189 files changed, 37 insertions, 10262 deletions

diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/Constraint.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/Constraint.java
deleted file mode 100644
index 916fb35c..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/Constraint.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query;
-
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.literal.*;
-import tools.refinery.store.query.term.*;
-
-import java.util.List;
-
-public interface Constraint {
-        String name();
-
-        List<Parameter> getParameters();
-
-        default int arity() {
-                return getParameters().size();
-        }
-
-        default boolean invalidIndex(int i) {
-                return i < 0 || i >= arity();
-        }
-
-        default Reduction getReduction() {
-                return Reduction.NOT_REDUCIBLE;
-        }
-
-        default boolean equals(LiteralEqualityHelper helper, Constraint other) {
-                return equals(other);
-        }
-
-        default String toReferenceString() {
-                return name();
-        }
-
-        default CallLiteral call(CallPolarity polarity, List<Variable> arguments) {
-                return new CallLiteral(polarity, this, arguments);
-        }
-
-        default CallLiteral call(CallPolarity polarity, Variable... arguments) {
-                return call(polarity, List.of(arguments));
-        }
-
-        default CallLiteral call(Variable... arguments) {
-                return call(CallPolarity.POSITIVE, arguments);
-        }
-
-        default CallLiteral callTransitive(NodeVariable left, NodeVariable right) {
-                return call(CallPolarity.TRANSITIVE, List.of(left, right));
-        }
-
-        default AssignedValue<Integer> count(List<Variable> arguments) {
-                return targetVariable -> new CountLiteral(targetVariable, this, arguments);
-        }
-
-        default AssignedValue<Integer> count(Variable... arguments) {
-                return count(List.of(arguments));
-        }
-
-        default <R, T> AssignedValue<R> aggregateBy(DataVariable<T> inputVariable, Aggregator<R, T> aggregator,
-                                                                                                List<Variable> arguments) {
-                return targetVariable -> new AggregationLiteral<>(targetVariable, aggregator, inputVariable, this, arguments);
-        }
-
-        default <R, T> AssignedValue<R> aggregateBy(DataVariable<T> inputVariable, Aggregator<R, T> aggregator,
-                                                                                                Variable... arguments) {
-                return aggregateBy(inputVariable, aggregator, List.of(arguments));
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/InvalidQueryException.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/InvalidQueryException.java
deleted file mode 100644
index c39277a0..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/InvalidQueryException.java
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query;
-
-public class InvalidQueryException extends RuntimeException {
-        public InvalidQueryException() {
-        }
-
-        public InvalidQueryException(String message) {
-                super(message);
-        }
-
-        public InvalidQueryException(String message, Throwable cause) {
-                super(message, cause);
-        }
-
-        public InvalidQueryException(Throwable cause) {
-                super(cause);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java
index 1fa96a07..513825b7 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryAdapter.java
@@ -6,8 +6,8 @@
 package tools.refinery.store.query;
 
 import tools.refinery.store.adapter.ModelAdapter;
-import tools.refinery.store.query.dnf.AnyQuery;
-import tools.refinery.store.query.dnf.Query;
+import tools.refinery.logic.dnf.AnyQuery;
+import tools.refinery.logic.dnf.Query;
 import tools.refinery.store.query.resultset.AnyResultSet;
 import tools.refinery.store.query.resultset.ResultSet;
 
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java
index 332e6381..71e2c5bf 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryBuilder.java
@@ -7,8 +7,8 @@ package tools.refinery.store.query;
 
 import tools.refinery.store.adapter.ModelAdapterBuilder;
 import tools.refinery.store.model.ModelStore;
-import tools.refinery.store.query.dnf.AnyQuery;
-import tools.refinery.store.query.rewriter.DnfRewriter;
+import tools.refinery.logic.dnf.AnyQuery;
+import tools.refinery.logic.rewriter.DnfRewriter;
 
 import java.util.Collection;
 import java.util.List;
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java
index 8b67c5c1..fec8c999 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/ModelQueryStoreAdapter.java
@@ -7,8 +7,8 @@ package tools.refinery.store.query;
 
 import tools.refinery.store.adapter.ModelStoreAdapter;
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.dnf.AnyQuery;
-import tools.refinery.store.query.dnf.Query;
+import tools.refinery.logic.dnf.AnyQuery;
+import tools.refinery.logic.dnf.Query;
 import tools.refinery.store.query.view.AnySymbolView;
 
 import java.util.Collection;
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AbstractQueryBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AbstractQueryBuilder.java
deleted file mode 100644
index 2a3e3ce0..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AbstractQueryBuilder.java
+++ /dev/null
@@ -1,175 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.dnf.callback.*;
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Collection;
-import java.util.List;
-import java.util.Set;
-
-public abstract class AbstractQueryBuilder<T extends AbstractQueryBuilder<T>> {
-        protected final DnfBuilder dnfBuilder;
-
-        protected AbstractQueryBuilder(DnfBuilder dnfBuilder) {
-                this.dnfBuilder = dnfBuilder;
-        }
-
-        protected abstract T self();
-
-        public NodeVariable parameter() {
-                return dnfBuilder.parameter();
-        }
-
-        public NodeVariable parameter(String name) {
-                return dnfBuilder.parameter(name);
-        }
-
-        public NodeVariable parameter(ParameterDirection direction) {
-                return dnfBuilder.parameter(direction);
-        }
-
-        public NodeVariable parameter(String name, ParameterDirection direction) {
-                return dnfBuilder.parameter(name, direction);
-        }
-
-        public T parameter(NodeVariable variable) {
-                dnfBuilder.parameter(variable);
-                return self();
-        }
-
-        public T parameter(NodeVariable variable, ParameterDirection direction) {
-                dnfBuilder.parameter(variable, direction);
-                return self();
-        }
-
-        public T parameters(NodeVariable... variables) {
-                dnfBuilder.parameters(variables);
-                return self();
-        }
-
-        public T parameters(List<NodeVariable> variables) {
-                dnfBuilder.parameters(variables);
-                return self();
-        }
-
-        public T parameters(List<NodeVariable> variables, ParameterDirection direction) {
-                dnfBuilder.parameters(variables, direction);
-                return self();
-        }
-
-        public T symbolicParameters(List<SymbolicParameter> parameters) {
-                dnfBuilder.symbolicParameters(parameters);
-                return self();
-        }
-
-        public T functionalDependencies(Collection<FunctionalDependency<Variable>> functionalDependencies) {
-                dnfBuilder.functionalDependencies(functionalDependencies);
-                return self();
-        }
-
-        public T functionalDependency(FunctionalDependency<Variable> functionalDependency) {
-                dnfBuilder.functionalDependency(functionalDependency);
-                return self();
-        }
-
-        public T functionalDependency(Set<? extends Variable> forEach, Set<? extends Variable> unique) {
-                dnfBuilder.functionalDependency(forEach, unique);
-                return self();
-        }
-
-        public T clause(ClauseCallback0 callback) {
-                dnfBuilder.clause(callback);
-                return self();
-        }
-
-        public T clause(ClauseCallback1Data0 callback) {
-                dnfBuilder.clause(callback);
-                return self();
-        }
-
-        public <U1> T clause(Class<U1> type1, ClauseCallback1Data1<U1> callback) {
-                dnfBuilder.clause(type1, callback);
-                return self();
-        }
-
-        public T clause(ClauseCallback2Data0 callback) {
-                dnfBuilder.clause(callback);
-                return self();
-        }
-
-        public <U1> T clause(Class<U1> type1, ClauseCallback2Data1<U1> callback) {
-                dnfBuilder.clause(type1, callback);
-                return self();
-        }
-
-        public <U1, U2> T clause(Class<U1> type1, Class<U2> type2, ClauseCallback2Data2<U1, U2> callback) {
-                dnfBuilder.clause(type1, type2, callback);
-                return self();
-        }
-
-        public T clause(ClauseCallback3Data0 callback) {
-                dnfBuilder.clause(callback);
-                return self();
-        }
-
-        public <U1> T clause(Class<U1> type1, ClauseCallback3Data1<U1> callback) {
-                dnfBuilder.clause(type1, callback);
-                return self();
-        }
-
-        public <U1, U2> T clause(Class<U1> type1, Class<U2> type2, ClauseCallback3Data2<U1, U2> callback) {
-                dnfBuilder.clause(type1, type2, callback);
-                return self();
-        }
-
-        public <U1, U2, U3> T clause(Class<U1> type1, Class<U2> type2, Class<U3> type3,
-                                                                 ClauseCallback3Data3<U1, U2, U3> callback) {
-                dnfBuilder.clause(type1, type2, type3, callback);
-                return self();
-        }
-
-        public T clause(ClauseCallback4Data0 callback) {
-                dnfBuilder.clause(callback);
-                return self();
-        }
-
-        public <U1> T clause(Class<U1> type1, ClauseCallback4Data1<U1> callback) {
-                dnfBuilder.clause(type1, callback);
-                return self();
-        }
-
-        public <U1, U2> T clause(Class<U1> type1, Class<U2> type2, ClauseCallback4Data2<U1, U2> callback) {
-                dnfBuilder.clause(type1, type2, callback);
-                return self();
-        }
-
-        public <U1, U2, U3> T clause(Class<U1> type1, Class<U2> type2, Class<U3> type3,
-                                                                 ClauseCallback4Data3<U1, U2, U3> callback) {
-                dnfBuilder.clause(type1, type2, type3, callback);
-                return self();
-        }
-
-        public <U1, U2, U3, U4> T clause(Class<U1> type1, Class<U2> type2, Class<U3> type3, Class<U4> type4,
-                                                                         ClauseCallback4Data4<U1, U2, U3, U4> callback) {
-                dnfBuilder.clause(type1, type2, type3, type4, callback);
-                return self();
-        }
-
-        public T clause(Literal... literals) {
-                dnfBuilder.clause(literals);
-                return self();
-        }
-
-        public T clause(Collection<? extends Literal> literals) {
-                dnfBuilder.clause(literals);
-                return self();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AnyQuery.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AnyQuery.java
deleted file mode 100644
index 5e28af68..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/AnyQuery.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-public sealed interface AnyQuery permits Query {
-        String name();
-
-        int arity();
-
-        Class<?> valueType();
-
-        Dnf getDnf();
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/ClausePostProcessor.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/ClausePostProcessor.java
deleted file mode 100644
index 8800a155..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/ClausePostProcessor.java
+++ /dev/null
@@ -1,362 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import org.jetbrains.annotations.NotNull;
-import tools.refinery.store.query.Constraint;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.literal.*;
-import tools.refinery.store.query.substitution.MapBasedSubstitution;
-import tools.refinery.store.query.substitution.StatelessSubstitution;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.*;
-import java.util.function.Function;
-
-class ClausePostProcessor {
-        private final Map<Variable, ParameterInfo> parameters;
-        private final List<Literal> literals;
-        private final Map<Variable, Variable> representatives = new LinkedHashMap<>();
-        private final Map<Variable, Set<Variable>> equivalencePartition = new HashMap<>();
-        private List<Literal> substitutedLiterals;
-        private final Set<Variable> existentiallyQuantifiedVariables = new LinkedHashSet<>();
-        private Set<Variable> positiveVariables;
-        private Map<Variable, Set<SortableLiteral>> variableToLiteralInputMap;
-        private PriorityQueue<SortableLiteral> literalsWithAllInputsBound;
-        private LinkedHashSet<Literal> topologicallySortedLiterals;
-
-        public ClausePostProcessor(Map<Variable, ParameterInfo> parameters, List<Literal> literals) {
-                this.parameters = parameters;
-                this.literals = literals;
-        }
-
-        public Result postProcessClause() {
-                mergeEquivalentNodeVariables();
-                substitutedLiterals = new ArrayList<>(literals.size());
-                keepParameterEquivalences();
-                substituteLiterals();
-                computeExistentiallyQuantifiedVariables();
-                computePositiveVariables();
-                validatePositiveRepresentatives();
-                validatePrivateVariables();
-                topologicallySortLiterals();
-                var filteredLiterals = new ArrayList<Literal>(topologicallySortedLiterals.size());
-                for (var literal : topologicallySortedLiterals) {
-                        var reducedLiteral = literal.reduce();
-                        if (BooleanLiteral.FALSE.equals(reducedLiteral)) {
-                                return ConstantResult.ALWAYS_FALSE;
-                        } else if (!BooleanLiteral.TRUE.equals(reducedLiteral)) {
-                                filteredLiterals.add(reducedLiteral);
-                        }
-                }
-                if (filteredLiterals.isEmpty()) {
-                        return ConstantResult.ALWAYS_TRUE;
-                }
-                if (hasContradictoryCall(filteredLiterals)) {
-                        return ConstantResult.ALWAYS_FALSE;
-                }
-                var clause = new DnfClause(Collections.unmodifiableSet(positiveVariables),
-                                Collections.unmodifiableList(filteredLiterals));
-                return new ClauseResult(clause);
-        }
-
-        private void mergeEquivalentNodeVariables() {
-                for (var literal : literals) {
-                        if (isPositiveEquivalence(literal)) {
-                                var equivalenceLiteral = (EquivalenceLiteral) literal;
-                                mergeVariables(equivalenceLiteral.getLeft(), equivalenceLiteral.getRight());
-                        }
-                }
-        }
-
-        private static boolean isPositiveEquivalence(Literal literal) {
-                return literal instanceof EquivalenceLiteral equivalenceLiteral && equivalenceLiteral.isPositive();
-        }
-
-        private void mergeVariables(Variable left, Variable right) {
-                var leftRepresentative = getRepresentative(left);
-                var rightRepresentative = getRepresentative(right);
-                var leftInfo = parameters.get(leftRepresentative);
-                var rightInfo = parameters.get(rightRepresentative);
-                if (leftInfo != null && (rightInfo == null || leftInfo.index() <= rightInfo.index())) {
-                        // Prefer the variable occurring earlier in the parameter list as a representative.
-                        doMergeVariables(leftRepresentative, rightRepresentative);
-                } else {
-                        doMergeVariables(rightRepresentative, leftRepresentative);
-                }
-        }
-
-        private void doMergeVariables(Variable parentRepresentative, Variable newChildRepresentative) {
-                var parentSet = getEquivalentVariables(parentRepresentative);
-                var childSet = getEquivalentVariables(newChildRepresentative);
-                parentSet.addAll(childSet);
-                equivalencePartition.remove(newChildRepresentative);
-                for (var childEquivalentNodeVariable : childSet) {
-                        representatives.put(childEquivalentNodeVariable, parentRepresentative);
-                }
-        }
-
-        private Variable getRepresentative(Variable variable) {
-                return representatives.computeIfAbsent(variable, Function.identity());
-        }
-
-        private Set<Variable> getEquivalentVariables(Variable variable) {
-                var representative = getRepresentative(variable);
-                if (!representative.equals(variable)) {
-                        throw new AssertionError("NodeVariable %s already has a representative %s"
-                                        .formatted(variable, representative));
-                }
-                return equivalencePartition.computeIfAbsent(variable, key -> {
-                        var set = new HashSet<Variable>(1);
-                        set.add(key);
-                        return set;
-                });
-        }
-
-        private void keepParameterEquivalences() {
-                for (var pair : representatives.entrySet()) {
-                        var left = pair.getKey();
-                        var right = pair.getValue();
-                        if (!left.equals(right) && parameters.containsKey(left) && parameters.containsKey(right)) {
-                                substitutedLiterals.add(new EquivalenceLiteral(true, left, right));
-                        }
-                }
-        }
-
-        private void substituteLiterals() {
-                Substitution substitution;
-                if (representatives.isEmpty()) {
-                        substitution = null;
-                } else {
-                        substitution = new MapBasedSubstitution(Collections.unmodifiableMap(representatives),
-                                        StatelessSubstitution.IDENTITY);
-                }
-                for (var literal : literals) {
-                        if (isPositiveEquivalence(literal)) {
-                                // We already retained all equivalences that cannot be replaced with substitutions in
-                                // {@link#keepParameterEquivalences()}.
-                                continue;
-                        }
-                        var substitutedLiteral = substitution == null ? literal : literal.substitute(substitution);
-                        substitutedLiterals.add(substitutedLiteral);
-                }
-        }
-
-        private void computeExistentiallyQuantifiedVariables() {
-                for (var literal : substitutedLiterals) {
-                        existentiallyQuantifiedVariables.addAll(literal.getOutputVariables());
-                }
-        }
-
-        private void computePositiveVariables() {
-                positiveVariables = new LinkedHashSet<>();
-                for (var pair : parameters.entrySet()) {
-                        var variable = pair.getKey();
-                        if (pair.getValue().direction() == ParameterDirection.IN) {
-                                // Inputs count as positive, because they are already bound when we evaluate literals.
-                                positiveVariables.add(variable);
-                        } else if (!existentiallyQuantifiedVariables.contains(variable)) {
-                                throw new InvalidQueryException("Unbound %s parameter %s"
-                                                .formatted(ParameterDirection.OUT, variable));
-                        }
-                }
-                positiveVariables.addAll(existentiallyQuantifiedVariables);
-        }
-
-        private void validatePositiveRepresentatives() {
-                for (var pair : equivalencePartition.entrySet()) {
-                        var representative = pair.getKey();
-                        if (!positiveVariables.contains(representative)) {
-                                var variableSet = pair.getValue();
-                                throw new InvalidQueryException("Variables %s were merged by equivalence but are not bound"
-                                                .formatted(variableSet));
-                        }
-                }
-        }
-
-        private void validatePrivateVariables() {
-                var negativeVariablesMap = new HashMap<Variable, Literal>();
-                for (var literal : substitutedLiterals) {
-                        for (var variable : literal.getPrivateVariables(positiveVariables)) {
-                                var oldLiteral = negativeVariablesMap.put(variable, literal);
-                                if (oldLiteral != null) {
-                                        throw new InvalidQueryException("Unbound variable %s appears in multiple literals %s and %s"
-                                                        .formatted(variable, oldLiteral, literal));
-                                }
-                        }
-                }
-        }
-
-        private void topologicallySortLiterals() {
-                topologicallySortedLiterals = new LinkedHashSet<>(substitutedLiterals.size());
-                variableToLiteralInputMap = new HashMap<>();
-                literalsWithAllInputsBound = new PriorityQueue<>();
-                int size = substitutedLiterals.size();
-                for (int i = 0; i < size; i++) {
-                        var literal = substitutedLiterals.get(i);
-                        var sortableLiteral = new SortableLiteral(i, literal);
-                        sortableLiteral.enqueue();
-                }
-                while (!literalsWithAllInputsBound.isEmpty()) {
-                        var variable = literalsWithAllInputsBound.remove();
-                        variable.addToSortedLiterals();
-                }
-                if (!variableToLiteralInputMap.isEmpty()) {
-                        throw new InvalidQueryException("Unbound input variables %s"
-                                        .formatted(variableToLiteralInputMap.keySet()));
-                }
-        }
-
-        private boolean hasContradictoryCall(Collection<Literal> filteredLiterals) {
-                var positiveCalls = new HashMap<Constraint, Set<CallLiteral>>();
-                for (var literal : filteredLiterals) {
-                        if (literal instanceof CallLiteral callLiteral && callLiteral.getPolarity() == CallPolarity.POSITIVE) {
-                                var callsOfTarget = positiveCalls.computeIfAbsent(callLiteral.getTarget(), key -> new HashSet<>());
-                                callsOfTarget.add(callLiteral);
-                        }
-                }
-                for (var literal : filteredLiterals) {
-                        if (literal instanceof CallLiteral callLiteral && callLiteral.getPolarity() == CallPolarity.NEGATIVE) {
-                                var callsOfTarget = positiveCalls.get(callLiteral.getTarget());
-                                if (contradicts(callLiteral, callsOfTarget)) {
-                                        return true;
-                                }
-                        }
-                }
-                return false;
-        }
-
-        private boolean contradicts(CallLiteral negativeCall, Collection<CallLiteral> positiveCalls) {
-                if (positiveCalls == null) {
-                        return false;
-                }
-                for (var positiveCall : positiveCalls) {
-                        if (contradicts(negativeCall, positiveCall)) {
-                                return true;
-                        }
-                }
-                return false;
-        }
-
-        private boolean contradicts(CallLiteral negativeCall, CallLiteral positiveCall) {
-                var privateVariables = negativeCall.getPrivateVariables(positiveVariables);
-                var negativeArguments = negativeCall.getArguments();
-                var positiveArguments = positiveCall.getArguments();
-                int arity = negativeArguments.size();
-                for (int i = 0; i < arity; i++) {
-                        var negativeArgument = negativeArguments.get(i);
-                        if (privateVariables.contains(negativeArgument)) {
-                                continue;
-                        }
-                        var positiveArgument = positiveArguments.get(i);
-                        if (!negativeArgument.equals(positiveArgument)) {
-                                return false;
-                        }
-                }
-                return true;
-        }
-
-        private class SortableLiteral implements Comparable<SortableLiteral> {
-                private final int index;
-                private final Literal literal;
-                private final Set<Variable> remainingInputs;
-
-                private SortableLiteral(int index, Literal literal) {
-                        this.index = index;
-                        this.literal = literal;
-                        remainingInputs = new HashSet<>(literal.getInputVariables(positiveVariables));
-                        for (var pair : parameters.entrySet()) {
-                                if (pair.getValue().direction() == ParameterDirection.IN) {
-                                        remainingInputs.remove(pair.getKey());
-                                }
-                        }
-                }
-
-                public void enqueue() {
-                        if (allInputsBound()) {
-                                addToAllInputsBoundQueue();
-                        } else {
-                                addToVariableToLiteralInputMap();
-                        }
-                }
-
-                private void bindVariable(Variable input) {
-                        if (!remainingInputs.remove(input)) {
-                                throw new AssertionError("Already processed input %s of literal %s".formatted(input, literal));
-                        }
-                        if (allInputsBound()) {
-                                addToAllInputsBoundQueue();
-                        }
-                }
-
-                private boolean allInputsBound() {
-                        return remainingInputs.isEmpty();
-                }
-
-                private void addToVariableToLiteralInputMap() {
-                        for (var inputVariable : remainingInputs) {
-                                var literalSetForInput = variableToLiteralInputMap.computeIfAbsent(
-                                                inputVariable, key -> new HashSet<>());
-                                literalSetForInput.add(this);
-                        }
-                }
-
-                private void addToAllInputsBoundQueue() {
-                        literalsWithAllInputsBound.add(this);
-                }
-
-                public void addToSortedLiterals() {
-                        if (!allInputsBound()) {
-                                throw new AssertionError("Inputs %s of %s are not yet bound".formatted(remainingInputs, literal));
-                        }
-                        // Add literal if we haven't yet added a duplicate of this literal.
-                        topologicallySortedLiterals.add(literal);
-                        for (var variable : literal.getOutputVariables()) {
-                                var literalSetForInput = variableToLiteralInputMap.remove(variable);
-                                if (literalSetForInput == null) {
-                                        continue;
-                                }
-                                for (var targetSortableLiteral : literalSetForInput) {
-                                        targetSortableLiteral.bindVariable(variable);
-                                }
-                        }
-                }
-
-                @Override
-                public int compareTo(@NotNull ClausePostProcessor.SortableLiteral other) {
-                        return Integer.compare(index, other.index);
-                }
-
-                @Override
-                public boolean equals(Object o) {
-                        if (this == o) return true;
-                        if (o == null || getClass() != o.getClass()) return false;
-                        SortableLiteral that = (SortableLiteral) o;
-                        return index == that.index && Objects.equals(literal, that.literal);
-                }
-
-                @Override
-                public int hashCode() {
-                        return Objects.hash(index, literal);
-                }
-        }
-
-        public sealed interface Result permits ClauseResult, ConstantResult {
-        }
-
-        public record ClauseResult(DnfClause clause) implements Result {
-        }
-
-        public enum ConstantResult implements Result {
-                ALWAYS_TRUE,
-                ALWAYS_FALSE
-        }
-
-        public record ParameterInfo(ParameterDirection direction, int index) {
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Dnf.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Dnf.java
deleted file mode 100644
index 86a1b6b2..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Dnf.java
+++ /dev/null
@@ -1,235 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.Constraint;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.DnfEqualityChecker;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.SubstitutingLiteralEqualityHelper;
-import tools.refinery.store.query.equality.SubstitutingLiteralHashCodeHelper;
-import tools.refinery.store.query.literal.Reduction;
-import tools.refinery.store.query.term.Parameter;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-import java.util.Set;
-import java.util.function.Consumer;
-import java.util.stream.Collectors;
-
-public final class Dnf implements Constraint {
-        private static final String INDENTATION = "    ";
-
-        private final String name;
-        private final String uniqueName;
-        private final List<SymbolicParameter> symbolicParameters;
-        private final List<FunctionalDependency<Variable>> functionalDependencies;
-        private final List<DnfClause> clauses;
-
-        Dnf(String name, List<SymbolicParameter> symbolicParameters,
-                List<FunctionalDependency<Variable>> functionalDependencies, List<DnfClause> clauses) {
-                validateFunctionalDependencies(symbolicParameters, functionalDependencies);
-                this.name = name;
-                this.uniqueName = DnfUtils.generateUniqueName(name);
-                this.symbolicParameters = symbolicParameters;
-                this.functionalDependencies = functionalDependencies;
-                this.clauses = clauses;
-        }
-
-        private static void validateFunctionalDependencies(
-                        Collection<SymbolicParameter> symbolicParameters,
-                        Collection<FunctionalDependency<Variable>> functionalDependencies) {
-                var parameterSet = symbolicParameters.stream().map(SymbolicParameter::getVariable).collect(Collectors.toSet());
-                for (var functionalDependency : functionalDependencies) {
-                        validateParameters(symbolicParameters, parameterSet, functionalDependency.forEach(), functionalDependency);
-                        validateParameters(symbolicParameters, parameterSet, functionalDependency.unique(), functionalDependency);
-                }
-        }
-
-        private static void validateParameters(Collection<SymbolicParameter> symbolicParameters,
-                                                                                   Set<Variable> parameterSet, Collection<Variable> toValidate,
-                                                                                   FunctionalDependency<Variable> functionalDependency) {
-                for (var variable : toValidate) {
-                        if (!parameterSet.contains(variable)) {
-                                throw new InvalidQueryException(
-                                                "Variable %s of functional dependency %s does not appear in the parameter list %s"
-                                                                .formatted(variable, functionalDependency, symbolicParameters));
-                        }
-                }
-        }
-
-        @Override
-        public String name() {
-                return name == null ? uniqueName : name;
-        }
-
-        public boolean isExplicitlyNamed() {
-                return name != null;
-        }
-
-        public String getUniqueName() {
-                return uniqueName;
-        }
-
-        public List<SymbolicParameter> getSymbolicParameters() {
-                return symbolicParameters;
-        }
-
-        public List<Parameter> getParameters() {
-                return Collections.unmodifiableList(symbolicParameters);
-        }
-
-        public List<FunctionalDependency<Variable>> getFunctionalDependencies() {
-                return functionalDependencies;
-        }
-
-        @Override
-        public int arity() {
-                return symbolicParameters.size();
-        }
-
-        public List<DnfClause> getClauses() {
-                return clauses;
-        }
-
-        public RelationalQuery asRelation() {
-                return new RelationalQuery(this);
-        }
-
-        public <T> FunctionalQuery<T> asFunction(Class<T> type) {
-                return new FunctionalQuery<>(this, type);
-        }
-
-        @Override
-        public Reduction getReduction() {
-                if (clauses.isEmpty()) {
-                        return Reduction.ALWAYS_FALSE;
-                }
-                for (var clause : clauses) {
-                        if (clause.literals().isEmpty()) {
-                                return Reduction.ALWAYS_TRUE;
-                        }
-                }
-                return Reduction.NOT_REDUCIBLE;
-        }
-
-        public boolean equalsWithSubstitution(DnfEqualityChecker callEqualityChecker, Dnf other) {
-                if (arity() != other.arity()) {
-                        return false;
-                }
-                for (int i = 0; i < arity(); i++) {
-                        if (!symbolicParameters.get(i).getDirection().equals(other.getSymbolicParameters().get(i).getDirection())) {
-                                return false;
-                        }
-                }
-                int numClauses = clauses.size();
-                if (numClauses != other.clauses.size()) {
-                        return false;
-                }
-                for (int i = 0; i < numClauses; i++) {
-                        var literalEqualityHelper = new SubstitutingLiteralEqualityHelper(callEqualityChecker, symbolicParameters,
-                                        other.symbolicParameters);
-                        if (!clauses.get(i).equalsWithSubstitution(literalEqualityHelper, other.clauses.get(i))) {
-                                return false;
-                        }
-                }
-                return true;
-        }
-
-        @Override
-        public boolean equals(LiteralEqualityHelper helper, Constraint other) {
-                if (other instanceof Dnf otherDnf) {
-                        return helper.dnfEqual(this, otherDnf);
-                }
-                return false;
-        }
-
-        public int hashCodeWithSubstitution() {
-                var helper = new SubstitutingLiteralHashCodeHelper();
-                int result = 0;
-                for (var symbolicParameter : symbolicParameters) {
-                        result = result * 31 + symbolicParameter.hashCodeWithSubstitution(helper);
-                }
-                for (var clause : clauses) {
-                        result = result * 31 + clause.hashCodeWithSubstitution(helper);
-                }
-                return result;
-        }
-
-        @Override
-        public String toString() {
-                return "%s/%d".formatted(name(), arity());
-        }
-
-        @Override
-        public String toReferenceString() {
-                return "@Dnf " + name();
-        }
-
-        public String toDefinitionString() {
-                var builder = new StringBuilder();
-                builder.append("pred ").append(name()).append("(");
-                var parameterIterator = symbolicParameters.iterator();
-                if (parameterIterator.hasNext()) {
-                        builder.append(parameterIterator.next());
-                        while (parameterIterator.hasNext()) {
-                                builder.append(", ").append(parameterIterator.next());
-                        }
-                }
-                builder.append(") <->");
-                var clauseIterator = clauses.iterator();
-                if (clauseIterator.hasNext()) {
-                        appendClause(clauseIterator.next(), builder);
-                        while (clauseIterator.hasNext()) {
-                                builder.append("\n;");
-                                appendClause(clauseIterator.next(), builder);
-                        }
-                } else {
-                        builder.append("\n").append(INDENTATION).append("<no clauses>");
-                }
-                builder.append(".\n");
-                return builder.toString();
-        }
-
-        private static void appendClause(DnfClause clause, StringBuilder builder) {
-                var iterator = clause.literals().iterator();
-                if (!iterator.hasNext()) {
-                        builder.append("\n").append(INDENTATION).append("<empty>");
-                        return;
-                }
-                builder.append("\n").append(INDENTATION).append(iterator.next());
-                while (iterator.hasNext()) {
-                        builder.append(",\n").append(INDENTATION).append(iterator.next());
-                }
-        }
-
-        public static DnfBuilder builder() {
-                return builder(null);
-        }
-
-        public static DnfBuilder builder(String name) {
-                return new DnfBuilder(name);
-        }
-
-        public static DnfBuilder builderFrom(Dnf original) {
-                var builder = builder(original.name());
-                builder.symbolicParameters(original.getSymbolicParameters());
-                builder.functionalDependencies(original.getFunctionalDependencies());
-                return builder;
-        }
-
-        public static Dnf of(Consumer<DnfBuilder> callback) {
-                return of(null, callback);
-        }
-
-        public static Dnf of(String name, Consumer<DnfBuilder> callback) {
-                var builder = builder(name);
-                callback.accept(builder);
-                return builder.build();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfBuilder.java
deleted file mode 100644
index 0f9fd366..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfBuilder.java
+++ /dev/null
@@ -1,225 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.dnf.callback.*;
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.*;
-
-import java.util.*;
-
-@SuppressWarnings("UnusedReturnValue")
-public final class DnfBuilder {
-        private final String name;
-        private final Set<Variable> parameterVariables = new LinkedHashSet<>();
-        private final List<SymbolicParameter> parameters = new ArrayList<>();
-        private final List<FunctionalDependency<Variable>> functionalDependencies = new ArrayList<>();
-        private final List<List<Literal>> clauses = new ArrayList<>();
-
-        DnfBuilder(String name) {
-                this.name = name;
-        }
-
-        public NodeVariable parameter() {
-                return parameter((String) null);
-        }
-
-        public NodeVariable parameter(String name) {
-                return parameter(name, ParameterDirection.OUT);
-        }
-
-        public NodeVariable parameter(ParameterDirection direction) {
-                return parameter((String) null, direction);
-        }
-
-        public NodeVariable parameter(String name, ParameterDirection direction) {
-                var variable = Variable.of(name);
-                parameter(variable, direction);
-                return variable;
-        }
-
-        public <T> DataVariable<T> parameter(Class<T> type) {
-                return parameter(null, type);
-        }
-
-        public <T> DataVariable<T> parameter(String name, Class<T> type) {
-                return parameter(name, type, ParameterDirection.OUT);
-        }
-
-        public <T> DataVariable<T> parameter(Class<T> type, ParameterDirection direction) {
-                return parameter(null, type, direction);
-        }
-
-        public <T> DataVariable<T> parameter(String name, Class<T> type, ParameterDirection direction) {
-                var variable = Variable.of(name, type);
-                parameter(variable, direction);
-                return variable;
-        }
-
-        public Variable parameter(Parameter parameter) {
-                return parameter(null, parameter);
-        }
-
-        public Variable parameter(String name, Parameter parameter) {
-                var type = parameter.tryGetType();
-                if (type.isPresent()) {
-                        return parameter(name, type.get(), parameter.getDirection());
-                }
-                return parameter(name, parameter.getDirection());
-        }
-
-        public DnfBuilder parameter(Variable variable) {
-                return parameter(variable, ParameterDirection.OUT);
-        }
-
-        public DnfBuilder parameter(Variable variable, ParameterDirection direction) {
-                return symbolicParameter(new SymbolicParameter(variable, direction));
-        }
-
-        public DnfBuilder parameters(Variable... variables) {
-                return parameters(List.of(variables));
-        }
-
-        public DnfBuilder parameters(Collection<? extends Variable> variables) {
-                return parameters(variables, ParameterDirection.OUT);
-        }
-
-        public DnfBuilder parameters(Collection<? extends Variable> variables, ParameterDirection direction) {
-                for (var variable : variables) {
-                        parameter(variable, direction);
-                }
-                return this;
-        }
-
-        public DnfBuilder symbolicParameter(SymbolicParameter symbolicParameter) {
-                var variable = symbolicParameter.getVariable();
-                if (!parameterVariables.add(variable)) {
-                        throw new InvalidQueryException("Variable %s is already on the parameter list %s"
-                                        .formatted(variable, parameters));
-                }
-                parameters.add(symbolicParameter);
-                return this;
-        }
-
-        public DnfBuilder symbolicParameters(SymbolicParameter... symbolicParameters) {
-                return symbolicParameters(List.of(symbolicParameters));
-        }
-
-        public DnfBuilder symbolicParameters(Collection<SymbolicParameter> symbolicParameters) {
-                for (var symbolicParameter : symbolicParameters) {
-                        symbolicParameter(symbolicParameter);
-                }
-                return this;
-        }
-
-        public DnfBuilder functionalDependencies(Collection<FunctionalDependency<Variable>> functionalDependencies) {
-                this.functionalDependencies.addAll(functionalDependencies);
-                return this;
-        }
-
-        public DnfBuilder functionalDependency(FunctionalDependency<Variable> functionalDependency) {
-                functionalDependencies.add(functionalDependency);
-                return this;
-        }
-
-        public DnfBuilder functionalDependency(Set<? extends Variable> forEach, Set<? extends Variable> unique) {
-                return functionalDependency(new FunctionalDependency<>(Set.copyOf(forEach), Set.copyOf(unique)));
-        }
-
-        public DnfBuilder clause(ClauseCallback0 callback) {
-                return clause(callback.toLiterals());
-        }
-
-        public DnfBuilder clause(ClauseCallback1Data0 callback) {
-                return clause(callback.toLiterals(Variable.of("v1")));
-        }
-
-        public <T> DnfBuilder clause(Class<T> type1, ClauseCallback1Data1<T> callback) {
-                return clause(callback.toLiterals(Variable.of("d1", type1)));
-        }
-
-        public DnfBuilder clause(ClauseCallback2Data0 callback) {
-                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2")));
-        }
-
-        public <T> DnfBuilder clause(Class<T> type1, ClauseCallback2Data1<T> callback) {
-                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("d1", type1)));
-        }
-
-        public <T1, T2> DnfBuilder clause(Class<T1> type1, Class<T2> type2, ClauseCallback2Data2<T1, T2> callback) {
-                return clause(callback.toLiterals(Variable.of("d1", type1), Variable.of("d2", type2)));
-        }
-
-        public DnfBuilder clause(ClauseCallback3Data0 callback) {
-                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("v3")));
-        }
-
-        public <T> DnfBuilder clause(Class<T> type1, ClauseCallback3Data1<T> callback) {
-                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("d1", type1)));
-        }
-
-        public <T1, T2> DnfBuilder clause(Class<T1> type1, Class<T2> type2, ClauseCallback3Data2<T1, T2> callback) {
-                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("d1", type1), Variable.of("d2", type2)));
-        }
-
-        public <T1, T2, T3> DnfBuilder clause(Class<T1> type1, Class<T2> type2, Class<T3> type3,
-                                                                                  ClauseCallback3Data3<T1, T2, T3> callback) {
-                return clause(callback.toLiterals(Variable.of("d1", type1), Variable.of("d2", type2),
-                                Variable.of("d3", type3)));
-        }
-
-        public DnfBuilder clause(ClauseCallback4Data0 callback) {
-                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("v3"), Variable.of("v4")));
-        }
-
-        public <T> DnfBuilder clause(Class<T> type1, ClauseCallback4Data1<T> callback) {
-                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("v3"), Variable.of("d1",
-                                type1)));
-        }
-
-        public <T1, T2> DnfBuilder clause(Class<T1> type1, Class<T2> type2, ClauseCallback4Data2<T1, T2> callback) {
-                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("v2"), Variable.of("d1", type1),
-                                Variable.of("d2", type2)));
-        }
-
-        public <T1, T2, T3> DnfBuilder clause(Class<T1> type1, Class<T2> type2, Class<T3> type3,
-                                                                                  ClauseCallback4Data3<T1, T2, T3> callback) {
-                return clause(callback.toLiterals(Variable.of("v1"), Variable.of("d1", type1), Variable.of("d2", type2),
-                                Variable.of("d3", type3)));
-        }
-
-        public <T1, T2, T3, T4> DnfBuilder clause(Class<T1> type1, Class<T2> type2, Class<T3> type3, Class<T4> type4,
-                                                                                          ClauseCallback4Data4<T1, T2, T3, T4> callback) {
-                return clause(callback.toLiterals(Variable.of("d1", type1), Variable.of("d2", type2),
-                                Variable.of("d3", type3), Variable.of("d4", type4)));
-        }
-
-        public DnfBuilder clause(Literal... literals) {
-                clause(List.of(literals));
-                return this;
-        }
-
-        public DnfBuilder clause(Collection<? extends Literal> literals) {
-                clauses.add(List.copyOf(literals));
-                return this;
-        }
-
-        <T> void output(DataVariable<T> outputVariable) {
-                // Copy parameter variables to exclude the newly added {@code outputVariable}.
-                var fromParameters = Set.copyOf(parameterVariables);
-                parameter(outputVariable, ParameterDirection.OUT);
-                functionalDependency(fromParameters, Set.of(outputVariable));
-        }
-
-        public Dnf build() {
-                var postProcessor = new DnfPostProcessor(parameters, clauses);
-                var postProcessedClauses = postProcessor.postProcessClauses();
-                return new Dnf(name, Collections.unmodifiableList(parameters),
-                                Collections.unmodifiableList(functionalDependencies),
-                                Collections.unmodifiableList(postProcessedClauses));
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfClause.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfClause.java
deleted file mode 100644
index 94327bad..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfClause.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.List;
-import java.util.Set;
-
-public record DnfClause(Set<Variable> positiveVariables, List<Literal> literals) {
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, DnfClause other) {
-                int size = literals.size();
-                if (size != other.literals.size()) {
-                        return false;
-                }
-                for (int i = 0; i < size; i++) {
-                        if (!literals.get(i).equalsWithSubstitution(helper, other.literals.get(i))) {
-                                return false;
-                        }
-                }
-                return true;
-        }
-
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                int result = 0;
-                for (var literal : literals) {
-                        result = result * 31 + literal.hashCodeWithSubstitution(helper);
-                }
-                return result;
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfPostProcessor.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfPostProcessor.java
deleted file mode 100644
index 50236642..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfPostProcessor.java
+++ /dev/null
@@ -1,112 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.DnfEqualityChecker;
-import tools.refinery.store.query.equality.SubstitutingLiteralEqualityHelper;
-import tools.refinery.store.query.equality.SubstitutingLiteralHashCodeHelper;
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.*;
-
-class DnfPostProcessor {
-        private final List<SymbolicParameter> parameters;
-        private final List<List<Literal>> clauses;
-
-        public DnfPostProcessor(List<SymbolicParameter> parameters, List<List<Literal>> clauses) {
-                this.parameters = parameters;
-                this.clauses = clauses;
-        }
-
-        public List<DnfClause> postProcessClauses() {
-                var parameterInfoMap = getParameterInfoMap();
-                var postProcessedClauses = new LinkedHashSet<CanonicalClause>(clauses.size());
-                int index = 0;
-                for (var literals : clauses) {
-                        var postProcessor = new ClausePostProcessor(parameterInfoMap, literals);
-                        ClausePostProcessor.Result result;
-                        try {
-                                result = postProcessor.postProcessClause();
-                        } catch (InvalidQueryException e) {
-                                throw new InvalidClauseException(index, e);
-                        }
-                        if (result instanceof ClausePostProcessor.ClauseResult clauseResult) {
-                                postProcessedClauses.add(new CanonicalClause(clauseResult.clause()));
-                        } else if (result instanceof ClausePostProcessor.ConstantResult constantResult) {
-                                switch (constantResult) {
-                                case ALWAYS_TRUE -> {
-                                        var inputVariables = getInputVariables();
-                                        return List.of(new DnfClause(inputVariables, List.of()));
-                                }
-                                case ALWAYS_FALSE -> {
-                                        // Skip this clause because it can never match.
-                                }
-                                default -> throw new IllegalStateException("Unexpected ClausePostProcessor.ConstantResult: " +
-                                                constantResult);
-                                }
-                        } else {
-                                throw new IllegalStateException("Unexpected ClausePostProcessor.Result: " + result);
-                        }
-                        index++;
-                }
-                return postProcessedClauses.stream().map(CanonicalClause::getDnfClause).toList();
-        }
-
-        private Map<Variable, ClausePostProcessor.ParameterInfo> getParameterInfoMap() {
-                var mutableParameterInfoMap = new LinkedHashMap<Variable, ClausePostProcessor.ParameterInfo>();
-                int arity = parameters.size();
-                for (int i = 0; i < arity; i++) {
-                        var parameter = parameters.get(i);
-                        mutableParameterInfoMap.put(parameter.getVariable(),
-                                        new ClausePostProcessor.ParameterInfo(parameter.getDirection(), i));
-                }
-                return Collections.unmodifiableMap(mutableParameterInfoMap);
-        }
-
-        private Set<Variable> getInputVariables() {
-                var inputParameters = new LinkedHashSet<Variable>();
-                for (var parameter : parameters) {
-                        if (parameter.getDirection() == ParameterDirection.IN) {
-                                inputParameters.add(parameter.getVariable());
-                        }
-                }
-                return Collections.unmodifiableSet(inputParameters);
-        }
-
-        private class CanonicalClause {
-                private final DnfClause dnfClause;
-
-                public CanonicalClause(DnfClause dnfClause) {
-                        this.dnfClause = dnfClause;
-                }
-
-                public DnfClause getDnfClause() {
-                        return dnfClause;
-                }
-
-                @Override
-                public boolean equals(Object obj) {
-                        if (this == obj) {
-                                return true;
-                        }
-                        if (obj == null || getClass() != obj.getClass()) {
-                                return false;
-                        }
-                        var otherCanonicalClause = (CanonicalClause) obj;
-                        var helper = new SubstitutingLiteralEqualityHelper(DnfEqualityChecker.DEFAULT, parameters, parameters);
-                        return dnfClause.equalsWithSubstitution(helper, otherCanonicalClause.dnfClause);
-                }
-
-                @Override
-                public int hashCode() {
-                        var helper = new SubstitutingLiteralHashCodeHelper(parameters);
-                        return dnfClause.hashCodeWithSubstitution(helper);
-                }
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfUtils.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfUtils.java
deleted file mode 100644
index 65ab3634..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/DnfUtils.java
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import java.util.UUID;
-
-public final class DnfUtils {
-        private DnfUtils() {
-                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
-        }
-
-        public static String generateUniqueName(String originalName) {
-                UUID uuid = UUID.randomUUID();
-                String uniqueString = "_" + uuid.toString().replace('-', '_');
-                if (originalName == null) {
-                        return uniqueString;
-                } else {
-                        return originalName + uniqueString;
-                }
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalDependency.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalDependency.java
deleted file mode 100644
index aef07ee3..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalDependency.java
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.InvalidQueryException;
-
-import java.util.HashSet;
-import java.util.Set;
-
-public record FunctionalDependency<T>(Set<T> forEach, Set<T> unique) {
-        public FunctionalDependency {
-                var uniqueForEach = new HashSet<>(unique);
-                uniqueForEach.retainAll(forEach);
-                if (!uniqueForEach.isEmpty()) {
-                        throw new InvalidQueryException("Variables %s appear on both sides of the functional dependency"
-                                        .formatted(uniqueForEach));
-                }
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQuery.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQuery.java
deleted file mode 100644
index 225f6844..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQuery.java
+++ /dev/null
@@ -1,110 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.literal.CallPolarity;
-import tools.refinery.store.query.term.Aggregator;
-import tools.refinery.store.query.term.AssignedValue;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-
-public final class FunctionalQuery<T> extends Query<T> {
-        private final Class<T> type;
-
-        FunctionalQuery(Dnf dnf, Class<T> type) {
-                super(dnf);
-                var parameters = dnf.getSymbolicParameters();
-                int outputIndex = dnf.arity() - 1;
-                for (int i = 0; i < outputIndex; i++) {
-                        var parameter = parameters.get(i);
-                        var parameterType = parameter.tryGetType();
-                        if (parameterType.isPresent()) {
-                                throw new InvalidQueryException("Expected parameter %s of %s to be a node variable, got %s instead"
-                                                .formatted(parameter, dnf, parameterType.get().getName()));
-                        }
-                }
-                var outputParameter = parameters.get(outputIndex);
-                var outputParameterType = outputParameter.tryGetType();
-                if (outputParameterType.isEmpty() || !outputParameterType.get().equals(type)) {
-                        throw new InvalidQueryException("Expected parameter %s of %s to be %s, but got %s instead".formatted(
-                                        outputParameter, dnf, type, outputParameterType.map(Class::getName).orElse("node")));
-                }
-                this.type = type;
-        }
-
-        @Override
-        public int arity() {
-                return getDnf().arity() - 1;
-        }
-
-        @Override
-        public Class<T> valueType() {
-                return type;
-        }
-
-        @Override
-        public T defaultValue() {
-                return null;
-        }
-
-        @Override
-        protected FunctionalQuery<T> withDnfInternal(Dnf newDnf) {
-                return newDnf.asFunction(type);
-        }
-
-        @Override
-        public FunctionalQuery<T> withDnf(Dnf newDnf) {
-                return (FunctionalQuery<T>) super.withDnf(newDnf);
-        }
-
-        public AssignedValue<T> call(List<NodeVariable> arguments) {
-                return targetVariable -> {
-                        var argumentsWithTarget = new ArrayList<Variable>(arguments.size() + 1);
-                        argumentsWithTarget.addAll(arguments);
-                        argumentsWithTarget.add(targetVariable);
-                        return getDnf().call(CallPolarity.POSITIVE, argumentsWithTarget);
-                };
-        }
-
-        public AssignedValue<T> call(NodeVariable... arguments) {
-                return call(List.of(arguments));
-        }
-
-        public <R> AssignedValue<R> aggregate(Aggregator<R, T> aggregator, List<NodeVariable> arguments) {
-                return targetVariable -> {
-                        var placeholderVariable = Variable.of(type);
-                        var argumentsWithPlaceholder = new ArrayList<Variable>(arguments.size() + 1);
-                        argumentsWithPlaceholder.addAll(arguments);
-                        argumentsWithPlaceholder.add(placeholderVariable);
-                        return getDnf()
-                                        .aggregateBy(placeholderVariable, aggregator, argumentsWithPlaceholder)
-                                        .toLiteral(targetVariable);
-                };
-        }
-
-        public <R> AssignedValue<R> aggregate(Aggregator<R, T> aggregator, NodeVariable... arguments) {
-                return aggregate(aggregator, List.of(arguments));
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                if (!super.equals(o)) return false;
-                FunctionalQuery<?> that = (FunctionalQuery<?>) o;
-                return Objects.equals(type, that.type);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(super.hashCode(), type);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQueryBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQueryBuilder.java
deleted file mode 100644
index d1cd7ba8..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/FunctionalQueryBuilder.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.term.DataVariable;
-
-public final class FunctionalQueryBuilder<T> extends AbstractQueryBuilder<FunctionalQueryBuilder<T>> {
-        private final DataVariable<T> outputVariable;
-        private final Class<T> type;
-
-        FunctionalQueryBuilder(DataVariable<T> outputVariable, DnfBuilder dnfBuilder, Class<T> type) {
-                super(dnfBuilder);
-                this.outputVariable = outputVariable;
-                this.type = type;
-        }
-
-        @Override
-        protected FunctionalQueryBuilder<T> self() {
-                return this;
-        }
-
-        public FunctionalQuery<T> build() {
-                dnfBuilder.output(outputVariable);
-                return dnfBuilder.build().asFunction(type);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/InvalidClauseException.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/InvalidClauseException.java
deleted file mode 100644
index 747574b9..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/InvalidClauseException.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.InvalidQueryException;
-
-public class InvalidClauseException extends InvalidQueryException {
-        private final int clauseIndex;
-
-        public InvalidClauseException(int clauseIndex) {
-                this.clauseIndex = clauseIndex;
-        }
-
-        public InvalidClauseException(int clauseIndex, String message) {
-                super(message);
-                this.clauseIndex = clauseIndex;
-        }
-
-        public InvalidClauseException(int clauseIndex, String message, Throwable cause) {
-                super(message, cause);
-                this.clauseIndex = clauseIndex;
-        }
-
-        public InvalidClauseException(int clauseIndex, Throwable cause) {
-                super(cause);
-                this.clauseIndex = clauseIndex;
-        }
-
-        public int getClauseIndex() {
-                return clauseIndex;
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Query.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Query.java
deleted file mode 100644
index 83fe6ccd..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/Query.java
+++ /dev/null
@@ -1,202 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.dnf.callback.*;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Objects;
-
-public abstract sealed class Query<T> implements AnyQuery permits FunctionalQuery, RelationalQuery {
-        private static final String OUTPUT_VARIABLE_NAME = "output";
-
-        private final Dnf dnf;
-
-        protected Query(Dnf dnf) {
-                for (var parameter : dnf.getSymbolicParameters()) {
-                        if (parameter.getDirection() != ParameterDirection.OUT) {
-                                throw new IllegalArgumentException("Query parameter %s with direction %s is not allowed"
-                                                .formatted(parameter.getVariable(), parameter.getDirection()));
-                        }
-                }
-                this.dnf = dnf;
-        }
-
-        @Override
-        public String name() {
-                return dnf.name();
-        }
-
-        @Override
-        public Dnf getDnf() {
-                return dnf;
-        }
-
-        // Allow redeclaration of the method with refined return type.
-        @SuppressWarnings("squid:S3038")
-        @Override
-        public abstract Class<T> valueType();
-
-        public abstract T defaultValue();
-
-        public Query<T> withDnf(Dnf newDnf) {
-                if (dnf.equals(newDnf)) {
-                        return this;
-                }
-                int arity = dnf.arity();
-                if (newDnf.arity() != arity) {
-                        throw new IllegalArgumentException("Arity of %s and %s do not match".formatted(dnf, newDnf));
-                }
-                var parameters = dnf.getParameters();
-                var newParameters = newDnf.getParameters();
-                for (int i = 0; i < arity; i++) {
-                        var parameter = parameters.get(i);
-                        var newParameter = newParameters.get(i);
-                        if (!parameter.matches(newParameter)) {
-                                throw new IllegalArgumentException("Parameter #%d mismatch: %s does not match %s"
-                                                .formatted(i, parameter, newParameter));
-                        }
-                }
-                return withDnfInternal(newDnf);
-        }
-
-        protected abstract Query<T> withDnfInternal(Dnf newDnf);
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                Query<?> that = (Query<?>) o;
-                return Objects.equals(dnf, that.dnf);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(dnf);
-        }
-
-        @Override
-        public String toString() {
-                return dnf.toString();
-        }
-
-        public static QueryBuilder builder() {
-                return builder(null);
-        }
-
-        public static QueryBuilder builder(String name) {
-                return new QueryBuilder(name);
-        }
-
-        public static RelationalQuery of(QueryCallback0 callback) {
-                return of(null, callback);
-        }
-
-        public static RelationalQuery of(String name, QueryCallback0 callback) {
-                var builder = builder(name);
-                callback.accept(builder);
-                return builder.build();
-        }
-
-        public static RelationalQuery of(QueryCallback1 callback) {
-                return of(null, callback);
-        }
-
-        public static RelationalQuery of(String name, QueryCallback1 callback) {
-                var builder = builder(name);
-                callback.accept(builder, builder.parameter("p1"));
-                return builder.build();
-        }
-
-        public static RelationalQuery of(QueryCallback2 callback) {
-                return of(null, callback);
-        }
-
-        public static RelationalQuery of(String name, QueryCallback2 callback) {
-                var builder = builder(name);
-                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"));
-                return builder.build();
-        }
-
-        public static RelationalQuery of(QueryCallback3 callback) {
-                return of(null, callback);
-        }
-
-        public static RelationalQuery of(String name, QueryCallback3 callback) {
-                var builder = builder(name);
-                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), builder.parameter("p3"));
-                return builder.build();
-        }
-
-        public static RelationalQuery of(QueryCallback4 callback) {
-                return of(null, callback);
-        }
-
-        public static RelationalQuery of(String name, QueryCallback4 callback) {
-                var builder = builder(name);
-                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), builder.parameter("p3"),
-                                builder.parameter("p4"));
-                return builder.build();
-        }
-
-        public static <T> FunctionalQuery<T> of(Class<T> type, FunctionalQueryCallback0<T> callback) {
-                return of(null, type, callback);
-        }
-
-        public static <T> FunctionalQuery<T> of(String name, Class<T> type, FunctionalQueryCallback0<T> callback) {
-                var outputVariable = Variable.of(OUTPUT_VARIABLE_NAME, type);
-                var builder = builder(name).output(outputVariable);
-                callback.accept(builder, outputVariable);
-                return builder.build();
-        }
-
-        public static <T> FunctionalQuery<T> of(Class<T> type, FunctionalQueryCallback1<T> callback) {
-                return of(null, type, callback);
-        }
-
-        public static <T> FunctionalQuery<T> of(String name, Class<T> type, FunctionalQueryCallback1<T> callback) {
-                var outputVariable = Variable.of(OUTPUT_VARIABLE_NAME, type);
-                var builder = builder(name).output(outputVariable);
-                callback.accept(builder, builder.parameter("p1"), outputVariable);
-                return builder.build();
-        }
-
-        public static <T> FunctionalQuery<T> of(Class<T> type, FunctionalQueryCallback2<T> callback) {
-                return of(null, type, callback);
-        }
-
-        public static <T> FunctionalQuery<T> of(String name, Class<T> type, FunctionalQueryCallback2<T> callback) {
-                var outputVariable = Variable.of(OUTPUT_VARIABLE_NAME, type);
-                var builder = builder(name).output(outputVariable);
-                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), outputVariable);
-                return builder.build();
-        }
-
-        public static <T> FunctionalQuery<T> of(Class<T> type, FunctionalQueryCallback3<T> callback) {
-                return of(null, type, callback);
-        }
-
-        public static <T> FunctionalQuery<T> of(String name, Class<T> type, FunctionalQueryCallback3<T> callback) {
-                var outputVariable = Variable.of(OUTPUT_VARIABLE_NAME, type);
-                var builder = builder(name).output(outputVariable);
-                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), builder.parameter("p3"),
-                                outputVariable);
-                return builder.build();
-        }
-
-        public static <T> FunctionalQuery<T> of(Class<T> type, FunctionalQueryCallback4<T> callback) {
-                return of(null, type, callback);
-        }
-
-        public static <T> FunctionalQuery<T> of(String name, Class<T> type, FunctionalQueryCallback4<T> callback) {
-                var outputVariable = Variable.of(OUTPUT_VARIABLE_NAME, type);
-                var builder = builder(name).output(outputVariable);
-                callback.accept(builder, builder.parameter("p1"), builder.parameter("p2"), builder.parameter("p3"),
-                                builder.parameter("p4"), outputVariable);
-                return builder.build();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/QueryBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/QueryBuilder.java
deleted file mode 100644
index 138911bc..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/QueryBuilder.java
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.term.DataVariable;
-
-public final class QueryBuilder extends AbstractQueryBuilder<QueryBuilder> {
-        QueryBuilder(String name) {
-                super(Dnf.builder(name));
-        }
-
-        @Override
-        protected QueryBuilder self() {
-                return this;
-        }
-
-        public <T> FunctionalQueryBuilder<T> output(DataVariable<T> outputVariable) {
-                return new FunctionalQueryBuilder<>(outputVariable, dnfBuilder, outputVariable.getType());
-        }
-
-        public RelationalQuery build() {
-                return dnfBuilder.build().asRelation();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/RelationalQuery.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/RelationalQuery.java
deleted file mode 100644
index 98f71e11..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/RelationalQuery.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.literal.CallLiteral;
-import tools.refinery.store.query.literal.CallPolarity;
-import tools.refinery.store.query.term.AssignedValue;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collections;
-import java.util.List;
-
-public final class RelationalQuery extends Query<Boolean> {
-        RelationalQuery(Dnf dnf) {
-                super(dnf);
-                for (var parameter : dnf.getSymbolicParameters()) {
-                        var parameterType = parameter.tryGetType();
-                        if (parameterType.isPresent()) {
-                                throw new InvalidQueryException("Expected parameter %s of %s to be a node variable, got %s instead"
-                                                .formatted(parameter, dnf, parameterType.get().getName()));
-                        }
-                }
-        }
-
-        @Override
-        public int arity() {
-                return getDnf().arity();
-        }
-
-        @Override
-        public Class<Boolean> valueType() {
-                return Boolean.class;
-        }
-
-        @Override
-        public Boolean defaultValue() {
-                return false;
-        }
-
-        @Override
-        protected RelationalQuery withDnfInternal(Dnf newDnf) {
-                return newDnf.asRelation();
-        }
-
-        @Override
-        public RelationalQuery withDnf(Dnf newDnf) {
-                return (RelationalQuery) super.withDnf(newDnf);
-        }
-
-        public CallLiteral call(CallPolarity polarity, List<NodeVariable> arguments) {
-                return getDnf().call(polarity, Collections.unmodifiableList(arguments));
-        }
-
-        public CallLiteral call(CallPolarity polarity, NodeVariable... arguments) {
-                return getDnf().call(polarity, arguments);
-        }
-
-        public CallLiteral call(NodeVariable... arguments) {
-                return getDnf().call(arguments);
-        }
-
-        public CallLiteral callTransitive(NodeVariable left, NodeVariable right) {
-                return getDnf().callTransitive(left, right);
-        }
-
-        public AssignedValue<Integer> count(List<NodeVariable> arguments) {
-                return getDnf().count(Collections.unmodifiableList(arguments));
-        }
-
-        public AssignedValue<Integer> count(NodeVariable... arguments) {
-                return getDnf().count(arguments);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/SymbolicParameter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/SymbolicParameter.java
deleted file mode 100644
index fe9cefcc..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/SymbolicParameter.java
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.term.Parameter;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Objects;
-
-public final class SymbolicParameter extends Parameter {
-        private final Variable variable;
-
-        public SymbolicParameter(Variable variable, ParameterDirection direction) {
-                super(variable.tryGetType().orElse(null), direction);
-                this.variable = variable;
-        }
-
-        public Variable getVariable() {
-                return variable;
-        }
-
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCode(), helper.getVariableHashCode(variable));
-        }
-
-        @Override
-        public String toString() {
-                var direction = getDirection();
-                if (direction == ParameterDirection.OUT) {
-                        return variable.toString();
-                }
-                return "%s %s".formatted(getDirection(), variable);
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                if (!super.equals(o)) return false;
-                SymbolicParameter that = (SymbolicParameter) o;
-                return Objects.equals(variable, that.variable);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(super.hashCode(), variable);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback0.java
deleted file mode 100644
index d98dda2e..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback0.java
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback0 {
-        Collection<Literal> toLiterals();
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data0.java
deleted file mode 100644
index 4c01a527..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data0.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback1Data0 {
-        Collection<Literal> toLiterals(NodeVariable v1);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data1.java
deleted file mode 100644
index 2c0cb6eb..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback1Data1.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback1Data1<T> {
-        Collection<Literal> toLiterals(DataVariable<T> d1);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data0.java
deleted file mode 100644
index d764bdba..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data0.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback2Data0 {
-        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data1.java
deleted file mode 100644
index 140af03a..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data1.java
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback2Data1<T> {
-        Collection<Literal> toLiterals(NodeVariable v1, DataVariable<T> x1);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data2.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data2.java
deleted file mode 100644
index bfc8637c..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback2Data2.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback2Data2<T1, T2> {
-        Collection<Literal> toLiterals(DataVariable<T1> x1, DataVariable<T2> x2);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data0.java
deleted file mode 100644
index 074df65b..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data0.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback3Data0 {
-        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2, NodeVariable v3);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data1.java
deleted file mode 100644
index 24ba5187..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data1.java
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback3Data1<T> {
-        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2, DataVariable<T> d1);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data2.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data2.java
deleted file mode 100644
index 2a2e837a..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data2.java
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback3Data2<T1, T2> {
-        Collection<Literal> toLiterals(NodeVariable v1, DataVariable<T1> d1, DataVariable<T2> d2);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data3.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data3.java
deleted file mode 100644
index 8f4bdd01..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback3Data3.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback3Data3<T1, T2, T3> {
-        Collection<Literal> toLiterals(DataVariable<T1> d1, DataVariable<T2> d2, DataVariable<T3> d3);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data0.java
deleted file mode 100644
index ed0f87b2..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data0.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback4Data0 {
-        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2, NodeVariable v3, NodeVariable v4);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data1.java
deleted file mode 100644
index 9b27e2e1..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data1.java
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback4Data1<T> {
-        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2, NodeVariable v3, DataVariable<T> d1);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data2.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data2.java
deleted file mode 100644
index cbc4808e..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data2.java
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback4Data2<T1, T2> {
-        Collection<Literal> toLiterals(NodeVariable v1, NodeVariable v2, DataVariable<T1> d1, DataVariable<T2> d2);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data3.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data3.java
deleted file mode 100644
index a6258f36..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data3.java
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback4Data3<T1, T2, T3> {
-        Collection<Literal> toLiterals(NodeVariable v1, DataVariable<T1> d1, DataVariable<T2> d2, DataVariable<T3> d3);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data4.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data4.java
deleted file mode 100644
index b52a911a..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/ClauseCallback4Data4.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-
-import java.util.Collection;
-
-@FunctionalInterface
-public interface ClauseCallback4Data4<T1, T2, T3, T4> {
-        Collection<Literal> toLiterals(DataVariable<T1> d1, DataVariable<T2> d2, DataVariable<T3> d3, DataVariable<T4> d4);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback0.java
deleted file mode 100644
index 63b3eee6..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback0.java
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.dnf.FunctionalQueryBuilder;
-import tools.refinery.store.query.term.DataVariable;
-
-@FunctionalInterface
-public interface FunctionalQueryCallback0<T> {
-        void accept(FunctionalQueryBuilder<T> builder, DataVariable<T> output);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback1.java
deleted file mode 100644
index 1295a118..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback1.java
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.dnf.FunctionalQueryBuilder;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-
-@FunctionalInterface
-public interface FunctionalQueryCallback1<T> {
-        void accept(FunctionalQueryBuilder<T> builder, NodeVariable p1, DataVariable<T> output);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback2.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback2.java
deleted file mode 100644
index d5b7f9ff..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback2.java
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.dnf.FunctionalQueryBuilder;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-
-@FunctionalInterface
-public interface FunctionalQueryCallback2<T> {
-        void accept(FunctionalQueryBuilder<T> builder, NodeVariable p1, NodeVariable p2, DataVariable<T> output);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback3.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback3.java
deleted file mode 100644
index dc8404a0..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback3.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.dnf.FunctionalQueryBuilder;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-
-@FunctionalInterface
-public interface FunctionalQueryCallback3<T> {
-        void accept(FunctionalQueryBuilder<T> builder, NodeVariable p1, NodeVariable p2, NodeVariable p3,
-                                DataVariable<T> output);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback4.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback4.java
deleted file mode 100644
index b6d3ddb0..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/FunctionalQueryCallback4.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.dnf.FunctionalQueryBuilder;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-
-@FunctionalInterface
-public interface FunctionalQueryCallback4<T> {
-        void accept(FunctionalQueryBuilder<T> builder, NodeVariable p1, NodeVariable p2, NodeVariable p3, NodeVariable p4,
-                                DataVariable<T> output);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback0.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback0.java
deleted file mode 100644
index 3cf1de48..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback0.java
+++ /dev/null
@@ -1,13 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.dnf.QueryBuilder;
-
-@FunctionalInterface
-public interface QueryCallback0 {
-        void accept(QueryBuilder builder);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback1.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback1.java
deleted file mode 100644
index 0a150955..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback1.java
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.dnf.QueryBuilder;
-import tools.refinery.store.query.term.NodeVariable;
-
-@FunctionalInterface
-public interface QueryCallback1 {
-        void accept(QueryBuilder builder, NodeVariable p1);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback2.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback2.java
deleted file mode 100644
index 9493a7b4..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback2.java
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.dnf.QueryBuilder;
-import tools.refinery.store.query.term.NodeVariable;
-
-@FunctionalInterface
-public interface QueryCallback2 {
-        void accept(QueryBuilder builder, NodeVariable p1, NodeVariable p2);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback3.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback3.java
deleted file mode 100644
index 358c7da7..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback3.java
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.dnf.QueryBuilder;
-import tools.refinery.store.query.term.NodeVariable;
-
-@FunctionalInterface
-public interface QueryCallback3 {
-        void accept(QueryBuilder builder, NodeVariable p1, NodeVariable p2, NodeVariable p3);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback4.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback4.java
deleted file mode 100644
index 890dda16..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/dnf/callback/QueryCallback4.java
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf.callback;
-
-import tools.refinery.store.query.dnf.QueryBuilder;
-import tools.refinery.store.query.term.NodeVariable;
-
-@FunctionalInterface
-public interface QueryCallback4 {
-        void accept(QueryBuilder builder, NodeVariable p1, NodeVariable p2, NodeVariable p3, NodeVariable p4);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DeepDnfEqualityChecker.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DeepDnfEqualityChecker.java
deleted file mode 100644
index d6171314..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DeepDnfEqualityChecker.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.equality;
-
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.DnfClause;
-import tools.refinery.store.query.dnf.SymbolicParameter;
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.util.CycleDetectingMapper;
-
-import java.util.List;
-
-public class DeepDnfEqualityChecker implements DnfEqualityChecker {
-        private final CycleDetectingMapper<Pair, Boolean> mapper = new CycleDetectingMapper<>(this::doCheckEqual);
-
-        @Override
-        public boolean dnfEqual(Dnf left, Dnf right) {
-                return mapper.map(new Pair(left, right));
-        }
-
-        public boolean dnfEqualRaw(List<SymbolicParameter> symbolicParameters,
-                                                           List<? extends List<? extends Literal>> clauses, Dnf other) {
-                int arity = symbolicParameters.size();
-                if (arity != other.arity()) {
-                        return false;
-                }
-                for (int i = 0; i < arity; i++) {
-                        if (!symbolicParameters.get(i).getDirection().equals(other.getSymbolicParameters().get(i).getDirection())) {
-                                return false;
-                        }
-                }
-                int numClauses = clauses.size();
-                if (numClauses != other.getClauses().size()) {
-                        return false;
-                }
-                for (int i = 0; i < numClauses; i++) {
-                        var literalEqualityHelper = new SubstitutingLiteralEqualityHelper(this, symbolicParameters,
-                                        other.getSymbolicParameters());
-                        if (!equalsWithSubstitutionRaw(literalEqualityHelper, clauses.get(i), other.getClauses().get(i))) {
-                                return false;
-                        }
-                }
-                return true;
-        }
-
-        private boolean equalsWithSubstitutionRaw(LiteralEqualityHelper helper, List<? extends Literal> literals,
-                                                                                          DnfClause other) {
-                int size = literals.size();
-                if (size != other.literals().size()) {
-                        return false;
-                }
-                for (int i = 0; i < size; i++) {
-                        if (!literals.get(i).equalsWithSubstitution(helper, other.literals().get(i))) {
-                                return false;
-                        }
-                }
-                return true;
-        }
-
-        protected boolean doCheckEqual(Pair pair) {
-                return pair.left.equalsWithSubstitution(this, pair.right);
-        }
-
-        protected List<Pair> getInProgress() {
-                return mapper.getInProgress();
-        }
-
-        protected record Pair(Dnf left, Dnf right) {
-                @Override
-                public String toString() {
-                        return "(%s, %s)".formatted(left.name(), right.name());
-                }
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DnfEqualityChecker.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DnfEqualityChecker.java
deleted file mode 100644
index e2cfd79b..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/DnfEqualityChecker.java
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.equality;
-
-import tools.refinery.store.query.dnf.Dnf;
-
-import java.util.Objects;
-
-@FunctionalInterface
-public interface DnfEqualityChecker {
-        DnfEqualityChecker DEFAULT = Objects::equals;
-
-        boolean dnfEqual(Dnf left, Dnf right);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/LiteralEqualityHelper.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/LiteralEqualityHelper.java
deleted file mode 100644
index 5abc76ce..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/LiteralEqualityHelper.java
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.equality;
-
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Objects;
-
-public interface LiteralEqualityHelper extends DnfEqualityChecker {
-        LiteralEqualityHelper DEFAULT = new LiteralEqualityHelper() {
-                @Override
-                public boolean variableEqual(Variable left, Variable right) {
-                        return Objects.equals(left, right);
-                }
-
-                @Override
-                public boolean dnfEqual(Dnf left, Dnf right) {
-                        return DnfEqualityChecker.DEFAULT.dnfEqual(left, right);
-                }
-        };
-
-        boolean variableEqual(Variable left, Variable right);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/LiteralHashCodeHelper.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/LiteralHashCodeHelper.java
deleted file mode 100644
index 5495160a..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/LiteralHashCodeHelper.java
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.equality;
-
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Objects;
-
-@FunctionalInterface
-public interface LiteralHashCodeHelper {
-        LiteralHashCodeHelper DEFAULT = Objects::hashCode;
-
-        int getVariableHashCode(Variable variable);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/SubstitutingLiteralEqualityHelper.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/SubstitutingLiteralEqualityHelper.java
deleted file mode 100644
index 50a79e07..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/SubstitutingLiteralEqualityHelper.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.equality;
-
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.SymbolicParameter;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-public class SubstitutingLiteralEqualityHelper implements LiteralEqualityHelper {
-        private final DnfEqualityChecker dnfEqualityChecker;
-        private final Map<Variable, Variable> leftToRight;
-        private final Map<Variable, Variable> rightToLeft;
-
-        public SubstitutingLiteralEqualityHelper(DnfEqualityChecker dnfEqualityChecker,
-                                                                                         List<SymbolicParameter> leftParameters,
-                                                                                         List<SymbolicParameter> rightParameters) {
-                this.dnfEqualityChecker = dnfEqualityChecker;
-                var arity = leftParameters.size();
-                if (arity != rightParameters.size()) {
-                        throw new IllegalArgumentException("Parameter lists have unequal length");
-                }
-                leftToRight = new HashMap<>(arity);
-                rightToLeft = new HashMap<>(arity);
-                for (int i = 0; i < arity; i++) {
-                        if (!variableEqual(leftParameters.get(i).getVariable(), rightParameters.get(i).getVariable())) {
-                                throw new IllegalArgumentException("Parameter lists cannot be unified: duplicate parameter " + i);
-                        }
-                }
-        }
-
-        @Override
-        public boolean dnfEqual(Dnf left, Dnf right) {
-                return dnfEqualityChecker.dnfEqual(left, right);
-        }
-
-        @Override
-        public boolean variableEqual(Variable left, Variable right) {
-                if (left.tryGetType().equals(right.tryGetType()) &&
-                                checkMapping(leftToRight, left, right) &&
-                                checkMapping(rightToLeft, right, left)) {
-                        leftToRight.put(left, right);
-                        rightToLeft.put(right, left);
-                        return true;
-                }
-                return false;
-        }
-
-        private static boolean checkMapping(Map<Variable, Variable> map, Variable key, Variable expectedValue) {
-                var currentValue = map.get(key);
-                return currentValue == null || currentValue.equals(expectedValue);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/SubstitutingLiteralHashCodeHelper.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/SubstitutingLiteralHashCodeHelper.java
deleted file mode 100644
index 754f6976..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/equality/SubstitutingLiteralHashCodeHelper.java
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.equality;
-
-import tools.refinery.store.query.dnf.SymbolicParameter;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-public class SubstitutingLiteralHashCodeHelper implements LiteralHashCodeHelper {
-        private final Map<Variable, Integer> assignedHashCodes = new LinkedHashMap<>();
-
-        // 0 is for {@code null}, so we start with 1.
-        private int next = 1;
-
-        public SubstitutingLiteralHashCodeHelper() {
-                this(List.of());
-        }
-
-        public SubstitutingLiteralHashCodeHelper(List<SymbolicParameter> parameters) {
-                for (var parameter : parameters) {
-                        getVariableHashCode(parameter.getVariable());
-                }
-        }
-
-        @Override
-        public int getVariableHashCode(Variable variable) {
-                if (variable == null) {
-                        return 0;
-                }
-                return assignedHashCodes.computeIfAbsent(variable, key -> {
-                        int sequenceNumber = next;
-                        next++;
-                        return variable.hashCodeWithSubstitution(sequenceNumber);
-                });
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCallLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCallLiteral.java
deleted file mode 100644
index 0e99d441..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCallLiteral.java
+++ /dev/null
@@ -1,135 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.Constraint;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.*;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractLiteral}.
-@SuppressWarnings("squid:S2160")
-public abstract class AbstractCallLiteral extends AbstractLiteral {
-        private final Constraint target;
-        private final List<Variable> arguments;
-        private final Set<Variable> inArguments;
-        private final Set<Variable> outArguments;
-
-        // Use exhaustive switch over enums.
-        @SuppressWarnings("squid:S1301")
-        protected AbstractCallLiteral(Constraint target, List<Variable> arguments) {
-                int arity = target.arity();
-                if (arguments.size() != arity) {
-                        throw new InvalidQueryException("%s needs %d arguments, but got %s".formatted(target.name(),
-                                        target.arity(), arguments.size()));
-                }
-                this.target = target;
-                this.arguments = arguments;
-                var mutableInArguments = new LinkedHashSet<Variable>();
-                var mutableOutArguments = new LinkedHashSet<Variable>();
-                var parameters = target.getParameters();
-                for (int i = 0; i < arity; i++) {
-                        var argument = arguments.get(i);
-                        var parameter = parameters.get(i);
-                        if (!parameter.isAssignable(argument)) {
-                                throw new InvalidQueryException("Argument %d of %s is not assignable to parameter %s"
-                                                .formatted(i, target, parameter));
-                        }
-                        switch (parameter.getDirection()) {
-                        case IN -> {
-                                mutableOutArguments.remove(argument);
-                                mutableInArguments.add(argument);
-                        }
-                        case OUT -> {
-                                if (!mutableInArguments.contains(argument)) {
-                                        mutableOutArguments.add(argument);
-                                }
-                        }
-                        }
-                }
-                inArguments = Collections.unmodifiableSet(mutableInArguments);
-                outArguments = Collections.unmodifiableSet(mutableOutArguments);
-        }
-
-        public Constraint getTarget() {
-                return target;
-        }
-
-        public List<Variable> getArguments() {
-                return arguments;
-        }
-
-        protected Set<Variable> getArgumentsOfDirection(ParameterDirection direction) {
-                return switch (direction) {
-                        case IN -> inArguments;
-                        case OUT -> outArguments;
-                };
-        }
-
-        @Override
-        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
-                var inputVariables = new LinkedHashSet<>(getArgumentsOfDirection(ParameterDirection.OUT));
-                inputVariables.retainAll(positiveVariablesInClause);
-                inputVariables.addAll(getArgumentsOfDirection(ParameterDirection.IN));
-                return Collections.unmodifiableSet(inputVariables);
-        }
-
-        @Override
-        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
-                var privateVariables = new LinkedHashSet<>(getArgumentsOfDirection(ParameterDirection.OUT));
-                privateVariables.removeAll(positiveVariablesInClause);
-                return Collections.unmodifiableSet(privateVariables);
-        }
-
-        @Override
-        public Literal substitute(Substitution substitution) {
-                var substitutedArguments = arguments.stream().map(substitution::getSubstitute).toList();
-                return doSubstitute(substitution, substitutedArguments);
-        }
-
-        protected abstract Literal doSubstitute(Substitution substitution, List<Variable> substitutedArguments);
-
-        public AbstractCallLiteral withTarget(Constraint newTarget) {
-                if (Objects.equals(target, newTarget)) {
-                        return this;
-                }
-                return withArguments(newTarget, arguments);
-        }
-
-        public abstract AbstractCallLiteral withArguments(Constraint newTarget, List<Variable> newArguments);
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                if (!super.equalsWithSubstitution(helper, other)) {
-                        return false;
-                }
-                var otherCallLiteral = (AbstractCallLiteral) other;
-                var arity = arguments.size();
-                if (arity != otherCallLiteral.arguments.size()) {
-                        return false;
-                }
-                for (int i = 0; i < arity; i++) {
-                        if (!helper.variableEqual(arguments.get(i), otherCallLiteral.arguments.get(i))) {
-                                return false;
-                        }
-                }
-                return target.equals(helper, otherCallLiteral.target);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                int result = super.hashCodeWithSubstitution(helper) * 31 + target.hashCode();
-                for (var argument : arguments) {
-                        result = result * 31 + helper.getVariableHashCode(argument);
-                }
-                return result;
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCountLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCountLiteral.java
deleted file mode 100644
index 9bb572c0..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractCountLiteral.java
+++ /dev/null
@@ -1,107 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.Constraint;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.term.ConstantTerm;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractLiteral}.
-@SuppressWarnings("squid:S2160")
-public abstract class AbstractCountLiteral<T> extends AbstractCallLiteral {
-        private final Class<T> resultType;
-        private final DataVariable<T> resultVariable;
-
-        protected AbstractCountLiteral(Class<T> resultType, DataVariable<T> resultVariable, Constraint target,
-                                                                   List<Variable> arguments) {
-                super(target, arguments);
-                if (!resultVariable.getType().equals(resultType)) {
-                        throw new InvalidQueryException("Count result variable %s must be of type %s, got %s instead".formatted(
-                                        resultVariable, resultType, resultVariable.getType().getName()));
-                }
-                if (arguments.contains(resultVariable)) {
-                        throw new InvalidQueryException("Count result variable %s must not appear in the argument list"
-                                        .formatted(resultVariable));
-                }
-                this.resultType = resultType;
-                this.resultVariable = resultVariable;
-        }
-
-        public Class<T> getResultType() {
-                return resultType;
-        }
-
-        public DataVariable<T> getResultVariable() {
-                return resultVariable;
-        }
-
-        @Override
-        public Set<Variable> getOutputVariables() {
-                return Set.of(resultVariable);
-        }
-
-        protected abstract T zero();
-
-        protected abstract T one();
-
-        @Override
-        public Literal reduce() {
-                var reduction = getTarget().getReduction();
-                return switch (reduction) {
-                        case ALWAYS_FALSE -> getResultVariable().assign(new ConstantTerm<>(resultType, zero()));
-                        // The only way a constant {@code true} predicate can be called in a negative position is to have all of
-                        // its arguments bound as input variables. Thus, there will only be a single match.
-                        case ALWAYS_TRUE -> getResultVariable().assign(new ConstantTerm<>(resultType, one()));
-                        case NOT_REDUCIBLE -> this;
-                };
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                if (!super.equalsWithSubstitution(helper, other)) {
-                        return false;
-                }
-                var otherCountLiteral = (AbstractCountLiteral<?>) other;
-                return Objects.equals(resultType, otherCountLiteral.resultType) &&
-                                helper.variableEqual(resultVariable, otherCountLiteral.resultVariable);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCodeWithSubstitution(helper), resultType,
-                                helper.getVariableHashCode(resultVariable));
-        }
-
-        protected abstract String operatorName();
-
-        @Override
-        public String toString() {
-                var builder = new StringBuilder();
-                builder.append(resultVariable);
-                builder.append(" is ");
-                builder.append(operatorName());
-                builder.append(' ');
-                builder.append(getTarget().toReferenceString());
-                builder.append('(');
-                var argumentIterator = getArguments().iterator();
-                if (argumentIterator.hasNext()) {
-                        builder.append(argumentIterator.next());
-                        while (argumentIterator.hasNext()) {
-                                builder.append(", ").append(argumentIterator.next());
-                        }
-                }
-                builder.append(')');
-                return builder.toString();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractLiteral.java
deleted file mode 100644
index 7d3cabd7..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AbstractLiteral.java
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-
-public abstract class AbstractLiteral implements Literal {
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                return other != null && getClass() == other.getClass();
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return getClass().hashCode();
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                AbstractLiteral that = (AbstractLiteral) o;
-                return equalsWithSubstitution(LiteralEqualityHelper.DEFAULT, that);
-        }
-
-        @Override
-        public int hashCode() {
-                return hashCodeWithSubstitution(LiteralHashCodeHelper.DEFAULT);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AggregationLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AggregationLiteral.java
deleted file mode 100644
index e3acfacc..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AggregationLiteral.java
+++ /dev/null
@@ -1,138 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.Constraint;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.*;
-
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractLiteral}.
-@SuppressWarnings("squid:S2160")
-public class AggregationLiteral<R, T> extends AbstractCallLiteral {
-        private final DataVariable<R> resultVariable;
-        private final DataVariable<T> inputVariable;
-        private final Aggregator<R, T> aggregator;
-
-        public AggregationLiteral(DataVariable<R> resultVariable, Aggregator<R, T> aggregator,
-                                                          DataVariable<T> inputVariable, Constraint target, List<Variable> arguments) {
-                super(target, arguments);
-                if (!inputVariable.getType().equals(aggregator.getInputType())) {
-                        throw new InvalidQueryException("Input variable %s must of type %s, got %s instead".formatted(
-                                        inputVariable, aggregator.getInputType().getName(), inputVariable.getType().getName()));
-                }
-                if (!getArgumentsOfDirection(ParameterDirection.OUT).contains(inputVariable)) {
-                        throw new InvalidQueryException("Input variable %s must be bound with direction %s in the argument list"
-                                        .formatted(inputVariable, ParameterDirection.OUT));
-                }
-                if (!resultVariable.getType().equals(aggregator.getResultType())) {
-                        throw new InvalidQueryException("Result variable %s must of type %s, got %s instead".formatted(
-                                        resultVariable, aggregator.getResultType().getName(), resultVariable.getType().getName()));
-                }
-                if (arguments.contains(resultVariable)) {
-                        throw new InvalidQueryException("Result variable %s must not appear in the argument list".formatted(
-                                        resultVariable));
-                }
-                this.resultVariable = resultVariable;
-                this.inputVariable = inputVariable;
-                this.aggregator = aggregator;
-        }
-
-        public DataVariable<R> getResultVariable() {
-                return resultVariable;
-        }
-
-        public DataVariable<T> getInputVariable() {
-                return inputVariable;
-        }
-
-        public Aggregator<R, T> getAggregator() {
-                return aggregator;
-        }
-
-        @Override
-        public Set<Variable> getOutputVariables() {
-                return Set.of(resultVariable);
-        }
-
-        @Override
-        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
-                if (positiveVariablesInClause.contains(inputVariable)) {
-                        throw new InvalidQueryException("Aggregation variable %s must not be bound".formatted(inputVariable));
-                }
-                return super.getInputVariables(positiveVariablesInClause);
-        }
-
-        @Override
-        public Literal reduce() {
-                var reduction = getTarget().getReduction();
-                return switch (reduction) {
-                        case ALWAYS_FALSE -> {
-                                var emptyValue = aggregator.getEmptyResult();
-                                yield emptyValue == null ? BooleanLiteral.FALSE :
-                                                resultVariable.assign(new ConstantTerm<>(resultVariable.getType(), emptyValue));
-                        }
-                        case ALWAYS_TRUE -> throw new InvalidQueryException("Trying to aggregate over an infinite set");
-                        case NOT_REDUCIBLE -> this;
-                };
-        }
-
-        @Override
-        protected Literal doSubstitute(Substitution substitution, List<Variable> substitutedArguments) {
-                return new AggregationLiteral<>(substitution.getTypeSafeSubstitute(resultVariable), aggregator,
-                                substitution.getTypeSafeSubstitute(inputVariable), getTarget(), substitutedArguments);
-        }
-
-        @Override
-        public AbstractCallLiteral withArguments(Constraint newTarget, List<Variable> newArguments) {
-                return new AggregationLiteral<>(resultVariable, aggregator, inputVariable, newTarget, newArguments);
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                if (!super.equalsWithSubstitution(helper, other)) {
-                        return false;
-                }
-                var otherAggregationLiteral = (AggregationLiteral<?, ?>) other;
-                return helper.variableEqual(resultVariable, otherAggregationLiteral.resultVariable) &&
-                                aggregator.equals(otherAggregationLiteral.aggregator) &&
-                                helper.variableEqual(inputVariable, otherAggregationLiteral.inputVariable);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCodeWithSubstitution(helper), helper.getVariableHashCode(resultVariable),
-                                helper.getVariableHashCode(inputVariable), aggregator);
-        }
-
-        @Override
-        public String toString() {
-                var builder = new StringBuilder();
-                builder.append(resultVariable);
-                builder.append(" is ");
-                builder.append(getTarget().toReferenceString());
-                builder.append("(");
-                var argumentIterator = getArguments().iterator();
-                if (argumentIterator.hasNext()) {
-                        var argument = argumentIterator.next();
-                        if (inputVariable.equals(argument)) {
-                                builder.append("@Aggregate(\"").append(aggregator).append("\") ");
-                        }
-                        builder.append(argument);
-                        while (argumentIterator.hasNext()) {
-                                builder.append(", ").append(argumentIterator.next());
-                        }
-                }
-                builder.append(")");
-                return builder.toString();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AssignLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AssignLiteral.java
deleted file mode 100644
index dadf487f..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/AssignLiteral.java
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Collections;
-import java.util.Objects;
-import java.util.Set;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractLiteral}.
-@SuppressWarnings("squid:S2160")
-public class AssignLiteral<T> extends AbstractLiteral {
-        private final DataVariable<T> variable;
-        private final Term<T> term;
-
-        public AssignLiteral(DataVariable<T> variable, Term<T> term) {
-                if (!term.getType().equals(variable.getType())) {
-                        throw new InvalidQueryException("Term %s must be of type %s, got %s instead".formatted(
-                                        term, variable.getType().getName(), term.getType().getName()));
-                }
-                var inputVariables = term.getInputVariables();
-                if (inputVariables.contains(variable)) {
-                        throw new InvalidQueryException("Result variable %s must not appear in the term %s".formatted(
-                                        variable, term));
-                }
-                this.variable = variable;
-                this.term = term;
-        }
-
-        public DataVariable<T> getVariable() {
-                return variable;
-        }
-
-        public Term<T> getTerm() {
-                return term;
-        }
-
-        @Override
-        public Set<Variable> getOutputVariables() {
-                return Set.of(variable);
-        }
-
-        @Override
-        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Collections.unmodifiableSet(term.getInputVariables());
-        }
-
-        @Override
-        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of();
-        }
-
-        @Override
-        public Literal substitute(Substitution substitution) {
-                return new AssignLiteral<>(substitution.getTypeSafeSubstitute(variable), term.substitute(substitution));
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                if (other == null || getClass() != other.getClass()) {
-                        return false;
-                }
-                var otherAssignLiteral = (AssignLiteral<?>) other;
-                return helper.variableEqual(variable, otherAssignLiteral.variable) &&
-                                term.equalsWithSubstitution(helper, otherAssignLiteral.term);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCodeWithSubstitution(helper), helper.getVariableHashCode(variable),
-                                term.hashCodeWithSubstitution(helper));
-        }
-
-        @Override
-        public String toString() {
-                return "%s is (%s)".formatted(variable, term);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/BooleanLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/BooleanLiteral.java
deleted file mode 100644
index 6cd320da..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/BooleanLiteral.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Set;
-
-public enum BooleanLiteral implements CanNegate<BooleanLiteral> {
-        TRUE(true),
-        FALSE(false);
-
-        private final boolean value;
-
-        BooleanLiteral(boolean value) {
-                this.value = value;
-        }
-
-        @Override
-        public Set<Variable> getOutputVariables() {
-                return Set.of();
-        }
-
-        @Override
-        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of();
-        }
-
-        @Override
-        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of();
-        }
-
-        @Override
-        public Literal substitute(Substitution substitution) {
-                // No variables to substitute.
-                return this;
-        }
-
-        @Override
-        public BooleanLiteral negate() {
-                return fromBoolean(!value);
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                return equals(other);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return hashCode();
-        }
-
-        @Override
-        public String toString() {
-                return Boolean.toString(value);
-        }
-
-        public static BooleanLiteral fromBoolean(boolean value) {
-                return value ? TRUE : FALSE;
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallLiteral.java
deleted file mode 100644
index 2d0e4e97..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallLiteral.java
+++ /dev/null
@@ -1,134 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.Constraint;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.*;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractLiteral}.
-@SuppressWarnings("squid:S2160")
-public final class CallLiteral extends AbstractCallLiteral implements CanNegate<CallLiteral> {
-        private final CallPolarity polarity;
-
-        public CallLiteral(CallPolarity polarity, Constraint target, List<Variable> arguments) {
-                super(target, arguments);
-                var parameters = target.getParameters();
-                int arity = target.arity();
-                if (polarity.isTransitive()) {
-                        if (arity != 2) {
-                                throw new InvalidQueryException("Transitive closures can only take binary relations");
-                        }
-                        if (parameters.get(0).isDataVariable() || parameters.get(1).isDataVariable()) {
-                                throw new InvalidQueryException("Transitive closures can only be computed over nodes");
-                        }
-                        if (parameters.get(0).getDirection() != ParameterDirection.OUT ||
-                                        parameters.get(1).getDirection() != ParameterDirection.OUT) {
-                                throw new InvalidQueryException("Transitive closures cannot take input parameters");
-                        }
-                }
-                this.polarity = polarity;
-        }
-
-        public CallPolarity getPolarity() {
-                return polarity;
-        }
-
-        @Override
-        protected Literal doSubstitute(Substitution substitution, List<Variable> substitutedArguments) {
-                return new CallLiteral(polarity, getTarget(), substitutedArguments);
-        }
-
-        @Override
-        public Set<Variable> getOutputVariables() {
-                if (polarity.isPositive()) {
-                        return getArgumentsOfDirection(ParameterDirection.OUT);
-                }
-                return Set.of();
-        }
-
-        @Override
-        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
-                if (polarity.isPositive()) {
-                        return getArgumentsOfDirection(ParameterDirection.IN);
-                }
-                return super.getInputVariables(positiveVariablesInClause);
-        }
-
-        @Override
-        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
-                if (polarity.isPositive()) {
-                        return Set.of();
-                }
-                return super.getPrivateVariables(positiveVariablesInClause);
-        }
-
-        @Override
-        public Literal reduce() {
-                var reduction = getTarget().getReduction();
-                var negatedReduction = polarity.isPositive() ? reduction : reduction.negate();
-                return switch (negatedReduction) {
-                        case ALWAYS_TRUE -> BooleanLiteral.TRUE;
-                        case ALWAYS_FALSE -> BooleanLiteral.FALSE;
-                        default -> this;
-                };
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                if (!super.equalsWithSubstitution(helper, other)) {
-                        return false;
-                }
-                var otherCallLiteral = (CallLiteral) other;
-                return polarity.equals(otherCallLiteral.polarity);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCodeWithSubstitution(helper), polarity);
-        }
-
-        @Override
-        public CallLiteral negate() {
-                return new CallLiteral(polarity.negate(), getTarget(), getArguments());
-        }
-
-        @Override
-        public AbstractCallLiteral withArguments(Constraint newTarget, List<Variable> newArguments) {
-                return new CallLiteral(polarity, newTarget, newArguments);
-        }
-
-        @Override
-        public String toString() {
-                var builder = new StringBuilder();
-                if (!polarity.isPositive()) {
-                        builder.append("!(");
-                }
-                builder.append(getTarget().toReferenceString());
-                if (polarity.isTransitive()) {
-                        builder.append("+");
-                }
-                builder.append("(");
-                var argumentIterator = getArguments().iterator();
-                if (argumentIterator.hasNext()) {
-                        builder.append(argumentIterator.next());
-                        while (argumentIterator.hasNext()) {
-                                builder.append(", ").append(argumentIterator.next());
-                        }
-                }
-                builder.append(")");
-                if (!polarity.isPositive()) {
-                        builder.append(")");
-                }
-                return builder.toString();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallPolarity.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallPolarity.java
deleted file mode 100644
index 716c7109..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CallPolarity.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.InvalidQueryException;
-
-public enum CallPolarity {
-        POSITIVE(true, false),
-        NEGATIVE(false, false),
-        TRANSITIVE(true, true);
-
-        private final boolean positive;
-
-        private final boolean transitive;
-
-        CallPolarity(boolean positive, boolean transitive) {
-                this.positive = positive;
-                this.transitive = transitive;
-        }
-
-        public boolean isPositive() {
-                return positive;
-        }
-
-        public boolean isTransitive() {
-                return transitive;
-        }
-
-        public CallPolarity negate() {
-                return switch (this) {
-                        case POSITIVE -> NEGATIVE;
-                        case NEGATIVE -> POSITIVE;
-                        case TRANSITIVE -> throw new InvalidQueryException("Transitive polarity cannot be negated");
-                };
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CanNegate.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CanNegate.java
deleted file mode 100644
index 35dcb3fb..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CanNegate.java
+++ /dev/null
@@ -1,10 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-public interface CanNegate<T extends CanNegate<T>> extends Literal {
-        T negate();
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CheckLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CheckLiteral.java
deleted file mode 100644
index dfedd2cb..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CheckLiteral.java
+++ /dev/null
@@ -1,95 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.ConstantTerm;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.term.bool.BoolNotTerm;
-import tools.refinery.store.query.term.bool.BoolTerms;
-
-import java.util.Collections;
-import java.util.Objects;
-import java.util.Set;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractLiteral}.
-@SuppressWarnings("squid:S2160")
-public class CheckLiteral extends AbstractLiteral implements CanNegate<CheckLiteral> {
-        private final Term<Boolean> term;
-
-        public CheckLiteral(Term<Boolean> term) {
-                if (!term.getType().equals(Boolean.class)) {
-                        throw new InvalidQueryException("Term %s must be of type %s, got %s instead".formatted(
-                                        term, Boolean.class.getName(), term.getType().getName()));
-                }
-                this.term = term;
-        }
-
-        public Term<Boolean> getTerm() {
-                return term;
-        }
-
-        @Override
-        public Set<Variable> getOutputVariables() {
-                return Set.of();
-        }
-
-        @Override
-        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Collections.unmodifiableSet(term.getInputVariables());
-        }
-
-        @Override
-        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of();
-        }
-
-        @Override
-        public Literal substitute(Substitution substitution) {
-                return new CheckLiteral(term.substitute(substitution));
-        }
-
-        @Override
-        public CheckLiteral negate() {
-                if (term instanceof BoolNotTerm notTerm) {
-                        return new CheckLiteral(notTerm.getBody());
-                }
-                return new CheckLiteral(BoolTerms.not(term));
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                if (other == null || getClass() != other.getClass()) {
-                        return false;
-                }
-                var otherAssumeLiteral = (CheckLiteral) other;
-                return term.equalsWithSubstitution(helper, otherAssumeLiteral.term);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCodeWithSubstitution(helper), term.hashCodeWithSubstitution(helper));
-        }
-
-        @Override
-        public Literal reduce() {
-                if (term instanceof ConstantTerm<Boolean> constantTerm) {
-                        // Return {@link BooleanLiteral#FALSE} for {@code false} or {@code null} literals.
-                        return Boolean.TRUE.equals(constantTerm.getValue()) ? BooleanLiteral.TRUE :
-                                        BooleanLiteral.FALSE;
-                }
-                return this;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s)".formatted(term);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Connectivity.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Connectivity.java
deleted file mode 100644
index a058094d..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Connectivity.java
+++ /dev/null
@@ -1,18 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import java.util.Locale;
-
-public enum Connectivity {
-        WEAK,
-        STRONG;
-
-        @Override
-        public String toString() {
-                return name().toLowerCase(Locale.ROOT);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/ConstantLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/ConstantLiteral.java
deleted file mode 100644
index d83bd584..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/ConstantLiteral.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Objects;
-import java.util.Set;
-
-public class ConstantLiteral extends AbstractLiteral {
-        private final NodeVariable variable;
-        private final int nodeId;
-
-        public ConstantLiteral(NodeVariable variable, int nodeId) {
-                this.variable = variable;
-                this.nodeId = nodeId;
-        }
-
-        public NodeVariable getVariable() {
-                return variable;
-        }
-
-        public int getNodeId() {
-                return nodeId;
-        }
-
-
-        @Override
-        public Set<Variable> getOutputVariables() {
-                return Set.of(variable);
-        }
-
-        @Override
-        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of();
-        }
-
-        @Override
-        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of();
-        }
-
-        @Override
-        public ConstantLiteral substitute(Substitution substitution) {
-                return new ConstantLiteral(substitution.getTypeSafeSubstitute(variable), nodeId);
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                if (other.getClass() != getClass()) {
-                        return false;
-                }
-                var otherConstantLiteral = (ConstantLiteral) other;
-                return helper.variableEqual(variable, otherConstantLiteral.variable) && nodeId == otherConstantLiteral.nodeId;
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCodeWithSubstitution(helper), helper.getVariableHashCode(variable), nodeId);
-        }
-
-        @Override
-        public String toString() {
-                return "%s === @Constant %d".formatted(variable, nodeId);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CountLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CountLiteral.java
deleted file mode 100644
index 3d078d89..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/CountLiteral.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.Constraint;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.List;
-
-public class CountLiteral extends AbstractCountLiteral<Integer> {
-        public CountLiteral(DataVariable<Integer> resultVariable, Constraint target, List<Variable> arguments) {
-                super(Integer.class, resultVariable, target, arguments);
-        }
-
-        @Override
-        protected Integer zero() {
-                return 0;
-        }
-
-        @Override
-        protected Integer one() {
-                return 1;
-        }
-
-        @Override
-        protected Literal doSubstitute(Substitution substitution, List<Variable> substitutedArguments) {
-                return new CountLiteral(substitution.getTypeSafeSubstitute(getResultVariable()), getTarget(),
-                                substitutedArguments);
-        }
-
-        @Override
-        public AbstractCallLiteral withArguments(Constraint newTarget, List<Variable> newArguments) {
-                return new CountLiteral(getResultVariable(), newTarget, newArguments);
-        }
-
-        @Override
-        protected String operatorName() {
-                return "count";
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/EquivalenceLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/EquivalenceLiteral.java
deleted file mode 100644
index 7343f709..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/EquivalenceLiteral.java
+++ /dev/null
@@ -1,100 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Objects;
-import java.util.Set;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractLiteral}.
-@SuppressWarnings("squid:S2160")
-public final class EquivalenceLiteral extends AbstractLiteral implements CanNegate<EquivalenceLiteral> {
-        private final boolean positive;
-        private final Variable left;
-        private final Variable right;
-
-        public EquivalenceLiteral(boolean positive, Variable left, Variable right) {
-                if (!left.tryGetType().equals(right.tryGetType())) {
-                        throw new InvalidQueryException("Variables %s and %s of different type cannot be equivalent"
-                                        .formatted(left, right));
-                }
-                this.positive = positive;
-                this.left = left;
-                this.right = right;
-        }
-
-        public boolean isPositive() {
-                return positive;
-        }
-
-        public Variable getLeft() {
-                return left;
-        }
-
-        public Variable getRight() {
-                return right;
-        }
-
-        @Override
-        public Set<Variable> getOutputVariables() {
-                return Set.of(left);
-        }
-
-        @Override
-        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of(right);
-        }
-
-        @Override
-        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of();
-        }
-
-        @Override
-        public EquivalenceLiteral negate() {
-                return new EquivalenceLiteral(!positive, left, right);
-        }
-
-        @Override
-        public EquivalenceLiteral substitute(Substitution substitution) {
-                return new EquivalenceLiteral(positive, substitution.getSubstitute(left),
-                                substitution.getSubstitute(right));
-        }
-
-        @Override
-        public Literal reduce() {
-                if (left.equals(right)) {
-                        return positive ? BooleanLiteral.TRUE : BooleanLiteral.FALSE;
-                }
-                return this;
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                if (other.getClass() != getClass()) {
-                        return false;
-                }
-                var otherEquivalenceLiteral = (EquivalenceLiteral) other;
-                return helper.variableEqual(left, otherEquivalenceLiteral.left) &&
-                                helper.variableEqual(right, otherEquivalenceLiteral.right);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCodeWithSubstitution(helper), helper.getVariableHashCode(left),
-                                helper.getVariableHashCode(right));
-        }
-
-        @Override
-        public String toString() {
-                return "%s %s %s".formatted(left, positive ? "===" : "!==", right);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literal.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literal.java
deleted file mode 100644
index cb16ab00..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literal.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Set;
-
-public interface Literal {
-        Set<Variable> getOutputVariables();
-
-        Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause);
-
-        Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause);
-
-        Literal substitute(Substitution substitution);
-
-        default Literal reduce() {
-                return this;
-        }
-
-        @SuppressWarnings("BooleanMethodIsAlwaysInverted")
-        boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other);
-
-        int hashCodeWithSubstitution(LiteralHashCodeHelper helper);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literals.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literals.java
deleted file mode 100644
index 6056da45..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Literals.java
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.term.Term;
-
-public final class Literals {
-        private Literals() {
-                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
-        }
-
-        public static <T extends CanNegate<T>> T not(CanNegate<T> literal) {
-                return literal.negate();
-        }
-
-        public static CheckLiteral check(Term<Boolean> term) {
-                return new CheckLiteral(term);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Reduction.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Reduction.java
deleted file mode 100644
index ee155a9a..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/Reduction.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-public enum Reduction {
-        /**
-         * Signifies that a literal should be preserved in the clause.
-         */
-        NOT_REDUCIBLE,
-
-        /**
-         * Signifies that the literal may be omitted from the cause (if the model being queried is nonempty).
-         */
-        ALWAYS_TRUE,
-
-        /**
-         * Signifies that the clause with the literal may be omitted entirely.
-         */
-        ALWAYS_FALSE;
-
-        public Reduction negate() {
-                return switch (this) {
-                        case NOT_REDUCIBLE -> NOT_REDUCIBLE;
-                        case ALWAYS_TRUE -> ALWAYS_FALSE;
-                        case ALWAYS_FALSE -> ALWAYS_TRUE;
-                };
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/RepresentativeElectionLiteral.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/RepresentativeElectionLiteral.java
deleted file mode 100644
index f7323947..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/literal/RepresentativeElectionLiteral.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import tools.refinery.store.query.Constraint;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.List;
-import java.util.Set;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractLiteral}.
-@SuppressWarnings("squid:S2160")
-public class RepresentativeElectionLiteral extends AbstractCallLiteral {
-        private final Connectivity connectivity;
-
-        public RepresentativeElectionLiteral(Connectivity connectivity, Constraint target, NodeVariable specific,
-                                                                                 NodeVariable representative) {
-                this(connectivity, target, List.of(specific, representative));
-        }
-
-        private RepresentativeElectionLiteral(Connectivity connectivity, Constraint target, List<Variable> arguments) {
-                super(target, arguments);
-                this.connectivity = connectivity;
-                var parameters = target.getParameters();
-                int arity = target.arity();
-                if (arity != 2) {
-                        throw new InvalidQueryException("SCCs can only take binary relations");
-                }
-                if (parameters.get(0).isDataVariable() || parameters.get(1).isDataVariable()) {
-                        throw new InvalidQueryException("SCCs can only be computed over nodes");
-                }
-                if (parameters.get(0).getDirection() != ParameterDirection.OUT ||
-                                parameters.get(1).getDirection() != ParameterDirection.OUT) {
-                        throw new InvalidQueryException("SCCs cannot take input parameters");
-                }
-        }
-
-        public Connectivity getConnectivity() {
-                return connectivity;
-        }
-
-        @Override
-        protected Literal doSubstitute(Substitution substitution, List<Variable> substitutedArguments) {
-                return new RepresentativeElectionLiteral(connectivity, getTarget(), substitutedArguments);
-        }
-
-        @Override
-        public Set<Variable> getOutputVariables() {
-                return getArgumentsOfDirection(ParameterDirection.OUT);
-        }
-
-        @Override
-        public Set<Variable> getInputVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of();
-        }
-
-        @Override
-        public Set<Variable> getPrivateVariables(Set<? extends Variable> positiveVariablesInClause) {
-                return Set.of();
-        }
-
-        @Override
-        public Literal reduce() {
-                var reduction = getTarget().getReduction();
-                return switch (reduction) {
-                        case ALWAYS_FALSE -> BooleanLiteral.FALSE;
-                        case ALWAYS_TRUE -> throw new InvalidQueryException(
-                                        "Trying to elect representatives over an infinite set");
-                        case NOT_REDUCIBLE -> this;
-                };
-        }
-
-        @Override
-        public AbstractCallLiteral withArguments(Constraint newTarget, List<Variable> newArguments) {
-                return new RepresentativeElectionLiteral(connectivity, newTarget, newArguments);
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, Literal other) {
-                if (!super.equalsWithSubstitution(helper, other)) {
-                        return false;
-                }
-                var otherRepresentativeElectionLiteral = (RepresentativeElectionLiteral) other;
-                return connectivity.equals(otherRepresentativeElectionLiteral.connectivity);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return super.hashCodeWithSubstitution(helper) * 31 + connectivity.hashCode();
-        }
-
-        @Override
-        public String toString() {
-                var builder = new StringBuilder();
-                builder.append("@Representative(\"");
-                builder.append(connectivity);
-                builder.append("\") ");
-                builder.append(getTarget().toReferenceString());
-                builder.append("(");
-                var argumentIterator = getArguments().iterator();
-                if (argumentIterator.hasNext()) {
-                        builder.append(argumentIterator.next());
-                        while (argumentIterator.hasNext()) {
-                                builder.append(", ").append(argumentIterator.next());
-                        }
-                }
-                builder.append(")");
-                return builder.toString();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AbstractResultSet.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AbstractResultSet.java
index dcfe6cc5..f8290b48 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AbstractResultSet.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AbstractResultSet.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.query.resultset;
 
 import tools.refinery.store.query.ModelQueryAdapter;
-import tools.refinery.store.query.dnf.Query;
+import tools.refinery.logic.dnf.Query;
 import tools.refinery.store.tuple.Tuple;
 
 import java.util.ArrayList;
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AnyResultSet.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AnyResultSet.java
index 5b75b103..038ca7f9 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AnyResultSet.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/AnyResultSet.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.query.resultset;
 
 import tools.refinery.store.query.ModelQueryAdapter;
-import tools.refinery.store.query.dnf.AnyQuery;
+import tools.refinery.logic.dnf.AnyQuery;
 
 public sealed interface AnyResultSet permits ResultSet {
         ModelQueryAdapter getAdapter();
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/EmptyResultSet.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/EmptyResultSet.java
index 991b1e32..daebfe7c 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/EmptyResultSet.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/EmptyResultSet.java
@@ -8,7 +8,7 @@ package tools.refinery.store.query.resultset;
 import tools.refinery.store.map.Cursor;
 import tools.refinery.store.map.Cursors;
 import tools.refinery.store.query.ModelQueryAdapter;
-import tools.refinery.store.query.dnf.Query;
+import tools.refinery.logic.dnf.Query;
 import tools.refinery.store.tuple.Tuple;
 
 public record EmptyResultSet<T>(ModelQueryAdapter adapter, Query<T> query) implements ResultSet<T> {
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/OrderedResultSet.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/OrderedResultSet.java
index df12b967..606e197c 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/OrderedResultSet.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/OrderedResultSet.java
@@ -7,7 +7,7 @@ package tools.refinery.store.query.resultset;
 
 import tools.refinery.store.map.Cursor;
 import tools.refinery.store.query.ModelQueryAdapter;
-import tools.refinery.store.query.dnf.Query;
+import tools.refinery.logic.dnf.Query;
 import tools.refinery.store.query.utils.OrderStatisticTree;
 import tools.refinery.store.tuple.Tuple;
 
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/ResultSet.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/ResultSet.java
index a6e99784..e84634ac 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/ResultSet.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/resultset/ResultSet.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.query.resultset;
 
 import tools.refinery.store.map.Cursor;
-import tools.refinery.store.query.dnf.Query;
+import tools.refinery.logic.dnf.Query;
 import tools.refinery.store.tuple.Tuple;
 
 public non-sealed interface ResultSet<T> extends AnyResultSet {
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/AbstractRecursiveRewriter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/AbstractRecursiveRewriter.java
deleted file mode 100644
index fb4c14a7..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/AbstractRecursiveRewriter.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.rewriter;
-
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.equality.DnfEqualityChecker;
-import tools.refinery.store.util.CycleDetectingMapper;
-
-public abstract class AbstractRecursiveRewriter implements DnfRewriter {
-        private final CycleDetectingMapper<Dnf, Dnf> mapper = new CycleDetectingMapper<>(Dnf::name, this::map);
-
-        @Override
-        public Dnf rewrite(Dnf dnf) {
-                return mapper.map(dnf);
-        }
-
-        protected Dnf map(Dnf dnf) {
-                var result = doRewrite(dnf);
-                return dnf.equalsWithSubstitution(DnfEqualityChecker.DEFAULT, result) ? dnf : result;
-        }
-
-        protected abstract Dnf doRewrite(Dnf dnf);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/ClauseInputParameterResolver.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/ClauseInputParameterResolver.java
deleted file mode 100644
index aa06a05a..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/ClauseInputParameterResolver.java
+++ /dev/null
@@ -1,160 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.rewriter;
-
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.DnfClause;
-import tools.refinery.store.query.literal.*;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.*;
-
-class ClauseInputParameterResolver {
-        private final InputParameterResolver rewriter;
-        private final String dnfName;
-        private final int clauseIndex;
-        private final Set<Variable> positiveVariables = new LinkedHashSet<>();
-        private final List<Literal> inlinedLiterals = new ArrayList<>();
-        private final Deque<Literal> workList;
-        private int helperIndex = 0;
-
-        public ClauseInputParameterResolver(InputParameterResolver rewriter, List<Literal> context, DnfClause clause,
-                                                                                String dnfName, int clauseIndex) {
-                this.rewriter = rewriter;
-                this.dnfName = dnfName;
-                this.clauseIndex = clauseIndex;
-                workList = new ArrayDeque<>(clause.literals().size() + context.size());
-                for (var literal : context) {
-                        workList.addLast(literal);
-                }
-                for (var literal : clause.literals()) {
-                        workList.addLast(literal);
-                }
-        }
-
-        public List<Literal> rewriteClause() {
-                while (!workList.isEmpty()) {
-                        var literal = workList.removeFirst();
-                        processLiteral(literal);
-                }
-                return inlinedLiterals;
-        }
-
-        private void processLiteral(Literal literal) {
-                if (!(literal instanceof AbstractCallLiteral abstractCallLiteral) ||
-                                !(abstractCallLiteral.getTarget() instanceof Dnf targetDnf)) {
-                        markAsDone(literal);
-                        return;
-                }
-                boolean hasInputParameter = hasInputParameter(targetDnf);
-                if (!hasInputParameter) {
-                        targetDnf = rewriter.rewrite(targetDnf);
-                }
-                if (inlinePositiveClause(abstractCallLiteral, targetDnf)) {
-                        return;
-                }
-                if (eliminateDoubleNegation(abstractCallLiteral, targetDnf)) {
-                        return;
-                }
-                if (hasInputParameter) {
-                        rewriteWithCurrentContext(abstractCallLiteral, targetDnf);
-                        return;
-                }
-                markAsDone(abstractCallLiteral.withTarget(targetDnf));
-        }
-
-        private void markAsDone(Literal literal) {
-                positiveVariables.addAll(literal.getOutputVariables());
-                inlinedLiterals.add(literal);
-        }
-
-        private boolean inlinePositiveClause(AbstractCallLiteral abstractCallLiteral, Dnf targetDnf) {
-                var targetLiteral = getSingleLiteral(abstractCallLiteral, targetDnf, CallPolarity.POSITIVE);
-                if (targetLiteral == null) {
-                        return false;
-                }
-                var substitution = asSubstitution(abstractCallLiteral, targetDnf);
-                var substitutedLiteral = targetLiteral.substitute(substitution);
-                workList.addFirst(substitutedLiteral);
-                return true;
-        }
-
-        private boolean eliminateDoubleNegation(AbstractCallLiteral abstractCallLiteral, Dnf targetDnf) {
-                var targetLiteral = getSingleLiteral(abstractCallLiteral, targetDnf, CallPolarity.NEGATIVE);
-                if (!(targetLiteral instanceof CallLiteral targetCallLiteral) ||
-                                targetCallLiteral.getPolarity() != CallPolarity.NEGATIVE) {
-                        return false;
-                }
-                var substitution = asSubstitution(abstractCallLiteral, targetDnf);
-                var substitutedLiteral = (CallLiteral) targetCallLiteral.substitute(substitution);
-                workList.addFirst(substitutedLiteral.negate());
-                return true;
-        }
-
-        private void rewriteWithCurrentContext(AbstractCallLiteral abstractCallLiteral, Dnf targetDnf) {
-                var contextBuilder = Dnf.builder("%s#clause%d#helper%d".formatted(dnfName, clauseIndex, helperIndex));
-                helperIndex++;
-                contextBuilder.parameters(positiveVariables, ParameterDirection.OUT);
-                contextBuilder.clause(inlinedLiterals);
-                var contextDnf = contextBuilder.build();
-                var contextCall = new CallLiteral(CallPolarity.POSITIVE, contextDnf, List.copyOf(positiveVariables));
-                inlinedLiterals.clear();
-                var substitution = Substitution.builder().renewing().build();
-                var context = new ArrayList<Literal>();
-                context.add(contextCall.substitute(substitution));
-                int arity = targetDnf.arity();
-                for (int i = 0; i < arity; i++) {
-                        var parameter = targetDnf.getSymbolicParameters().get(i).getVariable();
-                        var argument = abstractCallLiteral.getArguments().get(i);
-                        context.add(new EquivalenceLiteral(true, parameter, substitution.getSubstitute(argument)));
-                }
-                var rewrittenDnf = rewriter.rewriteWithContext(context, targetDnf);
-                workList.addFirst(abstractCallLiteral.withTarget(rewrittenDnf));
-                workList.addFirst(contextCall);
-        }
-
-        private static boolean hasInputParameter(Dnf targetDnf) {
-                for (var parameter : targetDnf.getParameters()) {
-                        if (parameter.getDirection() != ParameterDirection.OUT) {
-                                return true;
-                        }
-                }
-                return false;
-        }
-
-        private static Literal getSingleLiteral(AbstractCallLiteral abstractCallLiteral, Dnf targetDnf,
-                                                                                        CallPolarity polarity) {
-                if (!(abstractCallLiteral instanceof CallLiteral callLiteral) ||
-                                callLiteral.getPolarity() != polarity) {
-                        return null;
-                }
-                var clauses = targetDnf.getClauses();
-                if (clauses.size() != 1) {
-                        return null;
-                }
-                var targetLiterals = clauses.get(0).literals();
-                if (targetLiterals.size() != 1) {
-                        return null;
-                }
-                return targetLiterals.get(0);
-        }
-
-        private static Substitution asSubstitution(AbstractCallLiteral callLiteral, Dnf targetDnf) {
-                var builder = Substitution.builder().renewing();
-                var arguments = callLiteral.getArguments();
-                var parameters = targetDnf.getSymbolicParameters();
-                int arity = arguments.size();
-                if (parameters.size() != arity) {
-                        throw new IllegalArgumentException("Call %s of %s arity mismatch".formatted(callLiteral, targetDnf));
-                }
-                for (int i = 0; i < arity; i++) {
-                        builder.putChecked(parameters.get(i).getVariable(), arguments.get(i));
-                }
-                return builder.build();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/CompositeRewriter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/CompositeRewriter.java
deleted file mode 100644
index 5b4f65e5..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/CompositeRewriter.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.rewriter;
-
-import tools.refinery.store.query.dnf.Dnf;
-
-import java.util.ArrayList;
-import java.util.List;
-
-public class CompositeRewriter implements DnfRewriter {
-        private final List<DnfRewriter> rewriterList = new ArrayList<>();
-
-        public void addFirst(DnfRewriter rewriter) {
-                rewriterList.add(rewriter);
-        }
-
-        @Override
-        public Dnf rewrite(Dnf dnf) {
-                Dnf rewrittenDnf = dnf;
-                for (int i = rewriterList.size() - 1; i >= 0; i--) {
-                        var rewriter = rewriterList.get(i);
-                        rewrittenDnf = rewriter.rewrite(rewrittenDnf);
-                }
-                return rewrittenDnf;
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/DnfRewriter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/DnfRewriter.java
deleted file mode 100644
index 5d8359d1..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/DnfRewriter.java
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.rewriter;
-
-import tools.refinery.store.query.dnf.AnyQuery;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.Query;
-
-@FunctionalInterface
-public interface DnfRewriter {
-        Dnf rewrite(Dnf dnf);
-
-        default AnyQuery rewrite(AnyQuery query) {
-                return rewrite((Query<?>) query);
-        }
-
-        default <T> Query<T> rewrite(Query<T> query) {
-                var rewrittenDnf = rewrite(query.getDnf());
-                return query.withDnf(rewrittenDnf);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/DuplicateDnfRemover.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/DuplicateDnfRemover.java
deleted file mode 100644
index 0c786470..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/DuplicateDnfRemover.java
+++ /dev/null
@@ -1,98 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.rewriter;
-
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.DnfClause;
-import tools.refinery.store.query.dnf.Query;
-import tools.refinery.store.query.equality.DnfEqualityChecker;
-import tools.refinery.store.query.literal.AbstractCallLiteral;
-import tools.refinery.store.query.literal.Literal;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-public class DuplicateDnfRemover extends AbstractRecursiveRewriter {
-        private final Map<CanonicalDnf, Dnf> dnfCache = new HashMap<>();
-        private final Map<Dnf, Query<?>> queryCache = new HashMap<>();
-
-        @Override
-        protected Dnf map(Dnf dnf) {
-                var result = super.map(dnf);
-                return dnfCache.computeIfAbsent(new CanonicalDnf(result), CanonicalDnf::getDnf);
-        }
-
-        @Override
-        protected Dnf doRewrite(Dnf dnf) {
-                var builder = Dnf.builderFrom(dnf);
-                for (var clause : dnf.getClauses()) {
-                        builder.clause(rewriteClause(clause));
-                }
-                return builder.build();
-        }
-
-        private List<Literal> rewriteClause(DnfClause clause) {
-                var originalLiterals = clause.literals();
-                var literals = new ArrayList<Literal>(originalLiterals.size());
-                for (var literal : originalLiterals) {
-                        var rewrittenLiteral = literal;
-                        if (literal instanceof AbstractCallLiteral abstractCallLiteral &&
-                                        abstractCallLiteral.getTarget() instanceof Dnf targetDnf) {
-                                var rewrittenTarget = rewrite(targetDnf);
-                                rewrittenLiteral = abstractCallLiteral.withTarget(rewrittenTarget);
-                        }
-                        literals.add(rewrittenLiteral);
-                }
-                return literals;
-        }
-
-        @Override
-        public <T> Query<T> rewrite(Query<T> query) {
-                var rewrittenDnf = rewrite(query.getDnf());
-                // {@code withDnf} will always return the appropriate type.
-                @SuppressWarnings("unchecked")
-                var rewrittenQuery = (Query<T>) queryCache.computeIfAbsent(rewrittenDnf, query::withDnf);
-                return rewrittenQuery;
-        }
-
-        private static class CanonicalDnf {
-                private final Dnf dnf;
-                private final int hash;
-
-                public CanonicalDnf(Dnf dnf) {
-                        this.dnf = dnf;
-                        hash = dnf.hashCodeWithSubstitution();
-                }
-
-                public Dnf getDnf() {
-                        return dnf;
-                }
-
-                @Override
-                public boolean equals(Object obj) {
-                        if (this == obj) {
-                                return true;
-                        }
-                        if (obj == null || getClass() != obj.getClass()) {
-                                return false;
-                        }
-                        var otherCanonicalDnf = (CanonicalDnf) obj;
-                        return dnf.equalsWithSubstitution(DnfEqualityChecker.DEFAULT, otherCanonicalDnf.dnf);
-                }
-
-                @Override
-                public int hashCode() {
-                        return hash;
-                }
-
-                @Override
-                public String toString() {
-                        return dnf.name();
-                }
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/InputParameterResolver.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/InputParameterResolver.java
deleted file mode 100644
index cd8a2e7d..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/rewriter/InputParameterResolver.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.rewriter;
-
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.DnfBuilder;
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.HashSet;
-import java.util.List;
-
-public class InputParameterResolver extends AbstractRecursiveRewriter {
-        @Override
-        protected Dnf doRewrite(Dnf dnf) {
-                return rewriteWithContext(List.of(), dnf);
-        }
-
-        Dnf rewriteWithContext(List<Literal> context, Dnf dnf) {
-                var dnfName = dnf.name();
-                var builder = Dnf.builder(dnfName);
-                createSymbolicParameters(context, dnf, builder);
-                builder.functionalDependencies(dnf.getFunctionalDependencies());
-                var clauses = dnf.getClauses();
-                int clauseCount = clauses.size();
-                for (int i = 0; i < clauseCount; i++) {
-                        var clause = clauses.get(i);
-                        var clauseRewriter = new ClauseInputParameterResolver(this, context, clause, dnfName, i);
-                        builder.clause(clauseRewriter.rewriteClause());
-                }
-                return builder.build();
-        }
-
-        private static void createSymbolicParameters(List<Literal> context, Dnf dnf, DnfBuilder builder) {
-                var positiveInContext = new HashSet<Variable>();
-                for (var literal : context) {
-                        positiveInContext.addAll(literal.getOutputVariables());
-                }
-                for (var symbolicParameter : dnf.getSymbolicParameters()) {
-                        var variable = symbolicParameter.getVariable();
-                        var isOutput = symbolicParameter.getDirection() == ParameterDirection.OUT ||
-                                        positiveInContext.contains(variable);
-                        var direction = isOutput ? ParameterDirection.OUT : ParameterDirection.IN;
-                        builder.parameter(variable, direction);
-                }
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/MapBasedSubstitution.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/MapBasedSubstitution.java
deleted file mode 100644
index a8201eef..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/MapBasedSubstitution.java
+++ /dev/null
@@ -1,18 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.substitution;
-
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Map;
-
-public record MapBasedSubstitution(Map<Variable, Variable> map, Substitution fallback) implements Substitution {
-        @Override
-        public Variable getSubstitute(Variable variable) {
-                var value = map.get(variable);
-                return value == null ? fallback.getSubstitute(variable) : value;
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/RenewingSubstitution.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/RenewingSubstitution.java
deleted file mode 100644
index 9b737ceb..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/RenewingSubstitution.java
+++ /dev/null
@@ -1,20 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.substitution;
-
-import tools.refinery.store.query.term.Variable;
-
-import java.util.HashMap;
-import java.util.Map;
-
-public class RenewingSubstitution implements Substitution {
-        private final Map<Variable, Variable> alreadyRenewed = new HashMap<>();
-
-        @Override
-        public Variable getSubstitute(Variable variable) {
-                return alreadyRenewed.computeIfAbsent(variable, Variable::renew);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/StatelessSubstitution.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/StatelessSubstitution.java
deleted file mode 100644
index bb3803d3..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/StatelessSubstitution.java
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.substitution;
-
-import tools.refinery.store.query.term.Variable;
-
-public enum StatelessSubstitution implements Substitution {
-        FAILING {
-                @Override
-                public Variable getSubstitute(Variable variable) {
-                        throw new IllegalArgumentException("No substitute for " + variable);
-                }
-        },
-        IDENTITY {
-                @Override
-                public Variable getSubstitute(Variable variable) {
-                        return variable;
-                }
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/Substitution.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/Substitution.java
deleted file mode 100644
index 834fce12..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/Substitution.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.substitution;
-
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.Variable;
-
-@FunctionalInterface
-public interface Substitution {
-        Variable getSubstitute(Variable variable);
-
-        default NodeVariable getTypeSafeSubstitute(NodeVariable variable) {
-                var substitute = getSubstitute(variable);
-                return substitute.asNodeVariable();
-        }
-
-        default <T> DataVariable<T> getTypeSafeSubstitute(DataVariable<T> variable) {
-                var substitute = getSubstitute(variable);
-                return substitute.asDataVariable(variable.getType());
-        }
-
-        static SubstitutionBuilder builder() {
-                return new SubstitutionBuilder();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/SubstitutionBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/SubstitutionBuilder.java
deleted file mode 100644
index 37fb6908..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/substitution/SubstitutionBuilder.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.substitution;
-
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-@SuppressWarnings("UnusedReturnValue")
-public class SubstitutionBuilder {
-        private final Map<Variable, Variable> map = new HashMap<>();
-        private Substitution fallback;
-
-        SubstitutionBuilder() {
-                total();
-        }
-
-        public SubstitutionBuilder put(NodeVariable original, NodeVariable substitute) {
-                return putChecked(original, substitute);
-        }
-
-        public <T> SubstitutionBuilder put(DataVariable<T> original, DataVariable<T> substitute) {
-                return putChecked(original, substitute);
-        }
-
-        public SubstitutionBuilder putChecked(Variable original, Variable substitute) {
-                if (!original.tryGetType().equals(substitute.tryGetType())) {
-                        throw new IllegalArgumentException("Cannot substitute variable %s of sort %s with variable %s of sort %s"
-                                        .formatted(original, original.tryGetType().map(Class::getName).orElse("node"), substitute,
-                                                        substitute.tryGetType().map(Class::getName).orElse("node")));
-                }
-                if (map.containsKey(original)) {
-                        throw new IllegalArgumentException("Already has substitution for variable %s".formatted(original));
-                }
-                map.put(original, substitute);
-                return this;
-        }
-
-        public SubstitutionBuilder putManyChecked(List<Variable> originals, List<Variable> substitutes) {
-                int size = originals.size();
-                if (size != substitutes.size()) {
-                        throw new IllegalArgumentException("Cannot substitute %d variables %s with %d variables %s"
-                                        .formatted(size, originals, substitutes.size(), substitutes));
-                }
-                for (int i = 0; i < size; i++) {
-                        putChecked(originals.get(i), substitutes.get(i));
-                }
-                return this;
-        }
-
-        public SubstitutionBuilder fallback(Substitution newFallback) {
-                fallback = newFallback;
-                return this;
-        }
-
-        public SubstitutionBuilder total() {
-                return fallback(StatelessSubstitution.FAILING);
-        }
-
-        public SubstitutionBuilder partial() {
-                return fallback(StatelessSubstitution.IDENTITY);
-        }
-
-        public SubstitutionBuilder renewing() {
-                return fallback(new RenewingSubstitution());
-        }
-
-        public Substitution build() {
-                return map.isEmpty() ? fallback : new MapBasedSubstitution(Collections.unmodifiableMap(map), fallback);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AbstractTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AbstractTerm.java
deleted file mode 100644
index 5cecc35b..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AbstractTerm.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-
-import java.util.Objects;
-
-public abstract class AbstractTerm<T> implements Term<T> {
-        private final Class<T> type;
-
-        protected AbstractTerm(Class<T> type) {
-                this.type = type;
-        }
-
-        @Override
-        public Class<T> getType() {
-                return type;
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
-                return other != null && getClass() == other.getClass() && type.equals(other.getType());
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(getClass(), type);
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                AbstractTerm<?> that = (AbstractTerm<?>) o;
-                return equalsWithSubstitution(LiteralEqualityHelper.DEFAULT, that);
-        }
-
-        @Override
-        public int hashCode() {
-                return hashCodeWithSubstitution(LiteralHashCodeHelper.DEFAULT);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Aggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Aggregator.java
deleted file mode 100644
index 0684a9d9..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Aggregator.java
+++ /dev/null
@@ -1,18 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import java.util.stream.Stream;
-
-public interface Aggregator<R, T> {
-        Class<R> getResultType();
-
-        Class<T> getInputType();
-
-        R aggregateStream(Stream<T> stream);
-
-        R getEmptyResult();
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyDataVariable.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyDataVariable.java
deleted file mode 100644
index 3801bc11..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyDataVariable.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import org.jetbrains.annotations.Nullable;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-
-import java.util.Optional;
-import java.util.Set;
-
-public abstract sealed class AnyDataVariable extends Variable implements AnyTerm permits DataVariable {
-        protected AnyDataVariable(String name) {
-                super(name);
-        }
-
-        @Override
-        public Optional<Class<?>> tryGetType() {
-                return Optional.of(getType());
-        }
-
-        @Override
-        public boolean isNodeVariable() {
-                return false;
-        }
-
-        @Override
-        public boolean isDataVariable() {
-                return true;
-        }
-
-        @Override
-        public NodeVariable asNodeVariable() {
-                throw new InvalidQueryException("%s is a data variable".formatted(this));
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
-                return other instanceof AnyDataVariable dataVariable && helper.variableEqual(this, dataVariable);
-        }
-
-        @Override
-        public Set<AnyDataVariable> getInputVariables() {
-                return Set.of(this);
-        }
-
-        @Override
-        public abstract AnyDataVariable renew(@Nullable String name);
-
-        @Override
-        public abstract AnyDataVariable renew();
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyTerm.java
deleted file mode 100644
index f136b68d..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AnyTerm.java
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-
-import java.util.Set;
-
-public sealed interface AnyTerm permits AnyDataVariable, Term {
-        Class<?> getType();
-
-        AnyTerm substitute(Substitution substitution);
-
-        boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other);
-
-        int hashCodeWithSubstitution(LiteralHashCodeHelper helper);
-
-        Set<AnyDataVariable> getInputVariables();
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AssignedValue.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AssignedValue.java
deleted file mode 100644
index 0cf30aa6..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/AssignedValue.java
+++ /dev/null
@@ -1,13 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import tools.refinery.store.query.literal.Literal;
-
-@FunctionalInterface
-public interface AssignedValue<T> {
-        Literal toLiteral(DataVariable<T> targetVariable);
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/BinaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/BinaryTerm.java
deleted file mode 100644
index cdbf592a..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/BinaryTerm.java
+++ /dev/null
@@ -1,106 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.valuation.Valuation;
-
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Objects;
-import java.util.Set;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractTerm}.
-@SuppressWarnings("squid:S2160")
-public abstract class BinaryTerm<R, T1, T2> extends AbstractTerm<R> {
-        private final Class<T1> leftType;
-        private final Class<T2> rightType;
-        private final Term<T1> left;
-        private final Term<T2> right;
-
-        protected BinaryTerm(Class<R> type, Class<T1> leftType, Class<T2> rightType, Term<T1> left, Term<T2> right) {
-                super(type);
-                if (!left.getType().equals(leftType)) {
-                        throw new InvalidQueryException("Expected left %s to be of type %s, got %s instead".formatted(
-                                        left, leftType.getName(), left.getType().getName()));
-                }
-                if (!right.getType().equals(rightType)) {
-                        throw new InvalidQueryException("Expected right %s to be of type %s, got %s instead".formatted(
-                                        right, rightType.getName(), right.getType().getName()));
-                }
-                this.leftType = leftType;
-                this.rightType = rightType;
-                this.left = left;
-                this.right = right;
-        }
-
-        public Class<T1> getLeftType() {
-                return leftType;
-        }
-
-        public Class<T2> getRightType() {
-                return rightType;
-        }
-
-        public Term<T1> getLeft() {
-                return left;
-        }
-
-        public Term<T2> getRight() {
-                return right;
-        }
-
-        @Override
-        public R evaluate(Valuation valuation) {
-                var leftValue = left.evaluate(valuation);
-                if (leftValue == null) {
-                        return null;
-                }
-                var rightValue = right.evaluate(valuation);
-                if (rightValue == null) {
-                        return null;
-                }
-                return doEvaluate(leftValue, rightValue);
-        }
-
-        protected abstract R doEvaluate(T1 leftValue, T2 rightValue);
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
-                if (!super.equalsWithSubstitution(helper, other)) {
-                        return false;
-                }
-                var otherBinaryTerm = (BinaryTerm<?, ?, ?>) other;
-                return leftType.equals(otherBinaryTerm.leftType) &&
-                                rightType.equals(otherBinaryTerm.rightType) &&
-                                left.equalsWithSubstitution(helper, otherBinaryTerm.left) &&
-                                right.equalsWithSubstitution(helper, otherBinaryTerm.right);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCodeWithSubstitution(helper), leftType.hashCode(), rightType.hashCode(),
-                                left.hashCodeWithSubstitution(helper), right.hashCodeWithSubstitution(helper));
-        }
-
-        @Override
-        public Term<R> substitute(Substitution substitution) {
-                return doSubstitute(substitution, left.substitute(substitution), right.substitute(substitution));
-        }
-
-        public abstract Term<R> doSubstitute(Substitution substitution, Term<T1> substitutedLeft,
-                                                                                 Term<T2> substitutedRight);
-
-        @Override
-        public Set<AnyDataVariable> getInputVariables() {
-                var inputVariables = new HashSet<>(left.getInputVariables());
-                inputVariables.addAll(right.getInputVariables());
-                return Collections.unmodifiableSet(inputVariables);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ConstantTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ConstantTerm.java
deleted file mode 100644
index 415ae286..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ConstantTerm.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.valuation.Valuation;
-
-import java.util.Objects;
-import java.util.Set;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractTerm}.
-@SuppressWarnings("squid:S2160")
-public final class ConstantTerm<T> extends AbstractTerm<T> {
-        private final T value;
-
-        public ConstantTerm(Class<T> type, T value) {
-                super(type);
-                if (value != null && !type.isInstance(value)) {
-                        throw new InvalidQueryException("Value %s is not an instance of %s".formatted(value, type.getName()));
-                }
-                this.value = value;
-        }
-
-        public T getValue() {
-                return value;
-        }
-
-        @Override
-        public T evaluate(Valuation valuation) {
-                return getValue();
-        }
-
-        @Override
-        public Term<T> substitute(Substitution substitution) {
-                return this;
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
-                if (!super.equalsWithSubstitution(helper, other)) {
-                        return false;
-                }
-                var otherConstantTerm = (ConstantTerm<?>) other;
-                return Objects.equals(value, otherConstantTerm.value);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCodeWithSubstitution(helper), Objects.hash(value));
-        }
-
-        @Override
-        public Set<AnyDataVariable> getInputVariables() {
-                return Set.of();
-        }
-
-        @Override
-        public String toString() {
-                return value.toString();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/DataVariable.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/DataVariable.java
deleted file mode 100644
index 2206b522..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/DataVariable.java
+++ /dev/null
@@ -1,103 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import org.jetbrains.annotations.Nullable;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.literal.EquivalenceLiteral;
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.valuation.Valuation;
-
-import java.util.Objects;
-
-public final class DataVariable<T> extends AnyDataVariable implements Term<T> {
-        private final Class<T> type;
-
-        DataVariable(String name, Class<T> type) {
-                super(name);
-                this.type = type;
-        }
-
-        @Override
-        public Class<T> getType() {
-                return type;
-        }
-
-        @Override
-        public DataVariable<T> renew(@Nullable String name) {
-                return new DataVariable<>(name, type);
-        }
-
-        @Override
-        public DataVariable<T> renew() {
-                return renew(getExplicitName());
-        }
-
-        @Override
-        public <U> DataVariable<U> asDataVariable(Class<U> newType) {
-                if (!getType().equals(newType)) {
-                        throw new InvalidQueryException("%s is not of type %s but of type %s"
-                                        .formatted(this, newType.getName(), getType().getName()));
-                }
-                @SuppressWarnings("unchecked")
-                var result = (DataVariable<U>) this;
-                return result;
-        }
-
-        @Override
-        public T evaluate(Valuation valuation) {
-                return valuation.getValue(this);
-        }
-
-        @Override
-        public Term<T> substitute(Substitution substitution) {
-                return substitution.getTypeSafeSubstitute(this);
-        }
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
-                return other instanceof DataVariable<?> dataVariable && helper.variableEqual(this, dataVariable);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return helper.getVariableHashCode(this);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(int sequenceNumber) {
-                return Objects.hash(type, sequenceNumber);
-        }
-
-        public Literal assign(AssignedValue<T> value) {
-                return value.toLiteral(this);
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                if (!super.equals(o)) return false;
-                DataVariable<?> that = (DataVariable<?>) o;
-                return type.equals(that.type);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(super.hashCode(), type);
-        }
-
-        public EquivalenceLiteral isEquivalent(DataVariable<T> other) {
-                return new EquivalenceLiteral(true, this, other);
-        }
-
-        public EquivalenceLiteral notEquivalent(DataVariable<T> other) {
-                return new EquivalenceLiteral(false, this, other);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ExtremeValueAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ExtremeValueAggregator.java
deleted file mode 100644
index 657cb631..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ExtremeValueAggregator.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import java.util.Comparator;
-import java.util.Objects;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
-public class ExtremeValueAggregator<T> implements StatefulAggregator<T, T> {
-        private final Class<T> type;
-        private final T emptyResult;
-        private final Comparator<T> comparator;
-
-        public ExtremeValueAggregator(Class<T> type, T emptyResult) {
-                this(type, emptyResult, null);
-        }
-
-        public ExtremeValueAggregator(Class<T> type, T emptyResult, Comparator<T> comparator) {
-                this.type = type;
-                this.emptyResult = emptyResult;
-                this.comparator = comparator;
-        }
-
-        @Override
-        public Class<T> getResultType() {
-                return getInputType();
-        }
-
-        @Override
-        public Class<T> getInputType() {
-                return type;
-        }
-
-        @Override
-        public StatefulAggregate<T, T> createEmptyAggregate() {
-                return new Aggregate();
-        }
-
-        @Override
-        public T getEmptyResult() {
-                return emptyResult;
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                ExtremeValueAggregator<?> that = (ExtremeValueAggregator<?>) o;
-                return type.equals(that.type) && Objects.equals(emptyResult, that.emptyResult) && Objects.equals(comparator,
-                                that.comparator);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(type, emptyResult, comparator);
-        }
-
-        private class Aggregate implements StatefulAggregate<T, T> {
-                private final SortedMap<T, Integer> values;
-
-                private Aggregate() {
-                        values = new TreeMap<>(comparator);
-                }
-
-                private Aggregate(Aggregate other) {
-                        values = new TreeMap<>(other.values);
-                }
-
-                @Override
-                public void add(T value) {
-                        values.compute(value, (ignoredValue, currentCount) -> currentCount == null ? 1 : currentCount + 1);
-                }
-
-                @Override
-                public void remove(T value) {
-                        values.compute(value, (theValue, currentCount) -> {
-                                if (currentCount == null || currentCount <= 0) {
-                                        throw new IllegalStateException("Invalid count %d for value %s".formatted(currentCount, theValue));
-                                }
-                                return currentCount.equals(1) ? null : currentCount - 1;
-                        });
-                }
-
-                @Override
-                public T getResult() {
-                        return isEmpty() ? emptyResult : values.firstKey();
-                }
-
-                @Override
-                public boolean isEmpty() {
-                        return values.isEmpty();
-                }
-
-                @Override
-                public StatefulAggregate<T, T> deepCopy() {
-                        return new Aggregate(this);
-                }
-
-                @Override
-                public boolean contains(T value) {
-                        return StatefulAggregate.super.contains(value);
-                }
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/NodeVariable.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/NodeVariable.java
deleted file mode 100644
index 53c32e20..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/NodeVariable.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import org.jetbrains.annotations.Nullable;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.literal.ConstantLiteral;
-import tools.refinery.store.query.literal.EquivalenceLiteral;
-
-import java.util.Optional;
-
-public final class NodeVariable extends Variable {
-        NodeVariable(@Nullable String name) {
-                super(name);
-        }
-
-        @Override
-        public Optional<Class<?>> tryGetType() {
-                return Optional.empty();
-        }
-
-        @Override
-        public NodeVariable renew(@Nullable String name) {
-                return Variable.of(name);
-        }
-
-        @Override
-        public NodeVariable renew() {
-                return renew(getExplicitName());
-        }
-
-        @Override
-        public boolean isNodeVariable() {
-                return true;
-        }
-
-        @Override
-        public boolean isDataVariable() {
-                return false;
-        }
-
-        @Override
-        public NodeVariable asNodeVariable() {
-                return this;
-        }
-
-        @Override
-        public <T> DataVariable<T> asDataVariable(Class<T> type) {
-                throw new InvalidQueryException("%s is a node variable".formatted(this));
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(int sequenceNumber) {
-                return sequenceNumber;
-        }
-
-        public ConstantLiteral isConstant(int value) {
-                return new ConstantLiteral(this, value);
-        }
-
-        public EquivalenceLiteral isEquivalent(NodeVariable other) {
-                return new EquivalenceLiteral(true, this, other);
-        }
-
-        public EquivalenceLiteral notEquivalent(NodeVariable other) {
-                return new EquivalenceLiteral(false, this, other);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Parameter.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Parameter.java
deleted file mode 100644
index 577ac6e0..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Parameter.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import java.util.Objects;
-import java.util.Optional;
-
-public class Parameter {
-        public static final Parameter NODE_OUT = new Parameter(null);
-
-        private final Class<?> dataType;
-        private final ParameterDirection direction;
-
-        public Parameter(Class<?> dataType) {
-                this(dataType, ParameterDirection.OUT);
-        }
-
-        public Parameter(Class<?> dataType, ParameterDirection direction) {
-                this.dataType = dataType;
-                this.direction = direction;
-        }
-
-        public boolean isNodeVariable() {
-                return dataType == null;
-        }
-
-        public boolean isDataVariable() {
-                return !isNodeVariable();
-        }
-
-        public Optional<Class<?>> tryGetType() {
-                return Optional.ofNullable(dataType);
-        }
-
-        public ParameterDirection getDirection() {
-                return direction;
-        }
-
-        public boolean matches(Parameter other) {
-                return Objects.equals(dataType, other.dataType) && direction == other.direction;
-        }
-
-        public boolean isAssignable(Variable variable) {
-                if (variable instanceof AnyDataVariable dataVariable) {
-                        return dataVariable.getType().equals(dataType);
-                } else if (variable instanceof NodeVariable) {
-                        return !isDataVariable();
-                } else {
-                        throw new IllegalArgumentException("Unknown variable " + variable);
-                }
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                Parameter parameter = (Parameter) o;
-                return matches(parameter);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(dataType, direction);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ParameterDirection.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ParameterDirection.java
deleted file mode 100644
index da83f3c3..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/ParameterDirection.java
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-public enum ParameterDirection {
-        OUT("out"),
-        IN("in");
-
-        private final String name;
-
-        ParameterDirection(String name) {
-                this.name = name;
-        }
-
-        @Override
-        public String toString() {
-                return name;
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregate.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregate.java
deleted file mode 100644
index ab310556..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregate.java
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-public interface StatefulAggregate<R, T> {
-        void add(T value);
-
-        void remove(T value);
-
-        R getResult();
-
-        boolean isEmpty();
-
-        StatefulAggregate<R, T> deepCopy();
-
-        default boolean contains(T value) {
-                throw new UnsupportedOperationException();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregator.java
deleted file mode 100644
index df746a90..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatefulAggregator.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import java.util.stream.Stream;
-
-public interface StatefulAggregator<R, T> extends Aggregator<R, T> {
-        StatefulAggregate<R, T> createEmptyAggregate();
-
-        @Override
-        default R aggregateStream(Stream<T> stream) {
-                var accumulator = createEmptyAggregate();
-                var iterator = stream.iterator();
-                while (iterator.hasNext()) {
-                        var value = iterator.next();
-                        accumulator.add(value);
-                }
-                return accumulator.getResult();
-        }
-
-        @Override
-        default R getEmptyResult() {
-                return createEmptyAggregate().getResult();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatelessAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatelessAggregator.java
deleted file mode 100644
index a094919e..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/StatelessAggregator.java
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import java.util.stream.Stream;
-
-public interface StatelessAggregator<R, T> extends Aggregator<R, T> {
-        R add(R current, T value);
-
-        R remove(R current, T value);
-
-        @Override
-        default R aggregateStream(Stream<T> stream) {
-                var accumulator = getEmptyResult();
-                var iterator = stream.iterator();
-                while (iterator.hasNext()) {
-                        var value = iterator.next();
-                        accumulator = add(accumulator, value);
-                }
-                return accumulator;
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Term.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Term.java
deleted file mode 100644
index e6818b88..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Term.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import tools.refinery.store.query.literal.AssignLiteral;
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.valuation.Valuation;
-
-public non-sealed interface Term<T> extends AnyTerm, AssignedValue<T> {
-        @Override
-        Class<T> getType();
-
-        T evaluate(Valuation valuation);
-
-        @Override
-        Term<T> substitute(Substitution substitution);
-
-        @Override
-        default Literal toLiteral(DataVariable<T> targetVariable) {
-                return new AssignLiteral<>(targetVariable, this);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/UnaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/UnaryTerm.java
deleted file mode 100644
index a464ece5..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/UnaryTerm.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.equality.LiteralEqualityHelper;
-import tools.refinery.store.query.equality.LiteralHashCodeHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.valuation.Valuation;
-
-import java.util.Objects;
-import java.util.Set;
-
-// {@link Object#equals(Object)} is implemented by {@link AbstractTerm}.
-@SuppressWarnings("squid:S2160")
-public abstract class UnaryTerm<R, T> extends AbstractTerm<R> {
-        private final Class<T> bodyType;
-        private final Term<T> body;
-
-        protected UnaryTerm(Class<R> type, Class<T> bodyType, Term<T> body) {
-                super(type);
-                if (!body.getType().equals(bodyType)) {
-                        throw new InvalidQueryException("Expected body %s to be of type %s, got %s instead".formatted(body,
-                                        bodyType.getName(), body.getType().getName()));
-                }
-                this.bodyType = bodyType;
-                this.body = body;
-        }
-
-        public Class<T> getBodyType() {
-                return bodyType;
-        }
-
-        public Term<T> getBody() {
-                return body;
-        }
-
-        @Override
-        public R evaluate(Valuation valuation) {
-                var bodyValue = body.evaluate(valuation);
-                return bodyValue == null ? null : doEvaluate(bodyValue);
-        }
-
-        protected abstract R doEvaluate(T bodyValue);
-
-        @Override
-        public boolean equalsWithSubstitution(LiteralEqualityHelper helper, AnyTerm other) {
-                if (!super.equalsWithSubstitution(helper, other)) {
-                        return false;
-                }
-                var otherUnaryTerm = (UnaryTerm<?, ?>) other;
-                return bodyType.equals(otherUnaryTerm.bodyType) && body.equalsWithSubstitution(helper, otherUnaryTerm.body);
-        }
-
-        @Override
-        public int hashCodeWithSubstitution(LiteralHashCodeHelper helper) {
-                return Objects.hash(super.hashCodeWithSubstitution(helper), bodyType, body.hashCodeWithSubstitution(helper));
-        }
-
-        @Override
-        public Term<R> substitute(Substitution substitution) {
-                return doSubstitute(substitution, body.substitute(substitution));
-        }
-
-        protected abstract Term<R> doSubstitute(Substitution substitution, Term<T> substitutedBody);
-
-        @Override
-        public Set<AnyDataVariable> getInputVariables() {
-                return body.getInputVariables();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Variable.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Variable.java
deleted file mode 100644
index 1b553704..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/Variable.java
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import org.jetbrains.annotations.Nullable;
-import tools.refinery.store.query.dnf.DnfUtils;
-
-import java.util.Objects;
-import java.util.Optional;
-
-public abstract sealed class Variable permits AnyDataVariable, NodeVariable {
-        private final String explicitName;
-        private final String uniqueName;
-
-        protected Variable(String name) {
-                this.explicitName = name;
-                uniqueName = DnfUtils.generateUniqueName(name);
-        }
-
-        public abstract Optional<Class<?>> tryGetType();
-
-        public String getName() {
-                return explicitName == null ? uniqueName : explicitName;
-        }
-
-        protected String getExplicitName() {
-                return explicitName;
-        }
-
-        public boolean isExplicitlyNamed() {
-                return explicitName != null;
-        }
-
-        public String getUniqueName() {
-                return uniqueName;
-        }
-
-        public abstract Variable renew(@Nullable String name);
-
-        public abstract Variable renew();
-
-        public abstract boolean isNodeVariable();
-
-        public abstract boolean isDataVariable();
-
-        public abstract NodeVariable asNodeVariable();
-
-        public abstract <T> DataVariable<T> asDataVariable(Class<T> type);
-
-        public abstract int hashCodeWithSubstitution(int sequenceNumber);
-
-        @Override
-        public String toString() {
-                return getName();
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                Variable variable = (Variable) o;
-                return Objects.equals(uniqueName, variable.uniqueName);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(uniqueName);
-        }
-
-        public static NodeVariable of(@Nullable String name) {
-                return new NodeVariable(name);
-        }
-
-        public static NodeVariable of() {
-                return of((String) null);
-        }
-
-        public static <T> DataVariable<T> of(@Nullable String name, Class<T> type) {
-                return new DataVariable<>(name, type);
-        }
-
-        public static <T> DataVariable<T> of(Class<T> type) {
-                return of(null, type);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolAndTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolAndTerm.java
deleted file mode 100644
index f9e1c06f..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolAndTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.bool;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class BoolAndTerm extends BoolBinaryTerm {
-        public BoolAndTerm(Term<Boolean> left, Term<Boolean> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Boolean> doSubstitute(Substitution substitution, Term<Boolean> substitutedLeft,
-                                                                          Term<Boolean> substitutedRight) {
-                return new BoolAndTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Boolean doEvaluate(Boolean leftValue, Boolean rightValue) {
-                return leftValue && rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s && %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolBinaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolBinaryTerm.java
deleted file mode 100644
index a85aa63a..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolBinaryTerm.java
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.bool;
-
-import tools.refinery.store.query.term.BinaryTerm;
-import tools.refinery.store.query.term.Term;
-
-public abstract class BoolBinaryTerm extends BinaryTerm<Boolean, Boolean, Boolean> {
-        protected BoolBinaryTerm(Term<Boolean> left, Term<Boolean> right) {
-                super(Boolean.class, Boolean.class, Boolean.class, left, right);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolNotTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolNotTerm.java
deleted file mode 100644
index 8d3382b3..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolNotTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.bool;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.query.term.UnaryTerm;
-
-public class BoolNotTerm extends UnaryTerm<Boolean, Boolean> {
-        protected BoolNotTerm(Term<Boolean> body) {
-                super(Boolean.class, Boolean.class, body);
-        }
-
-        @Override
-        protected Term<Boolean> doSubstitute(Substitution substitution, Term<Boolean> substitutedBody) {
-                return new BoolNotTerm(substitutedBody);
-        }
-
-        @Override
-        protected Boolean doEvaluate(Boolean bodyValue) {
-                return !bodyValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(!%s)".formatted(getBody());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolOrTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolOrTerm.java
deleted file mode 100644
index b5195d52..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolOrTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.bool;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class BoolOrTerm extends BoolBinaryTerm {
-        public BoolOrTerm(Term<Boolean> left, Term<Boolean> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Boolean> doSubstitute(Substitution substitution, Term<Boolean> substitutedLeft,
-                                                                          Term<Boolean> substitutedRight) {
-                return new BoolOrTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Boolean doEvaluate(Boolean leftValue, Boolean rightValue) {
-                return leftValue || rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s || %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolTerms.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolTerms.java
deleted file mode 100644
index fa54f686..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolTerms.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.bool;
-
-import tools.refinery.store.query.term.ConstantTerm;
-import tools.refinery.store.query.term.Term;
-
-public final class BoolTerms {
-        private BoolTerms() {
-                throw new IllegalArgumentException("This is a static utility class and should not be instantiated directly");
-        }
-
-        public static Term<Boolean> constant(Boolean value) {
-                return new ConstantTerm<>(Boolean.class, value);
-        }
-
-        public static Term<Boolean> not(Term<Boolean> body) {
-                return new BoolNotTerm(body);
-        }
-
-        public static Term<Boolean> and(Term<Boolean> left, Term<Boolean> right) {
-                return new BoolAndTerm(left, right);
-        }
-
-        public static Term<Boolean> or(Term<Boolean> left, Term<Boolean> right) {
-                return new BoolOrTerm(left, right);
-        }
-
-        public static Term<Boolean> xor(Term<Boolean> left, Term<Boolean> right) {
-                return new BoolXorTerm(left, right);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolXorTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolXorTerm.java
deleted file mode 100644
index 7478b8a5..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/bool/BoolXorTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.bool;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class BoolXorTerm extends BoolBinaryTerm {
-        public BoolXorTerm(Term<Boolean> left, Term<Boolean> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Boolean> doSubstitute(Substitution substitution, Term<Boolean> substitutedLeft,
-                                                                          Term<Boolean> substitutedRight) {
-                return new BoolXorTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Boolean doEvaluate(Boolean leftValue, Boolean rightValue) {
-                return leftValue ^ rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s ^^ %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/ComparisonTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/ComparisonTerm.java
deleted file mode 100644
index 5ca5a0a1..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/ComparisonTerm.java
+++ /dev/null
@@ -1,19 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.comparable;
-
-import tools.refinery.store.query.term.BinaryTerm;
-import tools.refinery.store.query.term.Term;
-
-public abstract class ComparisonTerm<T> extends BinaryTerm<Boolean, T, T> {
-        protected ComparisonTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
-                super(Boolean.class, argumentType, argumentType, left, right);
-        }
-
-        public Class<T> getArgumentType() {
-                return getLeftType();
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/EqTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/EqTerm.java
deleted file mode 100644
index b8cf36f8..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/EqTerm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.comparable;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class EqTerm<T> extends ComparisonTerm<T> {
-        public EqTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
-                super(argumentType, left, right);
-        }
-
-        @Override
-        protected Boolean doEvaluate(T leftValue, T rightValue) {
-                return leftValue.equals(rightValue);
-        }
-
-        @Override
-        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
-                return new EqTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        public String toString() {
-                return "(%s == %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterEqTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterEqTerm.java
deleted file mode 100644
index b109eb1a..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterEqTerm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.comparable;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class GreaterEqTerm<T extends Comparable<T>> extends ComparisonTerm<T> {
-        public GreaterEqTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
-                super(argumentType, left, right);
-        }
-
-        @Override
-        protected Boolean doEvaluate(T leftValue, T rightValue) {
-                return leftValue.compareTo(rightValue) >= 0;
-        }
-
-        @Override
-        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
-                return new GreaterEqTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        public String toString() {
-                return "(%s >= %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterTerm.java
deleted file mode 100644
index 1b67f8b5..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/GreaterTerm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.comparable;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class GreaterTerm<T extends Comparable<T>> extends ComparisonTerm<T> {
-        public GreaterTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
-                super(argumentType, left, right);
-        }
-
-        @Override
-        protected Boolean doEvaluate(T leftValue, T rightValue) {
-                return leftValue.compareTo(rightValue) > 0;
-        }
-
-        @Override
-        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
-                return new GreaterTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        public String toString() {
-                return "(%s > %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessEqTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessEqTerm.java
deleted file mode 100644
index 1b34535f..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessEqTerm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.comparable;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class LessEqTerm<T extends Comparable<T>> extends ComparisonTerm<T> {
-        public LessEqTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
-                super(argumentType, left, right);
-        }
-
-        @Override
-        protected Boolean doEvaluate(T leftValue, T rightValue) {
-                return leftValue.compareTo(rightValue) <= 0;
-        }
-
-        @Override
-        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
-                return new LessEqTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        public String toString() {
-                return "(%s <= %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessTerm.java
deleted file mode 100644
index 44e70902..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/LessTerm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.comparable;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class LessTerm<T extends Comparable<T>> extends ComparisonTerm<T> {
-        public LessTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
-                super(argumentType, left, right);
-        }
-
-        @Override
-        protected Boolean doEvaluate(T leftValue, T rightValue) {
-                return leftValue.compareTo(rightValue) < 0;
-        }
-
-        @Override
-        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
-                return new LessTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        public String toString() {
-                return "(%s < %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/NotEqTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/NotEqTerm.java
deleted file mode 100644
index 1f9734c4..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/comparable/NotEqTerm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.comparable;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class NotEqTerm<T> extends ComparisonTerm<T> {
-        public NotEqTerm(Class<T> argumentType, Term<T> left, Term<T> right) {
-                super(argumentType, left, right);
-        }
-
-        @Override
-        protected Boolean doEvaluate(T leftValue, T rightValue) {
-                return !leftValue.equals(rightValue);
-        }
-
-        @Override
-        public Term<Boolean> doSubstitute(Substitution substitution, Term<T> substitutedLeft, Term<T> substitutedRight) {
-                return new NotEqTerm<>(getArgumentType(), substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        public String toString() {
-                return "(%s != %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntAddTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntAddTerm.java
deleted file mode 100644
index dbea3efc..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntAddTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class IntAddTerm extends IntBinaryTerm {
-        public IntAddTerm(Term<Integer> left, Term<Integer> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
-                                                                          Term<Integer> substitutedRight) {
-                return new IntAddTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
-                return leftValue + rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s + %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntBinaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntBinaryTerm.java
deleted file mode 100644
index 27ced4e4..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntBinaryTerm.java
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.term.BinaryTerm;
-import tools.refinery.store.query.term.Term;
-
-public abstract class IntBinaryTerm extends BinaryTerm<Integer, Integer, Integer> {
-        protected IntBinaryTerm(Term<Integer> left, Term<Integer> right) {
-                super(Integer.class, Integer.class, Integer.class, left, right);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntDivTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntDivTerm.java
deleted file mode 100644
index 2a35058c..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntDivTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class IntDivTerm extends IntBinaryTerm {
-        public IntDivTerm(Term<Integer> left, Term<Integer> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
-                                                                          Term<Integer> substitutedRight) {
-                return new IntDivTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
-                return rightValue == 0 ? null : leftValue / rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s / %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMaxTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMaxTerm.java
deleted file mode 100644
index f81fc509..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMaxTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class IntMaxTerm extends IntBinaryTerm {
-        public IntMaxTerm(Term<Integer> left, Term<Integer> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
-                                                                          Term<Integer> substitutedRight) {
-                return new IntMaxTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
-                return Math.max(rightValue, leftValue);
-        }
-
-        @Override
-        public String toString() {
-                return "max(%s, %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinTerm.java
deleted file mode 100644
index 89182e26..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class IntMinTerm extends IntBinaryTerm {
-        public IntMinTerm(Term<Integer> left, Term<Integer> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
-                                                                          Term<Integer> substitutedRight) {
-                return new IntMinTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
-                return Math.min(rightValue, leftValue);
-        }
-
-        @Override
-        public String toString() {
-                return "min(%s, %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinusTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinusTerm.java
deleted file mode 100644
index 709aa5ba..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMinusTerm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class IntMinusTerm extends IntUnaryTerm {
-        public IntMinusTerm(Term<Integer> body) {
-                super(body);
-        }
-
-        @Override
-        protected Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedBody) {
-                return new IntMinusTerm(substitutedBody);
-        }
-
-        @Override
-        protected Integer doEvaluate(Integer bodyValue) {
-                return -bodyValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(-%s)".formatted(getBody());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMulTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMulTerm.java
deleted file mode 100644
index 89d4c5f4..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntMulTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class IntMulTerm extends IntBinaryTerm {
-        public IntMulTerm(Term<Integer> left, Term<Integer> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
-                                                                          Term<Integer> substitutedRight) {
-                return new IntMulTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
-                return leftValue * rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s * %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPlusTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPlusTerm.java
deleted file mode 100644
index aef83bb4..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPlusTerm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class IntPlusTerm extends IntUnaryTerm {
-        public IntPlusTerm(Term<Integer> body) {
-                super(body);
-        }
-
-        @Override
-        protected Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedBody) {
-                return new IntPlusTerm(substitutedBody);
-        }
-
-        @Override
-        protected Integer doEvaluate(Integer bodyValue) {
-                return bodyValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(+%s)".formatted(getBody());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPowTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPowTerm.java
deleted file mode 100644
index d5af97a1..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntPowTerm.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class IntPowTerm extends IntBinaryTerm {
-        public IntPowTerm(Term<Integer> left, Term<Integer> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
-                                                                          Term<Integer> substitutedRight) {
-                return new IntPowTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
-                return rightValue < 0 ? null : power(leftValue, rightValue);
-        }
-
-        private static int power(int base, int exponent) {
-                int accum = 1;
-                while (exponent > 0) {
-                        if (exponent % 2 == 1) {
-                                accum = accum * base;
-                        }
-                        base = base * base;
-                        exponent = exponent / 2;
-                }
-                return accum;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s ** %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSubTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSubTerm.java
deleted file mode 100644
index 2c27afb1..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSubTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class IntSubTerm extends IntBinaryTerm {
-        public IntSubTerm(Term<Integer> left, Term<Integer> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Integer> doSubstitute(Substitution substitution, Term<Integer> substitutedLeft,
-                                                                          Term<Integer> substitutedRight) {
-                return new IntSubTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Integer doEvaluate(Integer leftValue, Integer rightValue) {
-                return leftValue - rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s - %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSumAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSumAggregator.java
deleted file mode 100644
index cd718c53..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntSumAggregator.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.term.StatelessAggregator;
-
-public final class IntSumAggregator implements StatelessAggregator<Integer, Integer> {
-        public static final IntSumAggregator INSTANCE = new IntSumAggregator();
-
-        private IntSumAggregator() {
-        }
-
-        @Override
-        public Class<Integer> getResultType() {
-                return Integer.class;
-        }
-
-        @Override
-        public Class<Integer> getInputType() {
-                return Integer.class;
-        }
-
-        @Override
-        public Integer getEmptyResult() {
-                return 0;
-        }
-
-        @Override
-        public Integer add(Integer current, Integer value) {
-                return current + value;
-        }
-
-        @Override
-        public Integer remove(Integer current, Integer value) {
-                return current - value;
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntTerms.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntTerms.java
deleted file mode 100644
index acb98b94..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntTerms.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.term.Aggregator;
-import tools.refinery.store.query.term.ConstantTerm;
-import tools.refinery.store.query.term.ExtremeValueAggregator;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.query.term.comparable.*;
-
-import java.util.Comparator;
-
-public final class IntTerms {
-        public static final Aggregator<Integer, Integer> INT_SUM = IntSumAggregator.INSTANCE;
-        public static final Aggregator<Integer, Integer> INT_MIN = new ExtremeValueAggregator<>(Integer.class,
-                        Integer.MAX_VALUE);
-        public static final Aggregator<Integer, Integer> INT_MAX = new ExtremeValueAggregator<>(Integer.class,
-                        Integer.MIN_VALUE, Comparator.reverseOrder());
-
-        private IntTerms() {
-                throw new IllegalArgumentException("This is a static utility class and should not be instantiated directly");
-        }
-
-        public static Term<Integer> constant(Integer value) {
-                return new ConstantTerm<>(Integer.class, value);
-        }
-
-        public static Term<Integer> plus(Term<Integer> body) {
-                return new IntPlusTerm(body);
-        }
-
-        public static Term<Integer> minus(Term<Integer> body) {
-                return new IntMinusTerm(body);
-        }
-
-        public static Term<Integer> add(Term<Integer> left, Term<Integer> right) {
-                return new IntAddTerm(left, right);
-        }
-
-        public static Term<Integer> sub(Term<Integer> left, Term<Integer> right) {
-                return new IntSubTerm(left, right);
-        }
-
-        public static Term<Integer> mul(Term<Integer> left, Term<Integer> right) {
-                return new IntMulTerm(left, right);
-        }
-
-        public static Term<Integer> div(Term<Integer> left, Term<Integer> right) {
-                return new IntDivTerm(left, right);
-        }
-
-        public static Term<Integer> pow(Term<Integer> left, Term<Integer> right) {
-                return new IntPowTerm(left, right);
-        }
-
-        public static Term<Integer> min(Term<Integer> left, Term<Integer> right) {
-                return new IntMinTerm(left, right);
-        }
-
-        public static Term<Integer> max(Term<Integer> left, Term<Integer> right) {
-                return new IntMaxTerm(left, right);
-        }
-
-        public static Term<Boolean> eq(Term<Integer> left, Term<Integer> right) {
-                return new EqTerm<>(Integer.class, left, right);
-        }
-
-        public static Term<Boolean> notEq(Term<Integer> left, Term<Integer> right) {
-                return new NotEqTerm<>(Integer.class, left, right);
-        }
-
-        public static Term<Boolean> less(Term<Integer> left, Term<Integer> right) {
-                return new LessTerm<>(Integer.class, left, right);
-        }
-
-        public static Term<Boolean> lessEq(Term<Integer> left, Term<Integer> right) {
-                return new LessEqTerm<>(Integer.class, left, right);
-        }
-
-        public static Term<Boolean> greater(Term<Integer> left, Term<Integer> right) {
-                return new GreaterTerm<>(Integer.class, left, right);
-        }
-
-        public static Term<Boolean> greaterEq(Term<Integer> left, Term<Integer> right) {
-                return new GreaterEqTerm<>(Integer.class, left, right);
-        }
-
-        public static Term<Integer> asInt(Term<Double> body) {
-                return new RealToIntTerm(body);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntUnaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntUnaryTerm.java
deleted file mode 100644
index 49b4c647..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/IntUnaryTerm.java
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.query.term.UnaryTerm;
-
-public abstract class IntUnaryTerm extends UnaryTerm<Integer, Integer> {
-        protected IntUnaryTerm(Term<Integer> body) {
-                super(Integer.class, Integer.class, body);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/RealToIntTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/RealToIntTerm.java
deleted file mode 100644
index 7d383562..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/int_/RealToIntTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.query.term.UnaryTerm;
-
-public class RealToIntTerm extends UnaryTerm<Integer, Double> {
-        protected RealToIntTerm(Term<Double> body) {
-                super(Integer.class, Double.class, body);
-        }
-
-        @Override
-        protected Integer doEvaluate(Double bodyValue) {
-                return bodyValue.isNaN() ? null : bodyValue.intValue();
-        }
-
-        @Override
-        protected Term<Integer> doSubstitute(Substitution substitution, Term<Double> substitutedBody) {
-                return new RealToIntTerm(substitutedBody);
-        }
-
-        @Override
-        public String toString() {
-                return "(%s as int)".formatted(getBody());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/IntToRealTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/IntToRealTerm.java
deleted file mode 100644
index 2f53117a..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/IntToRealTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.query.term.UnaryTerm;
-
-public class IntToRealTerm extends UnaryTerm<Double, Integer> {
-        protected IntToRealTerm(Term<Integer> body) {
-                super(Double.class, Integer.class, body);
-        }
-
-        @Override
-        protected Term<Double> doSubstitute(Substitution substitution, Term<Integer> substitutedBody) {
-                return new IntToRealTerm(substitutedBody);
-        }
-
-        @Override
-        protected Double doEvaluate(Integer bodyValue) {
-                return bodyValue.doubleValue();
-        }
-
-        @Override
-        public String toString() {
-                return "(%s as real)".formatted(getBody());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealAddTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealAddTerm.java
deleted file mode 100644
index 33fc9e41..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealAddTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class RealAddTerm extends RealBinaryTerm {
-        public RealAddTerm(Term<Double> left, Term<Double> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
-                                                                         Term<Double> substitutedRight) {
-                return new RealAddTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Double doEvaluate(Double leftValue, Double rightValue) {
-                return leftValue + rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s + %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealBinaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealBinaryTerm.java
deleted file mode 100644
index 000f3623..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealBinaryTerm.java
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.term.BinaryTerm;
-import tools.refinery.store.query.term.Term;
-
-public abstract class RealBinaryTerm extends BinaryTerm<Double, Double, Double> {
-        protected RealBinaryTerm(Term<Double> left, Term<Double> right) {
-                super(Double.class, Double.class, Double.class, left, right);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealDivTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealDivTerm.java
deleted file mode 100644
index 1e55bf42..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealDivTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class RealDivTerm extends RealBinaryTerm {
-        public RealDivTerm(Term<Double> left, Term<Double> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
-                                                                         Term<Double> substitutedRight) {
-                return new RealDivTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Double doEvaluate(Double leftValue, Double rightValue) {
-                return leftValue / rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s / %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMaxTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMaxTerm.java
deleted file mode 100644
index 2a249496..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMaxTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class RealMaxTerm extends RealBinaryTerm {
-        public RealMaxTerm(Term<Double> left, Term<Double> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
-                                                                         Term<Double> substitutedRight) {
-                return new RealMaxTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Double doEvaluate(Double leftValue, Double rightValue) {
-                return Math.max(leftValue, rightValue);
-        }
-
-        @Override
-        public String toString() {
-                return "max(%s, %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinTerm.java
deleted file mode 100644
index 2eb4cc1e..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class RealMinTerm extends RealBinaryTerm {
-        public RealMinTerm(Term<Double> left, Term<Double> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
-                                                                         Term<Double> substitutedRight) {
-                return new RealMinTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Double doEvaluate(Double leftValue, Double rightValue) {
-                return Math.min(leftValue, rightValue);
-        }
-
-        @Override
-        public String toString() {
-                return "min(%s, %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinusTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinusTerm.java
deleted file mode 100644
index 4afec7a1..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMinusTerm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class RealMinusTerm extends RealUnaryTerm {
-        public RealMinusTerm(Term<Double> body) {
-                super(body);
-        }
-
-        @Override
-        protected Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedBody) {
-                return new RealMinusTerm(substitutedBody);
-        }
-
-        @Override
-        protected Double doEvaluate(Double bodyValue) {
-                return -bodyValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(-%s)".formatted(getBody());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMulTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMulTerm.java
deleted file mode 100644
index ec95ac6f..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealMulTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class RealMulTerm extends RealBinaryTerm {
-        public RealMulTerm(Term<Double> left, Term<Double> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
-                                                                         Term<Double> substitutedRight) {
-                return new RealMulTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Double doEvaluate(Double leftValue, Double rightValue) {
-                return leftValue * rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s * %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPlusTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPlusTerm.java
deleted file mode 100644
index 64dd2e70..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPlusTerm.java
+++ /dev/null
@@ -1,30 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class RealPlusTerm extends RealUnaryTerm {
-        public RealPlusTerm(Term<Double> body) {
-                super(body);
-        }
-
-        @Override
-        protected Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedBody) {
-                return new RealPlusTerm(substitutedBody);
-        }
-
-        @Override
-        protected Double doEvaluate(Double bodyValue) {
-                return bodyValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(+%s)".formatted(getBody());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPowTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPowTerm.java
deleted file mode 100644
index 11c952ea..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealPowTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class RealPowTerm extends RealBinaryTerm {
-        public RealPowTerm(Term<Double> left, Term<Double> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
-                                                                         Term<Double> substitutedRight) {
-                return new RealPowTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Double doEvaluate(Double leftValue, Double rightValue) {
-                return Math.pow(leftValue, rightValue);
-        }
-
-        @Override
-        public String toString() {
-                return "(%s ** %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSubTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSubTerm.java
deleted file mode 100644
index 8cc701ed..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSubTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-
-public class RealSubTerm extends RealBinaryTerm {
-        public RealSubTerm(Term<Double> left, Term<Double> right) {
-                super(left, right);
-        }
-
-        @Override
-        public Term<Double> doSubstitute(Substitution substitution, Term<Double> substitutedLeft,
-                                                                         Term<Double> substitutedRight) {
-                return new RealSubTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        protected Double doEvaluate(Double leftValue, Double rightValue) {
-                return leftValue - rightValue;
-        }
-
-        @Override
-        public String toString() {
-                return "(%s - %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSumAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSumAggregator.java
deleted file mode 100644
index d21048e9..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealSumAggregator.java
+++ /dev/null
@@ -1,90 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.term.StatefulAggregate;
-import tools.refinery.store.query.term.StatefulAggregator;
-
-import java.util.Map;
-import java.util.TreeMap;
-
-public final class RealSumAggregator implements StatefulAggregator<Double, Double> {
-        public static final RealSumAggregator INSTANCE = new RealSumAggregator();
-
-        private RealSumAggregator() {
-        }
-
-        @Override
-        public Class<Double> getResultType() {
-                return Double.class;
-        }
-
-        @Override
-        public Class<Double> getInputType() {
-                return Double.class;
-        }
-
-        @Override
-        public StatefulAggregate<Double, Double> createEmptyAggregate() {
-                return new Aggregate();
-        }
-
-        @Override
-        public Double getEmptyResult() {
-                return 0d;
-        }
-
-        private static class Aggregate implements StatefulAggregate<Double, Double> {
-                private final Map<Double, Integer> values;
-
-                public Aggregate() {
-                        values = new TreeMap<>();
-                }
-
-                private Aggregate(Aggregate other) {
-                        values = new TreeMap<>(other.values);
-                }
-
-                @Override
-                public void add(Double value) {
-                        values.compute(value, (ignoredValue, currentCount) -> currentCount == null ? 1 : currentCount + 1);
-                }
-
-                @Override
-                public void remove(Double value) {
-                        values.compute(value, (theValue, currentCount) -> {
-                                if (currentCount == null || currentCount <= 0) {
-                                        throw new IllegalStateException("Invalid count %d for value %f".formatted(currentCount, theValue));
-                                }
-                                return currentCount.equals(1) ? null : currentCount - 1;
-                        });
-                }
-
-                @Override
-                public Double getResult() {
-                        return values.entrySet()
-                                        .stream()
-                                        .mapToDouble(entry -> entry.getKey() * entry.getValue())
-                                        .reduce(Double::sum)
-                                        .orElse(0d);
-                }
-
-                @Override
-                public boolean isEmpty() {
-                        return values.isEmpty();
-                }
-
-                @Override
-                public StatefulAggregate<Double, Double> deepCopy() {
-                        return new Aggregate(this);
-                }
-
-                @Override
-                public boolean contains(Double value) {
-                        return values.containsKey(value);
-                }
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealTerms.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealTerms.java
deleted file mode 100644
index 79220358..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealTerms.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.term.Aggregator;
-import tools.refinery.store.query.term.ConstantTerm;
-import tools.refinery.store.query.term.ExtremeValueAggregator;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.query.term.comparable.*;
-
-import java.util.Comparator;
-
-public final class RealTerms {
-        public static final Aggregator<Double, Double> REAL_SUM = RealSumAggregator.INSTANCE;
-        public static final Aggregator<Double, Double> REAL_MIN = new ExtremeValueAggregator<>(Double.class,
-                        Double.POSITIVE_INFINITY);
-        public static final Aggregator<Double, Double> REAL_MAX = new ExtremeValueAggregator<>(Double.class,
-                        Double.NEGATIVE_INFINITY, Comparator.reverseOrder());
-
-        private RealTerms() {
-                throw new IllegalArgumentException("This is a static utility class and should not be instantiated directly");
-        }
-
-        public static Term<Double> constant(Double value) {
-                return new ConstantTerm<>(Double.class, value);
-        }
-
-        public static Term<Double> plus(Term<Double> body) {
-                return new RealPlusTerm(body);
-        }
-
-        public static Term<Double> minus(Term<Double> body) {
-                return new RealMinusTerm(body);
-        }
-
-        public static Term<Double> add(Term<Double> left, Term<Double> right) {
-                return new RealAddTerm(left, right);
-        }
-
-        public static Term<Double> sub(Term<Double> left, Term<Double> right) {
-                return new RealSubTerm(left, right);
-        }
-
-        public static Term<Double> mul(Term<Double> left, Term<Double> right) {
-                return new RealMulTerm(left, right);
-        }
-
-        public static Term<Double> div(Term<Double> left, Term<Double> right) {
-                return new RealDivTerm(left, right);
-        }
-
-        public static Term<Double> pow(Term<Double> left, Term<Double> right) {
-                return new RealPowTerm(left, right);
-        }
-
-        public static Term<Double> min(Term<Double> left, Term<Double> right) {
-                return new RealMinTerm(left, right);
-        }
-
-        public static Term<Double> max(Term<Double> left, Term<Double> right) {
-                return new RealMaxTerm(left, right);
-        }
-
-        public static Term<Boolean> eq(Term<Double> left, Term<Double> right) {
-                return new EqTerm<>(Double.class, left, right);
-        }
-
-        public static Term<Boolean> notEq(Term<Double> left, Term<Double> right) {
-                return new NotEqTerm<>(Double.class, left, right);
-        }
-
-        public static Term<Boolean> less(Term<Double> left, Term<Double> right) {
-                return new LessTerm<>(Double.class, left, right);
-        }
-
-        public static Term<Boolean> lessEq(Term<Double> left, Term<Double> right) {
-                return new LessEqTerm<>(Double.class, left, right);
-        }
-
-        public static Term<Boolean> greater(Term<Double> left, Term<Double> right) {
-                return new GreaterTerm<>(Double.class, left, right);
-        }
-
-        public static Term<Boolean> greaterEq(Term<Double> left, Term<Double> right) {
-                return new GreaterEqTerm<>(Double.class, left, right);
-        }
-
-        public static Term<Double> asReal(Term<Integer> body) {
-                return new IntToRealTerm(body);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealUnaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealUnaryTerm.java
deleted file mode 100644
index d41c4ed9..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/real/RealUnaryTerm.java
+++ /dev/null
@@ -1,15 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.query.term.UnaryTerm;
-
-public abstract class RealUnaryTerm extends UnaryTerm<Double, Double> {
-        protected RealUnaryTerm(Term<Double> body) {
-                super(Double.class, Double.class, body);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityAddTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityAddTerm.java
deleted file mode 100644
index 68905f51..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityAddTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.uppercardinality;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-public class UpperCardinalityAddTerm extends UpperCardinalityBinaryTerm {
-        protected UpperCardinalityAddTerm(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                super(left, right);
-        }
-
-        @Override
-        protected UpperCardinality doEvaluate(UpperCardinality leftValue, UpperCardinality rightValue) {
-                return leftValue.add(rightValue);
-        }
-
-        @Override
-        public Term<UpperCardinality> doSubstitute(Substitution substitution, Term<UpperCardinality> substitutedLeft, Term<UpperCardinality> substitutedRight) {
-                return new UpperCardinalityAddTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        public String toString() {
-                return "(%s + %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityBinaryTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityBinaryTerm.java
deleted file mode 100644
index 0cf8fe44..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityBinaryTerm.java
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.uppercardinality;
-
-import tools.refinery.store.query.term.BinaryTerm;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-public abstract class UpperCardinalityBinaryTerm extends BinaryTerm<UpperCardinality, UpperCardinality,
-                UpperCardinality> {
-        protected UpperCardinalityBinaryTerm(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                super(UpperCardinality.class, UpperCardinality.class, UpperCardinality.class, left, right);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMaxTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMaxTerm.java
deleted file mode 100644
index ff75f64e..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMaxTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.uppercardinality;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-public class UpperCardinalityMaxTerm extends UpperCardinalityBinaryTerm {
-        protected UpperCardinalityMaxTerm(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                super(left, right);
-        }
-
-        @Override
-        protected UpperCardinality doEvaluate(UpperCardinality leftValue, UpperCardinality rightValue) {
-                return leftValue.max(rightValue);
-        }
-
-        @Override
-        public Term<UpperCardinality> doSubstitute(Substitution substitution, Term<UpperCardinality> substitutedLeft, Term<UpperCardinality> substitutedRight) {
-                return new UpperCardinalityMaxTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        public String toString() {
-                return "max(%s, %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMinTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMinTerm.java
deleted file mode 100644
index 1e89e9f4..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMinTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.uppercardinality;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-public class UpperCardinalityMinTerm extends UpperCardinalityBinaryTerm {
-        protected UpperCardinalityMinTerm(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                super(left, right);
-        }
-
-        @Override
-        protected UpperCardinality doEvaluate(UpperCardinality leftValue, UpperCardinality rightValue) {
-                return leftValue.min(rightValue);
-        }
-
-        @Override
-        public Term<UpperCardinality> doSubstitute(Substitution substitution, Term<UpperCardinality> substitutedLeft, Term<UpperCardinality> substitutedRight) {
-                return new UpperCardinalityMinTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        public String toString() {
-                return "min(%s, %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMulTerm.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMulTerm.java
deleted file mode 100644
index 3b4970f4..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityMulTerm.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.uppercardinality;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-public class UpperCardinalityMulTerm extends UpperCardinalityBinaryTerm {
-        protected UpperCardinalityMulTerm(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                super(left, right);
-        }
-
-        @Override
-        protected UpperCardinality doEvaluate(UpperCardinality leftValue, UpperCardinality rightValue) {
-                return leftValue.multiply(rightValue);
-        }
-
-        @Override
-        public Term<UpperCardinality> doSubstitute(Substitution substitution, Term<UpperCardinality> substitutedLeft, Term<UpperCardinality> substitutedRight) {
-                return new UpperCardinalityMulTerm(substitutedLeft, substitutedRight);
-        }
-
-        @Override
-        public String toString() {
-                return "(%s * %s)".formatted(getLeft(), getRight());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregator.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregator.java
deleted file mode 100644
index d31f00a2..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregator.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.uppercardinality;
-
-import tools.refinery.store.query.term.StatefulAggregate;
-import tools.refinery.store.query.term.StatefulAggregator;
-import tools.refinery.store.representation.cardinality.FiniteUpperCardinality;
-import tools.refinery.store.representation.cardinality.UnboundedUpperCardinality;
-import tools.refinery.store.representation.cardinality.UpperCardinalities;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-public class UpperCardinalitySumAggregator implements StatefulAggregator<UpperCardinality, UpperCardinality> {
-        public static final UpperCardinalitySumAggregator INSTANCE = new UpperCardinalitySumAggregator();
-
-        private UpperCardinalitySumAggregator() {
-        }
-
-        @Override
-        public Class<UpperCardinality> getResultType() {
-                return UpperCardinality.class;
-        }
-
-        @Override
-        public Class<UpperCardinality> getInputType() {
-                return UpperCardinality.class;
-        }
-
-        @Override
-        public StatefulAggregate<UpperCardinality, UpperCardinality> createEmptyAggregate() {
-                return new Aggregate();
-        }
-
-        private static class Aggregate implements StatefulAggregate<UpperCardinality, UpperCardinality> {
-                private int sumFiniteUpperBounds;
-                private int countUnbounded;
-
-                public Aggregate() {
-                        this(0, 0);
-                }
-
-                private Aggregate(int sumFiniteUpperBounds, int countUnbounded) {
-                        this.sumFiniteUpperBounds = sumFiniteUpperBounds;
-                        this.countUnbounded = countUnbounded;
-                }
-
-                @Override
-                public void add(UpperCardinality value) {
-                        if (value instanceof FiniteUpperCardinality finiteUpperCardinality) {
-                                sumFiniteUpperBounds += finiteUpperCardinality.finiteUpperBound();
-                        } else if (value instanceof UnboundedUpperCardinality) {
-                                countUnbounded += 1;
-                        } else {
-                                throw new IllegalArgumentException("Unknown UpperCardinality: " + value);
-                        }
-                }
-
-                @Override
-                public void remove(UpperCardinality value) {
-                        if (value instanceof FiniteUpperCardinality finiteUpperCardinality) {
-                                sumFiniteUpperBounds -= finiteUpperCardinality.finiteUpperBound();
-                        } else if (value instanceof UnboundedUpperCardinality) {
-                                countUnbounded -= 1;
-                        } else {
-                                throw new IllegalArgumentException("Unknown UpperCardinality: " + value);
-                        }
-                }
-
-                @Override
-                public UpperCardinality getResult() {
-                        return countUnbounded > 0 ? UpperCardinalities.UNBOUNDED : UpperCardinalities.atMost(sumFiniteUpperBounds);
-                }
-
-                @Override
-                public boolean isEmpty() {
-                        return sumFiniteUpperBounds == 0 && countUnbounded == 0;
-                }
-
-                @Override
-                public StatefulAggregate<UpperCardinality, UpperCardinality> deepCopy() {
-                        return new Aggregate(sumFiniteUpperBounds, countUnbounded);
-                }
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTerms.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTerms.java
deleted file mode 100644
index 13914f2d..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTerms.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.uppercardinality;
-
-import tools.refinery.store.query.term.Aggregator;
-import tools.refinery.store.query.term.ConstantTerm;
-import tools.refinery.store.query.term.ExtremeValueAggregator;
-import tools.refinery.store.query.term.Term;
-import tools.refinery.store.query.term.comparable.*;
-import tools.refinery.store.representation.cardinality.UpperCardinalities;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-import java.util.Comparator;
-
-public final class UpperCardinalityTerms {
-        public static final Aggregator<UpperCardinality, UpperCardinality> UPPER_CARDINALITY_SUM =
-                        UpperCardinalitySumAggregator.INSTANCE;
-        public static final Aggregator<UpperCardinality, UpperCardinality> UPPER_CARDINALITY_MIN =
-                        new ExtremeValueAggregator<>(UpperCardinality.class, UpperCardinalities.UNBOUNDED);
-        public static final Aggregator<UpperCardinality, UpperCardinality> UPPER_CARDINALITY_MAX =
-                        new ExtremeValueAggregator<>(UpperCardinality.class, UpperCardinalities.ZERO, Comparator.reverseOrder());
-
-        private UpperCardinalityTerms() {
-                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
-        }
-
-        public static Term<UpperCardinality> constant(UpperCardinality value) {
-                return new ConstantTerm<>(UpperCardinality.class, value);
-        }
-
-        public static Term<UpperCardinality> add(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                return new UpperCardinalityAddTerm(left, right);
-        }
-
-        public static Term<UpperCardinality> mul(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                return new UpperCardinalityMulTerm(left, right);
-        }
-
-        public static Term<UpperCardinality> min(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                return new UpperCardinalityMinTerm(left, right);
-        }
-
-        public static Term<UpperCardinality> max(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                return new UpperCardinalityMaxTerm(left, right);
-        }
-
-        public static Term<Boolean> eq(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                return new EqTerm<>(UpperCardinality.class, left, right);
-        }
-
-        public static Term<Boolean> notEq(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                return new NotEqTerm<>(UpperCardinality.class, left, right);
-        }
-
-        public static Term<Boolean> less(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                return new LessTerm<>(UpperCardinality.class, left, right);
-        }
-
-        public static Term<Boolean> lessEq(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                return new LessEqTerm<>(UpperCardinality.class, left, right);
-        }
-
-        public static Term<Boolean> greater(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                return new GreaterTerm<>(UpperCardinality.class, left, right);
-        }
-
-        public static Term<Boolean> greaterEq(Term<UpperCardinality> left, Term<UpperCardinality> right) {
-                return new GreaterEqTerm<>(UpperCardinality.class, left, right);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/MapBasedValuation.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/MapBasedValuation.java
deleted file mode 100644
index 261ceaa5..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/MapBasedValuation.java
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.valuation;
-
-import tools.refinery.store.query.term.AnyDataVariable;
-import tools.refinery.store.query.term.DataVariable;
-
-import java.util.Map;
-
-record MapBasedValuation(Map<AnyDataVariable, Object> values) implements Valuation {
-        @Override
-        public <T> T getValue(DataVariable<T> variable) {
-                if (!values.containsKey(variable)) {
-                        throw new IllegalArgumentException("No value for variable %s".formatted(variable));
-                }
-                var value = values.get(variable);
-                return variable.getType().cast(value);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/RestrictedValuation.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/RestrictedValuation.java
deleted file mode 100644
index fc8406aa..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/RestrictedValuation.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.valuation;
-
-import tools.refinery.store.query.term.AnyDataVariable;
-import tools.refinery.store.query.term.DataVariable;
-
-import java.util.Set;
-
-public record RestrictedValuation(Valuation valuation, Set<AnyDataVariable> allowedVariables) implements Valuation {
-        @Override
-        public <T> T getValue(DataVariable<T> variable) {
-                if (!allowedVariables.contains(variable)) {
-                        throw new IllegalArgumentException("Variable %s is not in scope".formatted(variable));
-                }
-                return valuation.getValue(variable);
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/SubstitutedValuation.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/SubstitutedValuation.java
deleted file mode 100644
index 1c14112c..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/SubstitutedValuation.java
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.valuation;
-
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.DataVariable;
-
-public record SubstitutedValuation(Valuation originalValuation, Substitution substitution) implements Valuation {
-        @Override
-        public <T> T getValue(DataVariable<T> variable) {
-                return originalValuation.getValue(substitution.getTypeSafeSubstitute(variable));
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/Valuation.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/Valuation.java
deleted file mode 100644
index 1588e957..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/Valuation.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.valuation;
-
-import org.jetbrains.annotations.Nullable;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.AnyDataVariable;
-import tools.refinery.store.query.term.DataVariable;
-
-import java.util.Map;
-import java.util.Set;
-
-public interface Valuation {
-        <T> T getValue(DataVariable<T> variable);
-
-        default Valuation substitute(@Nullable Substitution substitution) {
-                if (substitution == null) {
-                        return this;
-                }
-                return new SubstitutedValuation(this, substitution);
-        }
-
-        default Valuation restrict(Set<? extends AnyDataVariable> allowedVariables) {
-                return new RestrictedValuation(this, Set.copyOf(allowedVariables));
-        }
-
-        static ValuationBuilder builder() {
-                return new ValuationBuilder();
-        }
-
-        static Valuation empty() {
-                return new MapBasedValuation(Map.of());
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/ValuationBuilder.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/ValuationBuilder.java
deleted file mode 100644
index 7337dbc3..00000000
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/valuation/ValuationBuilder.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.valuation;
-
-import tools.refinery.store.query.term.AnyDataVariable;
-import tools.refinery.store.query.term.DataVariable;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-
-public class ValuationBuilder {
-        private final Map<AnyDataVariable, Object> values = new HashMap<>();
-
-        ValuationBuilder() {
-        }
-
-        public <T> ValuationBuilder put(DataVariable<T> variable, T value) {
-                return putChecked(variable, value);
-        }
-
-        public ValuationBuilder putChecked(AnyDataVariable variable, Object value) {
-                if (value != null && !variable.getType().isInstance(value)) {
-                        throw new IllegalArgumentException("Value %s is not an instance of %s"
-                                        .formatted(value, variable.getType().getName()));
-                }
-                if (values.containsKey(variable)) {
-                        throw new IllegalArgumentException("Already has value for variable %s".formatted(variable));
-                }
-                values.put(variable, value);
-                return this;
-        }
-
-        public Valuation build() {
-                return new MapBasedValuation(Collections.unmodifiableMap(values));
-        }
-}
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java
index f130fa59..d9809991 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AbstractFunctionView.java
@@ -7,8 +7,8 @@ package tools.refinery.store.query.view;
 
 import tools.refinery.store.map.CursorAsIterator;
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.dnf.FunctionalDependency;
-import tools.refinery.store.query.term.Parameter;
+import tools.refinery.logic.dnf.FunctionalDependency;
+import tools.refinery.logic.term.Parameter;
 import tools.refinery.store.representation.Symbol;
 import tools.refinery.store.tuple.Tuple;
 import tools.refinery.store.tuple.Tuple1;
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AnySymbolView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AnySymbolView.java
index 7e9bf6df..b01c3988 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AnySymbolView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/AnySymbolView.java
@@ -5,10 +5,10 @@
  */
 package tools.refinery.store.query.view;
 
+import tools.refinery.logic.dnf.FunctionalDependency;
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.dnf.FunctionalDependency;
+import tools.refinery.logic.Constraint;
 import tools.refinery.store.representation.AnySymbol;
-import tools.refinery.store.query.Constraint;
 
 import java.util.Set;
 
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FilteredView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FilteredView.java
index 924277ed..7ce07442 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FilteredView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FilteredView.java
@@ -5,7 +5,7 @@
  */
 package tools.refinery.store.query.view;
 
-import tools.refinery.store.query.InvalidQueryException;
+import tools.refinery.logic.InvalidQueryException;
 import tools.refinery.store.tuple.Tuple;
 import tools.refinery.store.representation.Symbol;
 
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/ForbiddenView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/ForbiddenView.java
index c312330e..8323ace7 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/ForbiddenView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/ForbiddenView.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.query.view;
 
 import tools.refinery.store.representation.Symbol;
-import tools.refinery.store.representation.TruthValue;
+import tools.refinery.logic.term.truthvalue.TruthValue;
 import tools.refinery.store.tuple.Tuple;
 
 public class ForbiddenView extends TuplePreservingView<TruthValue> {
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FunctionView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FunctionView.java
index 74a5be07..5585f5f2 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FunctionView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/FunctionView.java
@@ -1,11 +1,11 @@
 /*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
+ * SPDX-FileCopyrightText: 2021-2024 The Refinery Authors <https://refinery.tools/>
  *
  * SPDX-License-Identifier: EPL-2.0
  */
 package tools.refinery.store.query.view;
 
-import tools.refinery.store.query.term.*;
+import tools.refinery.logic.term.*;
 import tools.refinery.store.representation.Symbol;
 
 import java.util.ArrayList;
@@ -33,4 +33,18 @@ public final class FunctionView<T> extends AbstractFunctionView<T> {
         public <R> AssignedValue<R> aggregate(Aggregator<R, T> aggregator, NodeVariable... arguments) {
                 return aggregate(aggregator, List.of(arguments));
         }
+
+        public AssignedValue<T> leftJoin(T defaultValue, List<NodeVariable> arguments) {
+                return targetVariable -> {
+                        var placeholderVariable = Variable.of(getSymbol().valueType());
+                        var argumentsWithPlaceholder = new ArrayList<Variable>(arguments.size() + 1);
+                        argumentsWithPlaceholder.addAll(arguments);
+                        argumentsWithPlaceholder.add(placeholderVariable);
+                        return leftJoinBy(placeholderVariable, defaultValue, argumentsWithPlaceholder).toLiteral(targetVariable);
+                };
+        }
+
+        public AssignedValue<T> leftJoin(T defaultValue, NodeVariable... arguments) {
+                return leftJoin(defaultValue, List.of(arguments));
+        }
 }
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MayView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MayView.java
index c322e220..3a6cc93b 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MayView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MayView.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.query.view;
 
 import tools.refinery.store.representation.Symbol;
-import tools.refinery.store.representation.TruthValue;
+import tools.refinery.logic.term.truthvalue.TruthValue;
 import tools.refinery.store.tuple.Tuple;
 
 public class MayView extends TuplePreservingView<TruthValue> {
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MustView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MustView.java
index 65bb4e4c..af984327 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MustView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/MustView.java
@@ -6,7 +6,7 @@
 package tools.refinery.store.query.view;
 
 import tools.refinery.store.representation.Symbol;
-import tools.refinery.store.representation.TruthValue;
+import tools.refinery.logic.term.truthvalue.TruthValue;
 import tools.refinery.store.tuple.Tuple;
 
 public class MustView extends TuplePreservingView<TruthValue> {
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java
index fcf11506..01865cbe 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/NodeFunctionView.java
@@ -5,7 +5,7 @@
  */
 package tools.refinery.store.query.view;
 
-import tools.refinery.store.query.term.Parameter;
+import tools.refinery.logic.term.Parameter;
 import tools.refinery.store.representation.Symbol;
 import tools.refinery.store.tuple.Tuple1;
 
diff --git a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java
index ed12cd9d..6841488d 100644
--- a/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java
+++ b/subprojects/store-query/src/main/java/tools/refinery/store/query/view/TuplePreservingView.java
@@ -7,7 +7,7 @@ package tools.refinery.store.query.view;
 
 import tools.refinery.store.map.CursorAsIterator;
 import tools.refinery.store.model.Model;
-import tools.refinery.store.query.term.Parameter;
+import tools.refinery.logic.term.Parameter;
 import tools.refinery.store.representation.Symbol;
 import tools.refinery.store.tuple.Tuple;
 import tools.refinery.store.tuple.Tuple1;
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderLiteralEliminationTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderLiteralEliminationTest.java
deleted file mode 100644
index 6a2dc0c7..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderLiteralEliminationTest.java
+++ /dev/null
@@ -1,259 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.CsvSource;
-import tools.refinery.store.query.literal.BooleanLiteral;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.term.bool.BoolTerms;
-import tools.refinery.store.query.view.KeyOnlyView;
-import tools.refinery.store.query.view.SymbolView;
-import tools.refinery.store.representation.Symbol;
-
-import java.util.List;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static tools.refinery.store.query.literal.Literals.check;
-import static tools.refinery.store.query.literal.Literals.not;
-import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
-
-class DnfBuilderLiteralEliminationTest {
-        private final Symbol<Boolean> friend = Symbol.of("friend", 2);
-        private final SymbolView<Boolean> friendView = new KeyOnlyView<>(friend);
-        private final NodeVariable p = Variable.of("p");
-        private final NodeVariable q = Variable.of("q");
-        private final Dnf trueDnf = Dnf.builder().parameter(p, ParameterDirection.IN).clause().build();
-        private final Dnf falseDnf = Dnf.builder().parameter(p).build();
-
-        @Test
-        void eliminateTrueTest() {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(BooleanLiteral.TRUE, friendView.call(p, q))
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void eliminateTrueAssumptionTest() {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(check(BoolTerms.constant(true)), friendView.call(p, q))
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void eliminateFalseTest() {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(friendView.call(p, q))
-                                .clause(friendView.call(q, p), BooleanLiteral.FALSE)
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @ParameterizedTest
-        @CsvSource(value = {
-                        "false",
-                        "null"
-        }, nullValues = "null")
-        void eliminateFalseAssumptionTest(Boolean value) {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(friendView.call(p, q))
-                                .clause(friendView.call(q, p), check(BoolTerms.constant(value)))
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void alwaysTrueTest() {
-                var actual = Dnf.builder()
-                                .parameters(List.of(p, q), ParameterDirection.IN)
-                                .clause(friendView.call(p, q))
-                                .clause(BooleanLiteral.TRUE)
-                                .build();
-                var expected = Dnf.builder().parameters(List.of(p, q), ParameterDirection.IN).clause().build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void alwaysFalseTest() {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(friendView.call(p, q), BooleanLiteral.FALSE)
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void eliminateTrueDnfTest() {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(trueDnf.call(q), friendView.call(p, q))
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void eliminateFalseDnfTest() {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(friendView.call(p, q))
-                                .clause(friendView.call(q, p), falseDnf.call(q))
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void alwaysTrueDnfTest() {
-                var actual = Dnf.builder()
-                                .parameters(List.of(p, q), ParameterDirection.IN)
-                                .clause(friendView.call(p, q))
-                                .clause(trueDnf.call(q))
-                                .build();
-                var expected = Dnf.builder().parameters(List.of(p, q), ParameterDirection.IN).clause().build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void alwaysFalseDnfTest() {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(friendView.call(p, q), falseDnf.call(q))
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void eliminateNotFalseDnfTest() {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(not(falseDnf.call(q)), friendView.call(p, q))
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void eliminateNotTrueDnfTest() {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(friendView.call(p, q))
-                                .clause(friendView.call(q, p), not(trueDnf.call(q)))
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).clause(friendView.call(p, q)).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void alwaysNotFalseDnfTest() {
-                var actual = Dnf.builder()
-                                .parameters(List.of(p, q), ParameterDirection.IN)
-                                .clause(friendView.call(p, q))
-                                .clause(not(falseDnf.call(q)))
-                                .build();
-                var expected = Dnf.builder().parameters(List.of(p, q), ParameterDirection.IN).clause().build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void alwaysNotTrueDnfTest() {
-                var actual = Dnf.builder()
-                                .parameters(p, q)
-                                .clause(friendView.call(p, q), not(trueDnf.call(q)))
-                                .build();
-                var expected = Dnf.builder().parameters(p, q).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void removeDuplicateTest() {
-                var actual = Dnf.of(builder -> builder.clause((p, q) -> List.of(
-                                friendView.call(p, q),
-                                friendView.call(p, q)
-                )));
-                var expected = Dnf.of(builder -> builder.clause((p, q) -> List.of(friendView.call(p, q))));
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void removeContradictoryTest() {
-                var actual = Dnf.of(builder -> builder.clause((p, q) -> List.of(
-                                friendView.call(p, q),
-                                not(friendView.call(p, q))
-                )));
-                var expected = Dnf.builder().build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void removeContradictoryUniversalTest() {
-                var actual = Dnf.of(builder -> builder.clause((p, q) -> List.of(
-                                friendView.call(q, q),
-                                friendView.call(p, q),
-                                not(friendView.call(p, Variable.of()))
-                )));
-                var expected = Dnf.builder().build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void removeContradictoryExistentialUniversalTest() {
-                var actual = Dnf.of(builder -> builder.clause((p) -> List.of(
-                                friendView.call(p, Variable.of()),
-                                not(friendView.call(p, Variable.of()))
-                )));
-                var expected = Dnf.builder().build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void removeContradictoryUniversalParameterTest() {
-                var actual = Dnf.of(builder -> {
-                        var p = builder.parameter("p");
-                        builder.clause((q) -> List.of(
-                                        friendView.call(q, q),
-                                        friendView.call(p, q),
-                                        not(friendView.call(p, Variable.of()))
-                        ));
-                });
-                var expected = Dnf.builder().parameter(p).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderVariableUnificationTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderVariableUnificationTest.java
deleted file mode 100644
index fc40c7b3..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfBuilderVariableUnificationTest.java
+++ /dev/null
@@ -1,325 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.view.KeyOnlyView;
-import tools.refinery.store.query.view.SymbolView;
-import tools.refinery.store.representation.Symbol;
-
-import java.util.List;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
-
-class DnfBuilderVariableUnificationTest {
-        private final Symbol<Boolean> friend = Symbol.of("friend", 2);
-        private final Symbol<Boolean> children = Symbol.of("children", 2);
-        private final SymbolView<Boolean> friendView = new KeyOnlyView<>(friend);
-        private final SymbolView<Boolean> childrenView = new KeyOnlyView<>(children);
-
-        @Test
-        void equalToParameterTest() {
-                var actual = Dnf.of(builder -> {
-                        var p = builder.parameter("p");
-                        builder.clause(q -> List.of(
-                                        friendView.call(p, q),
-                                        p.isEquivalent(q)
-                        ));
-                });
-
-                var expectedP = Variable.of("p");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(new SymbolicParameter(expectedP, ParameterDirection.OUT)),
-                                List.of(
-                                                List.of(friendView.call(expectedP, expectedP))
-                                )
-                ));
-        }
-
-        @Test
-        void equalToParameterReverseTest() {
-                var actual = Dnf.of(builder -> {
-                        var p = builder.parameter("p");
-                        builder.clause(q -> List.of(
-                                        friendView.call(p, q),
-                                        q.isEquivalent(p)
-                        ));
-                });
-
-                var expectedP = Variable.of("p");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(new SymbolicParameter(expectedP, ParameterDirection.OUT)),
-                                List.of(
-                                                List.of(friendView.call(expectedP, expectedP))
-                                )
-                ));
-        }
-
-        @Test
-        void equalQuantifiedTest() {
-                var actual = Dnf.of(builder -> builder.clause((p, q) -> List.of(
-                                friendView.call(p, q),
-                                p.isEquivalent(q)
-                )));
-
-                var expectedP = Variable.of("p");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(),
-                                List.of(
-                                                List.of(friendView.call(expectedP, expectedP))
-                                )
-                ));
-        }
-
-        @Test
-        void equalQuantifiedTransitiveTest() {
-                var actual = Dnf.of(builder -> builder.clause((p, q, r) -> List.of(
-                                friendView.call(p, q),
-                                p.isEquivalent(q),
-                                childrenView.call(p, r),
-                                q.isEquivalent(r)
-                )));
-
-                var expectedP = Variable.of("p");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(),
-                                List.of(
-                                                List.of(friendView.call(expectedP, expectedP), childrenView.call(expectedP, expectedP))
-                                )
-                ));
-        }
-
-        @Test
-        void equalQuantifiedTransitiveRemoveDuplicateTest() {
-                var actual = Dnf.of(builder -> builder.clause((p, q, r) -> List.of(
-                                friendView.call(p, q),
-                                p.isEquivalent(q),
-                                friendView.call(p, r),
-                                q.isEquivalent(r)
-                )));
-
-                var expectedP = Variable.of("p");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(),
-                                List.of(
-                                                List.of(friendView.call(expectedP, expectedP))
-                                )
-                ));
-        }
-
-        @Test
-        void parametersEqualTest() {
-                var actual = Dnf.of(builder -> {
-                        var p = builder.parameter("p");
-                        var q = builder.parameter("q");
-                        builder.clause(
-                                        friendView.call(p, q),
-                                        p.isEquivalent(q)
-                        );
-                });
-
-                var expectedP = Variable.of("p");
-                var expectedQ = Variable.of("q");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(
-                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
-                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
-                                ),
-                                List.of(
-                                                List.of(friendView.call(expectedP, expectedP), expectedQ.isEquivalent(expectedP))
-                                )
-                ));
-        }
-
-        @Test
-        void parametersEqualTransitiveTest() {
-                var actual = Dnf.of(builder -> {
-                        var p = builder.parameter("p");
-                        var q = builder.parameter("q");
-                        var r = builder.parameter("r");
-                        builder.clause(
-                                        friendView.call(p, q),
-                                        childrenView.call(p, r),
-                                        p.isEquivalent(q),
-                                        r.isEquivalent(q)
-                        );
-                });
-
-                var expectedP = Variable.of("p");
-                var expectedQ = Variable.of("q");
-                var expectedR = Variable.of("r");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(
-                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
-                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT),
-                                                new SymbolicParameter(expectedR, ParameterDirection.OUT)
-                                ),
-                                List.of(
-                                                List.of(
-                                                                friendView.call(expectedP, expectedP),
-                                                                expectedQ.isEquivalent(expectedP),
-                                                                expectedR.isEquivalent(expectedP),
-                                                                childrenView.call(expectedP, expectedP)
-                                                )
-                                )
-                ));
-        }
-
-        @Test
-        void parameterAndQuantifiedEqualsTest() {
-                var actual = Dnf.of(builder -> {
-                        var p = builder.parameter("p");
-                        var q = builder.parameter("q");
-                        builder.clause((r) -> List.of(
-                                        friendView.call(p, r),
-                                        p.isEquivalent(r),
-                                        childrenView.call(q, r),
-                                        q.isEquivalent(r)
-                        ));
-                });
-
-
-                var expectedP = Variable.of("p");
-                var expectedQ = Variable.of("q");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(
-                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
-                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
-                                ),
-                                List.of(
-                                                List.of(
-                                                                friendView.call(expectedP, expectedP),
-                                                                expectedQ.isEquivalent(expectedP),
-                                                                childrenView.call(expectedP, expectedP)
-                                                )
-                                )
-                ));
-        }
-
-        @Test
-        void parameterAndQuantifiedEqualsReverseFirstTest() {
-                var actual = Dnf.of(builder -> {
-                        var p = builder.parameter("p");
-                        var q = builder.parameter("q");
-                        builder.clause((r) -> List.of(
-                                        friendView.call(p, r),
-                                        r.isEquivalent(p),
-                                        childrenView.call(q, r),
-                                        q.isEquivalent(r)
-                        ));
-                });
-
-                var expectedP = Variable.of("p");
-                var expectedQ = Variable.of("q");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(
-                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
-                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
-                                ),
-                                List.of(
-                                                List.of(
-                                                                friendView.call(expectedP, expectedP),
-                                                                expectedQ.isEquivalent(expectedP),
-                                                                childrenView.call(expectedP, expectedP)
-                                                )
-                                )
-                ));
-        }
-
-        @Test
-        void parameterAndQuantifiedEqualsReverseSecondTest() {
-                var actual = Dnf.of(builder -> {
-                        var p = builder.parameter("p");
-                        var q = builder.parameter("q");
-                        builder.clause((r) -> List.of(
-                                        friendView.call(p, r),
-                                        p.isEquivalent(r),
-                                        childrenView.call(q, r),
-                                        r.isEquivalent(q)
-                        ));
-                });
-
-                var expectedP = Variable.of("p");
-                var expectedQ = Variable.of("q");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(
-                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
-                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
-                                ),
-                                List.of(
-                                                List.of(
-                                                                friendView.call(expectedP, expectedP),
-                                                                expectedQ.isEquivalent(expectedP),
-                                                                childrenView.call(expectedP, expectedP)
-                                                )
-                                )
-                ));
-        }
-
-        @Test
-        void parameterAndQuantifiedEqualsReverseBoth() {
-                var actual = Dnf.of(builder -> {
-                        var p = builder.parameter("p");
-                        var q = builder.parameter("q");
-                        builder.clause((r) -> List.of(
-                                        friendView.call(p, r),
-                                        p.isEquivalent(r),
-                                        childrenView.call(q, r),
-                                        r.isEquivalent(q)
-                        ));
-                });
-
-                var expectedP = Variable.of("p");
-                var expectedQ = Variable.of("q");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(
-                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
-                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
-                                ),
-                                List.of(
-                                                List.of(
-                                                                friendView.call(expectedP, expectedP),
-                                                                expectedQ.isEquivalent(expectedP),
-                                                                childrenView.call(expectedP, expectedP)
-                                                )
-                                )
-                ));
-        }
-
-        @Test
-        void parameterAndTwoQuantifiedEqualsTest() {
-                var actual = Dnf.of(builder -> {
-                        var p = builder.parameter("p");
-                        var q = builder.parameter("q");
-                        builder.clause((r, s) -> List.of(
-                                        r.isEquivalent(s),
-                                        friendView.call(p, r),
-                                        p.isEquivalent(r),
-                                        childrenView.call(q, s),
-                                        q.isEquivalent(s)
-                        ));
-                });
-
-                var expectedP = Variable.of("p");
-                var expectedQ = Variable.of("q");
-                assertThat(actual, structurallyEqualTo(
-                                List.of(
-                                                new SymbolicParameter(expectedP, ParameterDirection.OUT),
-                                                new SymbolicParameter(expectedQ, ParameterDirection.OUT)
-                                ),
-                                List.of(
-                                                List.of(
-                                                                friendView.call(expectedP, expectedP),
-                                                                expectedQ.isEquivalent(expectedP),
-                                                                childrenView.call(expectedP, expectedP)
-                                                )
-                                )
-                ));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfToDefinitionStringTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfToDefinitionStringTest.java
deleted file mode 100644
index 12cfaa4e..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/DnfToDefinitionStringTest.java
+++ /dev/null
@@ -1,157 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.view.AnySymbolView;
-import tools.refinery.store.query.view.KeyOnlyView;
-import tools.refinery.store.representation.Symbol;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.is;
-import static tools.refinery.store.query.literal.Literals.not;
-
-class DnfToDefinitionStringTest {
-        private static final Symbol<Boolean> person = Symbol.of("person", 1);
-        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
-        private static final AnySymbolView personView = new KeyOnlyView<>(person);
-        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
-        private static final NodeVariable p = Variable.of("p");
-        private static final NodeVariable q = Variable.of("q");
-
-        @Test
-        void noClausesTest() {
-                var dnf = Dnf.builder("Example").parameter(p).build();
-
-                assertThat(dnf.toDefinitionString(), is("""
-                                pred Example(p) <->
-                                    <no clauses>.
-                                """));
-        }
-
-        @Test
-        void noParametersTest() {
-                var dnf = Dnf.builder("Example").build();
-
-                assertThat(dnf.toDefinitionString(), is("""
-                                pred Example() <->
-                                    <no clauses>.
-                                """));
-        }
-
-        @Test
-        void emptyClauseTest() {
-                var dnf = Dnf.builder("Example").parameter(p, ParameterDirection.IN).clause().build();
-
-                assertThat(dnf.toDefinitionString(), is("""
-                                pred Example(in p) <->
-                                    <empty>.
-                                """));
-        }
-
-        @Test
-        void relationViewPositiveTest() {
-                var dnf = Dnf.builder("Example").parameter(p).clause(friendView.call(p, q)).build();
-
-                assertThat(dnf.toDefinitionString(), is("""
-                                pred Example(p) <->
-                                    @RelationView("key") friend(p, q).
-                                """));
-        }
-
-        @Test
-        void relationViewNegativeTest() {
-                var dnf = Dnf.builder("Example")
-                                .parameter(p, ParameterDirection.IN)
-                                .clause(not(friendView.call(p, q)))
-                                .build();
-
-                assertThat(dnf.toDefinitionString(), is("""
-                                pred Example(in p) <->
-                                    !(@RelationView("key") friend(p, q)).
-                                """));
-        }
-
-        @Test
-        void relationViewTransitiveTest() {
-                var dnf = Dnf.builder("Example").parameter(p).clause(friendView.callTransitive(p, q)).build();
-
-                assertThat(dnf.toDefinitionString(), is("""
-                                pred Example(p) <->
-                                    @RelationView("key") friend+(p, q).
-                                """));
-        }
-
-        @Test
-        void multipleParametersTest() {
-                var dnf = Dnf.builder("Example").parameters(p, q).clause(friendView.call(p, q)).build();
-
-                assertThat(dnf.toDefinitionString(), is("""
-                                pred Example(p, q) <->
-                                    @RelationView("key") friend(p, q).
-                                """));
-        }
-
-        @Test
-        void multipleLiteralsTest() {
-                var dnf = Dnf.builder("Example")
-                                .parameter(p)
-                                .clause(
-                                                personView.call(p),
-                                                personView.call(q),
-                                                friendView.call(p, q)
-                                )
-                                .build();
-
-                assertThat(dnf.toDefinitionString(), is("""
-                                pred Example(p) <->
-                                    @RelationView("key") person(p),
-                                    @RelationView("key") person(q),
-                                    @RelationView("key") friend(p, q).
-                                """));
-        }
-
-        @Test
-        void multipleClausesTest() {
-                var dnf = Dnf.builder("Example")
-                                .parameter(p)
-                                .clause(friendView.call(p, q))
-                                .clause(friendView.call(q, p))
-                                .build();
-
-                assertThat(dnf.toDefinitionString(), is("""
-                                pred Example(p) <->
-                                    @RelationView("key") friend(p, q)
-                                ;
-                                    @RelationView("key") friend(q, p).
-                                """));
-        }
-
-        @Test
-        void dnfTest() {
-                var r = Variable.of("r");
-                var s = Variable.of("s");
-                var called  = Dnf.builder("Called").parameters(r, s).clause(friendView.call(r, s)).build();
-                var dnf = Dnf.builder("Example")
-                                .parameter(p)
-                                .clause(
-                                                personView.call(p),
-                                                personView.call(q),
-                                                not(called.call(p, q))
-                                )
-                                .build();
-
-                assertThat(dnf.toDefinitionString(), is("""
-                                pred Example(p) <->
-                                    @RelationView("key") person(p),
-                                    @RelationView("key") person(q),
-                                    !(@Dnf Called(p, q)).
-                                """));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/HashCodeTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/HashCodeTest.java
deleted file mode 100644
index 0c8eaeed..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/HashCodeTest.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.view.AnySymbolView;
-import tools.refinery.store.query.view.KeyOnlyView;
-import tools.refinery.store.representation.Symbol;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.is;
-import static org.hamcrest.Matchers.not;
-
-class HashCodeTest {
-        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
-        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
-        private static final AnySymbolView personView = new KeyOnlyView<>(person);
-        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
-        private static final NodeVariable p = Variable.of("p");
-        private static final NodeVariable q = Variable.of("q");
-
-        @Test
-        void flatEqualsTest() {
-                var expected = Dnf.builder("Expected").parameters(q).clause(personView.call(q)).build();
-                var actual = Dnf.builder("Actual").parameters(p).clause(personView.call(p)).build();
-
-                assertThat(actual.hashCodeWithSubstitution(), is(expected.hashCodeWithSubstitution()));
-        }
-
-        @Test
-        void flatNotEqualsTest() {
-                var expected = Dnf.builder("Expected").parameters(q).clause(friendView.call(q, q)).build();
-                var actual = Dnf.builder("Actual").parameters(p).clause(friendView.call(p, q)).build();
-
-                assertThat(actual.hashCodeWithSubstitution(), not(expected.hashCodeWithSubstitution()));
-        }
-
-        @Test
-        void deepEqualsTest() {
-                var expected2 = Dnf.builder("Expected2").parameters(p).clause(personView.call(p)).build();
-                var expected = Dnf.builder("Expected").parameters(q).clause(
-                                expected2.call(q)
-                ).build();
-                var actual = Dnf.builder("Actual").parameters(q).clause(
-                                expected2.call(q)
-                ).build();
-
-                assertThat(actual.hashCodeWithSubstitution(), is(expected.hashCodeWithSubstitution()));
-        }
-
-        @Test
-        void deepNotEqualsTest() {
-                var expected = Dnf.builder("Expected").parameters(q).clause(
-                                Dnf.builder("Expected2").parameters(p).clause(personView.call(p)).build().call(q)
-                ).build();
-                var actual = Dnf.builder("Actual").parameters(q).clause(
-                                Dnf.builder("Actual2").parameters(p).clause(personView.call(p)).build().call(q)
-                ).build();
-
-                assertThat(actual.hashCodeWithSubstitution(), not(expected.hashCodeWithSubstitution()));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/TopologicalSortTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/TopologicalSortTest.java
deleted file mode 100644
index 854bd469..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/TopologicalSortTest.java
+++ /dev/null
@@ -1,113 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.view.AnySymbolView;
-import tools.refinery.store.query.view.KeyOnlyView;
-import tools.refinery.store.representation.Symbol;
-
-import java.util.List;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.junit.jupiter.api.Assertions.assertThrows;
-import static tools.refinery.store.query.literal.Literals.not;
-import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
-
-class TopologicalSortTest {
-        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
-        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
-        private static final Dnf example = Dnf.of("example", builder -> {
-                var a = builder.parameter("a", ParameterDirection.IN);
-                var b = builder.parameter("b", ParameterDirection.IN);
-                var c = builder.parameter("c", ParameterDirection.OUT);
-                var d = builder.parameter("d", ParameterDirection.OUT);
-                builder.clause(
-                                friendView.call(a, b),
-                                friendView.call(b, c),
-                                friendView.call(c, d)
-                );
-        });
-        private static final NodeVariable p = Variable.of("p");
-        private static final NodeVariable q = Variable.of("q");
-        private static final NodeVariable r = Variable.of("r");
-        private static final NodeVariable s = Variable.of("s");
-        private static final NodeVariable t = Variable.of("t");
-
-        @Test
-        void topologicalSortTest() {
-                var actual = Dnf.builder("Actual")
-                                .parameter(p, ParameterDirection.IN)
-                                .parameter(q, ParameterDirection.OUT)
-                                .clause(
-                                                not(friendView.call(p, q)),
-                                                example.call(p, q, r, s),
-                                                example.call(r, t, q, s),
-                                                friendView.call(r, t)
-                                )
-                                .build();
-
-                assertThat(actual, structurallyEqualTo(
-                                List.of(
-                                                new SymbolicParameter(p, ParameterDirection.IN),
-                                                new SymbolicParameter(q, ParameterDirection.OUT)
-                                ),
-                                List.of(
-                                                List.of(
-                                                                friendView.call(r, t),
-                                                                example.call(r, t, q, s),
-                                                                not(friendView.call(p, q)),
-                                                                example.call(p, q, r, s)
-                                                )
-                                )
-                ));
-        }
-
-        @Test
-        void missingInputTest() {
-                var builder = Dnf.builder("Actual")
-                                .parameter(p, ParameterDirection.OUT)
-                                .parameter(q, ParameterDirection.OUT)
-                                .clause(
-                                                not(friendView.call(p, q)),
-                                                example.call(p, q, r, s),
-                                                example.call(r, t, q, s),
-                                                friendView.call(r, t)
-                                );
-                assertThrows(InvalidQueryException.class, builder::build);
-        }
-
-        @Test
-        void missingVariableTest() {
-                var builder = Dnf.builder("Actual")
-                                .parameter(p, ParameterDirection.IN)
-                                .parameter(q, ParameterDirection.OUT)
-                                .clause(
-                                                not(friendView.call(p, q)),
-                                                example.call(p, q, r, s),
-                                                example.call(r, t, q, s)
-                                );
-                assertThrows(InvalidQueryException.class, builder::build);
-        }
-
-        @Test
-        void circularDependencyTest() {
-                var builder = Dnf.builder("Actual")
-                                .parameter(p, ParameterDirection.IN)
-                                .parameter(q, ParameterDirection.OUT)
-                                .clause(
-                                                not(friendView.call(p, q)),
-                                                example.call(p, q, r, s),
-                                                example.call(r, t, q, s),
-                                                example.call(p, q, r, t)
-                                );
-                assertThrows(InvalidQueryException.class, builder::build);
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/VariableDirectionTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/VariableDirectionTest.java
deleted file mode 100644
index fc3f5d48..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/dnf/VariableDirectionTest.java
+++ /dev/null
@@ -1,251 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.dnf;
-
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.Arguments;
-import org.junit.jupiter.params.provider.MethodSource;
-import tools.refinery.store.query.literal.BooleanLiteral;
-import tools.refinery.store.query.literal.Literal;
-import tools.refinery.store.query.term.DataVariable;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.view.AnySymbolView;
-import tools.refinery.store.query.view.FunctionView;
-import tools.refinery.store.query.view.KeyOnlyView;
-import tools.refinery.store.representation.Symbol;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.stream.Stream;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.hasItem;
-import static org.hamcrest.Matchers.not;
-import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
-import static org.junit.jupiter.api.Assertions.assertThrows;
-import static tools.refinery.store.query.literal.Literals.not;
-import static tools.refinery.store.query.term.int_.IntTerms.INT_SUM;
-
-class VariableDirectionTest {
-        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
-        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
-        private static final Symbol<Integer> age = Symbol.of("age", 1, Integer.class);
-        private static final AnySymbolView personView = new KeyOnlyView<>(person);
-        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
-        private static final FunctionView<Integer> ageView = new FunctionView<>(age);
-        private static final NodeVariable p = Variable.of("p");
-        private static final NodeVariable q = Variable.of("q");
-        private static final DataVariable<Integer> x = Variable.of("x", Integer.class);
-        private static final DataVariable<Integer> y = Variable.of("y", Integer.class);
-        private static final DataVariable<Integer> z = Variable.of("z", Integer.class);
-
-        @ParameterizedTest
-        @MethodSource("clausesWithVariableInput")
-        void unboundOutVariableTest(List<? extends Literal> clause) {
-                var builder = Dnf.builder().parameter(p, ParameterDirection.OUT).clause(clause);
-                assertThrows(InvalidClauseException.class, builder::build);
-        }
-
-        @ParameterizedTest
-        @MethodSource("clausesWithVariableInput")
-        void unboundInVariableTest(List<? extends Literal> clause) {
-                var builder = Dnf.builder().parameter(p, ParameterDirection.IN).clause(clause);
-                var dnf = assertDoesNotThrow(builder::build);
-                var clauses = dnf.getClauses();
-                if (clauses.size() > 0) {
-                        assertThat(clauses.get(0).positiveVariables(), hasItem(p));
-                }
-        }
-
-        @ParameterizedTest
-        @MethodSource("clausesWithVariableInput")
-        void boundPrivateVariableTest(List<? extends Literal> clause) {
-                var clauseWithBinding = new ArrayList<Literal>(clause);
-                clauseWithBinding.add(personView.call(p));
-                var builder = Dnf.builder().clause(clauseWithBinding);
-                var dnf = assertDoesNotThrow(builder::build);
-                var clauses = dnf.getClauses();
-                if (clauses.size() > 0) {
-                        assertThat(clauses.get(0).positiveVariables(), hasItem(p));
-                }
-        }
-
-        static Stream<Arguments> clausesWithVariableInput() {
-                return Stream.concat(
-                                clausesNotBindingVariable(),
-                                literalToClauseArgumentStream(literalsWithRequiredVariableInput())
-                );
-        }
-
-        @ParameterizedTest
-        @MethodSource("clausesNotBindingVariable")
-        void unboundPrivateVariableTest(List<? extends Literal> clause) {
-                var builder = Dnf.builder().clause(clause);
-                var dnf = assertDoesNotThrow(builder::build);
-                var clauses = dnf.getClauses();
-                if (clauses.size() > 0) {
-                        assertThat(clauses.get(0).positiveVariables(), not(hasItem(p)));
-                }
-        }
-
-        @ParameterizedTest
-        @MethodSource("clausesNotBindingVariable")
-        void unboundByEquivalencePrivateVariableTest(List<? extends Literal> clause) {
-                var r = Variable.of("r");
-                var clauseWithEquivalence = new ArrayList<Literal>(clause);
-                clauseWithEquivalence.add(r.isEquivalent(p));
-                var builder = Dnf.builder().clause(clauseWithEquivalence);
-                assertThrows(InvalidClauseException.class, builder::build);
-        }
-
-        static Stream<Arguments> clausesNotBindingVariable() {
-                return Stream.concat(
-                                Stream.of(
-                                        Arguments.of(List.of()),
-                                        Arguments.of(List.of(BooleanLiteral.TRUE)),
-                                        Arguments.of(List.of(BooleanLiteral.FALSE))
-                                ),
-                                literalToClauseArgumentStream(literalsWithPrivateVariable())
-                );
-        }
-
-        @ParameterizedTest
-        @MethodSource("literalsWithPrivateVariable")
-        void unboundTwicePrivateVariableTest(Literal literal) {
-                var builder = Dnf.builder().clause(not(personView.call(p)), literal);
-                assertThrows(InvalidClauseException.class, builder::build);
-        }
-
-        @ParameterizedTest
-        @MethodSource("literalsWithPrivateVariable")
-        void unboundTwiceByEquivalencePrivateVariableTest(Literal literal) {
-                var r = Variable.of("r");
-                var builder = Dnf.builder().clause(not(personView.call(r)), r.isEquivalent(p), literal);
-                assertThrows(InvalidClauseException.class, builder::build);
-        }
-
-        static Stream<Arguments> literalsWithPrivateVariable() {
-                var dnfWithOutput = Dnf.builder("WithOutput")
-                                .parameter(p, ParameterDirection.OUT)
-                                .parameter(q, ParameterDirection.OUT)
-                                .clause(friendView.call(p, q))
-                                .build();
-                var dnfWithOutputToAggregate = Dnf.builder("WithOutputToAggregate")
-                                .parameter(p, ParameterDirection.OUT)
-                                .parameter(q, ParameterDirection.OUT)
-                                .parameter(x, ParameterDirection.OUT)
-                                .clause(
-                                                friendView.call(p, q),
-                                                ageView.call(q, x)
-                                )
-                                .build();
-
-                return Stream.of(
-                                Arguments.of(not(friendView.call(p, q))),
-                                Arguments.of(y.assign(friendView.count(p, q))),
-                                Arguments.of(y.assign(ageView.aggregate(INT_SUM, p))),
-                                Arguments.of(not(dnfWithOutput.call(p, q))),
-                                Arguments.of(y.assign(dnfWithOutput.count(p, q))),
-                                Arguments.of(y.assign(dnfWithOutputToAggregate.aggregateBy(z, INT_SUM, p, q, z)))
-                );
-        }
-
-        @ParameterizedTest
-        @MethodSource("literalsWithRequiredVariableInput")
-        void unboundPrivateVariableTest(Literal literal) {
-                var builder = Dnf.builder().clause(literal);
-                assertThrows(InvalidClauseException.class, builder::build);
-        }
-
-        @ParameterizedTest
-        @MethodSource("literalsWithRequiredVariableInput")
-        void boundPrivateVariableInputTest(Literal literal) {
-                var builder = Dnf.builder().clause(personView.call(p), literal);
-                var dnf = assertDoesNotThrow(builder::build);
-                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(p));
-        }
-
-        static Stream<Arguments> literalsWithRequiredVariableInput() {
-                var dnfWithInput = Dnf.builder("WithInput")
-                                .parameter(p, ParameterDirection.IN)
-                                .parameter(q, ParameterDirection.OUT)
-                                .clause(friendView.call(p, q)).build();
-                var dnfWithInputToAggregate = Dnf.builder("WithInputToAggregate")
-                                .parameter(p, ParameterDirection.IN)
-                                .parameter(q, ParameterDirection.OUT)
-                                .parameter(x, ParameterDirection.OUT)
-                                .clause(
-                                                friendView.call(p, q),
-                                                ageView.call(q, x)
-                                ).build();
-
-                return Stream.of(
-                                Arguments.of(dnfWithInput.call(p, q)),
-                                Arguments.of(dnfWithInput.call(p, p)),
-                                Arguments.of(not(dnfWithInput.call(p, q))),
-                                Arguments.of(not(dnfWithInput.call(p, p))),
-                                Arguments.of(y.assign(dnfWithInput.count(p, q))),
-                                Arguments.of(y.assign(dnfWithInput.count(p, p))),
-                                Arguments.of(y.assign(dnfWithInputToAggregate.aggregateBy(z, INT_SUM, p, q, z))),
-                                Arguments.of(y.assign(dnfWithInputToAggregate.aggregateBy(z, INT_SUM, p, p, z)))
-                );
-        }
-
-        @ParameterizedTest
-        @MethodSource("literalsWithVariableOutput")
-        void boundParameterTest(Literal literal) {
-                var builder = Dnf.builder().parameter(p, ParameterDirection.OUT).clause(literal);
-                var dnf = assertDoesNotThrow(builder::build);
-                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(p));
-        }
-
-        @ParameterizedTest
-        @MethodSource("literalsWithVariableOutput")
-        void boundTwiceParameterTest(Literal literal) {
-                var builder = Dnf.builder().parameter(p, ParameterDirection.IN).clause(literal);
-                var dnf = assertDoesNotThrow(builder::build);
-                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(p));
-        }
-
-        @ParameterizedTest
-        @MethodSource("literalsWithVariableOutput")
-        void boundPrivateVariableOutputTest(Literal literal) {
-                var dnfWithInput = Dnf.builder("WithInput")
-                                .parameter(p, ParameterDirection.IN)
-                                .clause(personView.call(p))
-                                .build();
-                var builder = Dnf.builder().clause(dnfWithInput.call(p), literal);
-                var dnf = assertDoesNotThrow(builder::build);
-                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(p));
-        }
-
-        @ParameterizedTest
-        @MethodSource("literalsWithVariableOutput")
-        void boundTwicePrivateVariableOutputTest(Literal literal) {
-                var builder = Dnf.builder().clause(personView.call(p), literal);
-                var dnf = assertDoesNotThrow(builder::build);
-                assertThat(dnf.getClauses().get(0).positiveVariables(), hasItem(p));
-        }
-
-        static Stream<Arguments> literalsWithVariableOutput() {
-                var dnfWithOutput = Dnf.builder("WithOutput")
-                                .parameter(p, ParameterDirection.OUT)
-                                .parameter(q, ParameterDirection.OUT)
-                                .clause(friendView.call(p, q))
-                                .build();
-
-                return Stream.of(
-                                Arguments.of(friendView.call(p, q)),
-                                Arguments.of(dnfWithOutput.call(p, q))
-                );
-        }
-
-        private static Stream<Arguments> literalToClauseArgumentStream(Stream<Arguments> literalArgumentsStream) {
-                return literalArgumentsStream.map(arguments -> Arguments.of(List.of(arguments.get()[0])));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/AggregationLiteralTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/AggregationLiteralTest.java
deleted file mode 100644
index ddd57e96..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/AggregationLiteralTest.java
+++ /dev/null
@@ -1,89 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.Constraint;
-import tools.refinery.store.query.InvalidQueryException;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.InvalidClauseException;
-import tools.refinery.store.query.term.*;
-
-import java.util.List;
-import java.util.Set;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.*;
-import static org.junit.jupiter.api.Assertions.assertAll;
-import static org.junit.jupiter.api.Assertions.assertThrows;
-import static tools.refinery.store.query.literal.Literals.not;
-import static tools.refinery.store.query.term.int_.IntTerms.INT_SUM;
-import static tools.refinery.store.query.term.int_.IntTerms.constant;
-
-class AggregationLiteralTest {
-        private static final NodeVariable p = Variable.of("p");
-        private static final DataVariable<Integer> x = Variable.of("x", Integer.class);
-        private static final DataVariable<Integer> y = Variable.of("y", Integer.class);
-        private static final DataVariable<Integer> z = Variable.of("z", Integer.class);
-        private static final Constraint fakeConstraint = new Constraint() {
-                @Override
-                public String name() {
-                        return getClass().getName();
-                }
-
-                @Override
-                public List<Parameter> getParameters() {
-                        return List.of(
-                                        new Parameter(null, ParameterDirection.OUT),
-                                        new Parameter(Integer.class, ParameterDirection.OUT)
-                        );
-                }
-        };
-
-        @Test
-        void parameterDirectionTest() {
-                var literal = x.assign(fakeConstraint.aggregateBy(y, INT_SUM, p, y));
-                assertAll(
-                                () -> assertThat(literal.getOutputVariables(), containsInAnyOrder(x)),
-                                () -> assertThat(literal.getInputVariables(Set.of()), empty()),
-                                () -> assertThat(literal.getInputVariables(Set.of(p)), containsInAnyOrder(p)),
-                                () -> assertThat(literal.getPrivateVariables(Set.of()), containsInAnyOrder(p, y)),
-                                () -> assertThat(literal.getPrivateVariables(Set.of(p)), containsInAnyOrder(y))
-                );
-        }
-
-        @Test
-        void missingAggregationVariableTest() {
-                var aggregation = fakeConstraint.aggregateBy(y, INT_SUM, p, z);
-                assertThrows(InvalidQueryException.class, () -> x.assign(aggregation));
-        }
-
-        @Test
-        void circularAggregationVariableTest() {
-                var aggregation = fakeConstraint.aggregateBy(x, INT_SUM, p, x);
-                assertThrows(InvalidQueryException.class, () -> x.assign(aggregation));
-        }
-
-        @Test
-        void unboundTwiceVariableTest() {
-                var builder = Dnf.builder()
-                                .clause(
-                                                not(fakeConstraint.call(p, y)),
-                                                x.assign(fakeConstraint.aggregateBy(y, INT_SUM, p, y))
-                                );
-                assertThrows(InvalidClauseException.class, builder::build);
-        }
-
-        @Test
-        void unboundBoundVariableTest() {
-                var builder = Dnf.builder()
-                                .clause(
-                                                y.assign(constant(27)),
-                                                x.assign(fakeConstraint.aggregateBy(y, INT_SUM, p, y))
-                                );
-                assertThrows(InvalidClauseException.class, builder::build);
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/CallLiteralTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/CallLiteralTest.java
deleted file mode 100644
index a01c6586..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/literal/CallLiteralTest.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.literal;
-
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.Constraint;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.Parameter;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-
-import java.util.List;
-import java.util.Set;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.containsInAnyOrder;
-import static org.hamcrest.Matchers.empty;
-import static org.junit.jupiter.api.Assertions.assertAll;
-import static tools.refinery.store.query.literal.Literals.not;
-
-class CallLiteralTest {
-        private static final NodeVariable p = Variable.of("p");
-        private static final NodeVariable q = Variable.of("q");
-        private static final NodeVariable r = Variable.of("r");
-        private static final NodeVariable s = Variable.of("s");
-
-        private static final Constraint fakeConstraint = new Constraint() {
-                @Override
-                public String name() {
-                        return getClass().getName();
-                }
-
-                @Override
-                public List<Parameter> getParameters() {
-                        return List.of(
-                                        new Parameter(null, ParameterDirection.IN),
-                                        new Parameter(null, ParameterDirection.IN),
-                                        new Parameter(null, ParameterDirection.OUT),
-                                        new Parameter(null, ParameterDirection.OUT)
-                        );
-                }
-        };
-
-        @Test
-        void notRepeatedPositiveDirectionTest() {
-                var literal = fakeConstraint.call(p, q, r, s);
-                assertAll(
-                                () -> assertThat(literal.getOutputVariables(), containsInAnyOrder(r, s)),
-                                () -> assertThat(literal.getInputVariables(Set.of()), containsInAnyOrder(p, q)),
-                                () -> assertThat(literal.getInputVariables(Set.of(p, q, r)), containsInAnyOrder(p, q)),
-                                () -> assertThat(literal.getPrivateVariables(Set.of()), empty()),
-                                () -> assertThat(literal.getPrivateVariables(Set.of(p, q, r)), empty())
-                );
-        }
-
-        @Test
-        void notRepeatedNegativeDirectionTest() {
-                var literal = not(fakeConstraint.call(p, q, r, s));
-                assertAll(
-                                () -> assertThat(literal.getOutputVariables(), empty()),
-                                () -> assertThat(literal.getInputVariables(Set.of()), containsInAnyOrder(p, q)),
-                                () -> assertThat(literal.getInputVariables(Set.of(p, q, r)), containsInAnyOrder(p, q, r)),
-                                () -> assertThat(literal.getPrivateVariables(Set.of()), containsInAnyOrder(r, s)),
-                                () -> assertThat(literal.getPrivateVariables(Set.of(p, q, r)), containsInAnyOrder(s))
-                );
-        }
-
-        @Test
-        void repeatedPositiveDirectionTest() {
-                var literal = fakeConstraint.call(p, p, q, q);
-                assertAll(
-                                () -> assertThat(literal.getOutputVariables(), containsInAnyOrder(q)),
-                                () -> assertThat(literal.getInputVariables(Set.of()), containsInAnyOrder(p)),
-                                () -> assertThat(literal.getInputVariables(Set.of(p, q)), containsInAnyOrder(p)),
-                                () -> assertThat(literal.getPrivateVariables(Set.of()), empty()),
-                                () -> assertThat(literal.getPrivateVariables(Set.of(p, q)), empty())
-                );
-        }
-
-        @Test
-        void repeatedNegativeDirectionTest() {
-                var literal = not(fakeConstraint.call(p, p, q, q));
-                assertAll(
-                                () -> assertThat(literal.getOutputVariables(), empty()),
-                                () -> assertThat(literal.getInputVariables(Set.of()), containsInAnyOrder(p)),
-                                () -> assertThat(literal.getInputVariables(Set.of(p, q)), containsInAnyOrder(p, q)),
-                                () -> assertThat(literal.getPrivateVariables(Set.of()), containsInAnyOrder(q)),
-                                () -> assertThat(literal.getPrivateVariables(Set.of(p, q)), empty())
-                );
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/rewriter/DuplicateDnfRemoverTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/rewriter/DuplicateDnfRemoverTest.java
deleted file mode 100644
index ebb24ab5..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/rewriter/DuplicateDnfRemoverTest.java
+++ /dev/null
@@ -1,164 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.rewriter;
-
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.dnf.Query;
-import tools.refinery.store.query.literal.AbstractCallLiteral;
-import tools.refinery.store.query.literal.Reduction;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.view.AnySymbolView;
-import tools.refinery.store.query.view.KeyOnlyView;
-import tools.refinery.store.representation.Symbol;
-
-import java.util.List;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.is;
-import static org.hamcrest.Matchers.not;
-import static tools.refinery.store.query.literal.Literals.not;
-
-class DuplicateDnfRemoverTest {
-        private final static Symbol<Boolean> friend = Symbol.of("friend", 2);
-        private final static AnySymbolView friendView = new KeyOnlyView<>(friend);
-
-        private DuplicateDnfRemover sut;
-
-        @BeforeEach
-        void beforeEach() {
-                sut = new DuplicateDnfRemover();
-        }
-
-        @Test
-        void removeDuplicateSimpleTest() {
-                var one = Query.of("One", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-                var two = Query.of("Two", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-
-                var oneResult = sut.rewrite(one);
-                var twoResult = sut.rewrite(two);
-
-                assertThat(oneResult, is(twoResult));
-                assertThat(one, is(oneResult));
-        }
-
-        @Test
-        void notDuplicateSimpleTest() {
-                var one = Query.of("One", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-                var two = Query.of("Two", (builder, x, y) -> builder.clause((z) -> List.of(
-                                friendView.call(x, y),
-                                friendView.call(y, z)
-                )));
-
-                var oneResult = sut.rewrite(one);
-                var twoResult = sut.rewrite(two);
-
-                assertThat(one, is(oneResult));
-                assertThat(two, is(twoResult));
-        }
-
-        @Test
-        void removeDuplicateRecursiveTest() {
-                var oneSubQuery = Query.of("OneSubQuery", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-                var one = Query.of("One", (builder, x) -> builder.clause(
-                                oneSubQuery.call(x, Variable.of())
-                ));
-                var twoSubQuery = Query.of("TwoSubQuery", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-                var two = Query.of("Two", (builder, x) -> builder.clause(
-                                twoSubQuery.call(x, Variable.of())
-                ));
-
-                var oneResult = sut.rewrite(one);
-                var twoResult = sut.rewrite(two);
-
-                assertThat(oneResult, is(twoResult));
-                assertThat(one, is(oneResult));
-        }
-
-        @Test
-        void notDuplicateRecursiveTest() {
-                var oneSubQuery = Query.of("OneSubQuery", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-                var one = Query.of("One", (builder, x) -> builder.clause(
-                                oneSubQuery.call(x, Variable.of())
-                ));
-                var twoSubQuery = Query.of("TwoSubQuery", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-                var two = Query.of("Two", (builder, x) -> builder.clause(
-                                twoSubQuery.call(Variable.of(), x)
-                ));
-
-                var oneResult = sut.rewrite(one);
-                var twoResult = sut.rewrite(two);
-
-                assertThat(one, is(oneResult));
-                assertThat(oneResult, is(not(twoResult)));
-
-                var oneCall = (AbstractCallLiteral) oneResult.getDnf().getClauses().get(0).literals().get(0);
-                var twoCall = (AbstractCallLiteral) twoResult.getDnf().getClauses().get(0).literals().get(0);
-
-                assertThat(oneCall.getTarget(), is(twoCall.getTarget()));
-        }
-
-        @Test
-        void removeContradictionTest() {
-                var oneSubQuery = Query.of("OneSubQuery", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-                var twoSubQuery = Query.of("TwoSubQuery", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-                var query = Query.of("Contradiction", (builder, x, y) -> builder.clause(
-                                oneSubQuery.call(x, y),
-                                not(twoSubQuery.call(x, y))
-                ));
-
-                var result = sut.rewrite(query);
-
-                assertThat(result.getDnf().getReduction(), is(Reduction.ALWAYS_FALSE));
-        }
-
-        @Test
-        void removeQuantifiedContradictionTest() {
-                var oneSubQuery = Query.of("OneSubQuery", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-                var twoSubQuery = Query.of("TwoSubQuery", (builder, x, y) -> builder.clause(
-                                friendView.call(x, y),
-                                friendView.call(y, x)
-                ));
-                var query = Query.of("Contradiction", (builder, x) -> builder.clause(
-                                oneSubQuery.call(x, Variable.of()),
-                                not(twoSubQuery.call(x, Variable.of()))
-                ));
-
-                var result = sut.rewrite(query);
-
-                assertThat(result.getDnf().getReduction(), is(Reduction.ALWAYS_FALSE));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/rewriter/InputParameterResolverTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/rewriter/InputParameterResolverTest.java
deleted file mode 100644
index ef0077e4..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/rewriter/InputParameterResolverTest.java
+++ /dev/null
@@ -1,228 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.rewriter;
-
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.Query;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.view.AnySymbolView;
-import tools.refinery.store.query.view.KeyOnlyView;
-import tools.refinery.store.representation.Symbol;
-
-import java.util.List;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.is;
-import static tools.refinery.store.query.literal.Literals.not;
-import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
-
-class InputParameterResolverTest {
-        private final static Symbol<Boolean> person = Symbol.of("Person", 1);
-        private final static Symbol<Boolean> friend = Symbol.of("friend", 2);
-        private final static AnySymbolView personView = new KeyOnlyView<>(person);
-        private final static AnySymbolView friendView = new KeyOnlyView<>(friend);
-
-        private InputParameterResolver sut;
-
-        @BeforeEach
-        void beforeEach() {
-                sut = new InputParameterResolver();
-        }
-
-        @Test
-        void inlineSingleClauseTest() {
-                var dnf = Dnf.of("SubQuery", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.OUT);
-                        builder.clause(friendView.call(x, Variable.of()));
-                });
-                var query = Query.of("Actual", (builder, x) -> builder.clause(
-                                dnf.call(x),
-                                personView.call(x)
-                ));
-
-                var actual = sut.rewrite(query);
-
-                var expected = Query.of("Expected", (builder, x) -> builder.clause(
-                                friendView.call(x, Variable.of()),
-                                personView.call(x)
-                ));
-
-                assertThat(actual.getDnf(), structurallyEqualTo(expected.getDnf()));
-        }
-
-        @Test
-        void inlineSingleClauseWIthInputTest() {
-                var dnf = Dnf.of("SubQuery", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.IN);
-                        builder.clause(not(friendView.call(x, Variable.of())));
-                });
-                var query = Query.of("Actual", (builder, x) -> builder.clause(
-                                dnf.call(x),
-                                personView.call(x)
-                ));
-
-                var actual = sut.rewrite(query);
-
-                var expected = Query.of("Expected", (builder, x) -> builder.clause(
-                                personView.call(x),
-                                not(friendView.call(x, Variable.of()))
-                ));
-
-                assertThat(actual.getDnf(), structurallyEqualTo(expected.getDnf()));
-        }
-
-        @Test
-        void singleLiteralDemandSetTest() {
-                var dnf = Dnf.of("SubQuery", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.IN);
-                        builder.clause(not(friendView.call(x, Variable.of())));
-                        builder.clause(not(friendView.call(Variable.of(), x)));
-                });
-                var query = Query.of("Actual", (builder, x) -> builder.clause(
-                                dnf.call(x),
-                                personView.call(x)
-                ));
-
-                var actual = sut.rewrite(query);
-
-                var expectedSubQuery = Dnf.of("ExpectedSubQuery", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.OUT);
-                        builder.clause(
-                                        personView.call(x),
-                                        not(friendView.call(x, Variable.of()))
-                        );
-                        builder.clause(
-                                        personView.call(x),
-                                        not(friendView.call(Variable.of(), x))
-                        );
-                });
-                var expected = Query.of("Expected", (builder, x) -> builder.clause(
-                                personView.call(x),
-                                expectedSubQuery.call(x)
-                ));
-
-                assertThat(actual.getDnf(), structurallyEqualTo(expected.getDnf()));
-        }
-
-        @Test
-        void multipleLiteralDemandSetTest() {
-                var dnf = Dnf.of("SubQuery", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.IN);
-                        var y = builder.parameter("y", ParameterDirection.IN);
-                        builder.clause(not(friendView.call(x, y)));
-                        builder.clause(not(friendView.call(y, x)));
-                });
-                var query = Query.of("Actual", (builder, p1) -> builder.clause(p2 -> List.of(
-                                not(dnf.call(p1, p2)),
-                                personView.call(p1),
-                                personView.call(p2)
-                )));
-
-                var actual = sut.rewrite(query);
-
-                var context = Dnf.of("Context", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.OUT);
-                        var y = builder.parameter("y", ParameterDirection.OUT);
-                        builder.clause(
-                                        personView.call(x),
-                                        personView.call(y)
-                        );
-                });
-                var expectedSubQuery = Dnf.of("ExpectedSubQuery", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.OUT);
-                        var y = builder.parameter("x", ParameterDirection.OUT);
-                        builder.clause(
-                                        context.call(x, y),
-                                        not(friendView.call(x, y))
-                        );
-                        builder.clause(
-                                        context.call(x, y),
-                                        not(friendView.call(y, x))
-                        );
-                });
-                var expected = Query.of("Expected", (builder, p1) -> builder.clause(p2 -> List.of(
-                                context.call(p1, p2),
-                                not(expectedSubQuery.call(p1, p2))
-                )));
-
-                assertThat(actual.getDnf(), structurallyEqualTo(expected.getDnf()));
-        }
-
-        @Test
-        void multipleParameterDemandSetTest() {
-                var dnf = Dnf.of("SubQuery", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.IN);
-                        var y = builder.parameter("y", ParameterDirection.IN);
-                        builder.clause(not(friendView.call(x, y)));
-                        builder.clause(not(friendView.call(y, x)));
-                });
-                var query = Query.of("Actual", (builder, p1) -> builder.clause(
-                                not(dnf.call(p1, p1)),
-                                personView.call(p1)
-                ));
-
-                var actual = sut.rewrite(query);
-
-                var expectedSubQuery = Dnf.of("ExpectedSubQuery", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.OUT);
-                        var y = builder.parameter("y", ParameterDirection.OUT);
-                        builder.clause(
-                                        y.isEquivalent(x),
-                                        personView.call(x),
-                                        not(friendView.call(x, x))
-                        );
-                });
-                var expected = Query.of("Expected", (builder, p1) -> builder.clause(
-                                personView.call(p1),
-                                not(expectedSubQuery.call(p1, p1))
-                ));
-
-                assertThat(actual.getDnf(), structurallyEqualTo(expected.getDnf()));
-        }
-
-        @Test
-        void eliminateDoubleNegationTest() {
-                var dnf = Dnf.of("SubQuery", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.IN);
-                        builder.clause(not(friendView.call(x, Variable.of())));
-                });
-                var query = Query.of("Actual", (builder, p1) -> builder.clause(
-                                personView.call(p1),
-                                not(dnf.call(p1))
-                ));
-
-                var actual = sut.rewrite(query);
-
-                var expected = Query.of("Actual", (builder, p1) -> builder.clause(
-                                personView.call(p1),
-                                friendView.call(p1, Variable.of())
-                ));
-
-                assertThat(actual.getDnf(), structurallyEqualTo(expected.getDnf()));
-        }
-
-        @Test
-        void identityWhenNoWorkToDoTest() {
-                var dnf = Dnf.of("SubQuery", builder -> {
-                        var x = builder.parameter("x", ParameterDirection.OUT);
-                        builder.clause(
-                                        personView.call(x),
-                                        not(friendView.call(x, Variable.of()))
-                        );
-                });
-                var query = Query.of("Actual", (builder, p1) -> builder.clause(
-                                personView.call(p1),
-                                not(dnf.call(p1))
-                ));
-
-                var actual = sut.rewrite(query);
-
-                assertThat(actual, is(query));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/TermSubstitutionTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/TermSubstitutionTest.java
deleted file mode 100644
index 1fae2492..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/TermSubstitutionTest.java
+++ /dev/null
@@ -1,97 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term;
-
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.Arguments;
-import org.junit.jupiter.params.provider.MethodSource;
-import tools.refinery.store.query.equality.DnfEqualityChecker;
-import tools.refinery.store.query.equality.SubstitutingLiteralEqualityHelper;
-import tools.refinery.store.query.substitution.Substitution;
-import tools.refinery.store.query.term.bool.BoolTerms;
-import tools.refinery.store.query.term.int_.IntTerms;
-import tools.refinery.store.query.term.real.RealTerms;
-import tools.refinery.store.query.term.uppercardinality.UpperCardinalityTerms;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-import java.util.List;
-import java.util.stream.Stream;
-
-class TermSubstitutionTest {
-        private final static DataVariable<Integer> intA = Variable.of("intA", Integer.class);
-        private final static DataVariable<Integer> intB = Variable.of("intB", Integer.class);
-        private final static DataVariable<Double> realA = Variable.of("realA", Double.class);
-        private final static DataVariable<Double> realB = Variable.of("realB", Double.class);
-        private final static DataVariable<Boolean> boolA = Variable.of("boolA", Boolean.class);
-        private final static DataVariable<Boolean> boolB = Variable.of("boolB", Boolean.class);
-        private final static DataVariable<UpperCardinality> upperCardinalityA = Variable.of("upperCardinalityA",
-                        UpperCardinality.class);
-        private final static DataVariable<UpperCardinality> upperCardinalityB = Variable.of("upperCardinalityB",
-                        UpperCardinality.class);
-        private final static Substitution substitution = Substitution.builder()
-                        .put(intA, intB)
-                        .put(intB, intA)
-                        .put(realA, realB)
-                        .put(realB, realA)
-                        .put(boolA, boolB)
-                        .put(boolB, boolA)
-                        .put(upperCardinalityA, upperCardinalityB)
-                        .put(upperCardinalityB, upperCardinalityA)
-                        .build();
-
-        @ParameterizedTest
-        @MethodSource
-        void substitutionTest(AnyTerm term) {
-                var substitutedTerm1 = term.substitute(substitution);
-                Assertions.assertNotEquals(term, substitutedTerm1, "Original term is not equal to substituted term");
-                var helper = new SubstitutingLiteralEqualityHelper(DnfEqualityChecker.DEFAULT, List.of(), List.of());
-                Assertions.assertTrue(term.equalsWithSubstitution(helper, substitutedTerm1), "Terms are equal by helper");
-                // The {@link #substitution} is its own inverse.
-                var substitutedTerm2 = substitutedTerm1.substitute(substitution);
-                Assertions.assertEquals(term, substitutedTerm2, "Original term is not equal to back-substituted term");
-        }
-
-        static Stream<Arguments> substitutionTest() {
-                return Stream.of(
-                                Arguments.of(IntTerms.plus(intA)),
-                                Arguments.of(IntTerms.minus(intA)),
-                                Arguments.of(IntTerms.add(intA, intB)),
-                                Arguments.of(IntTerms.sub(intA, intB)),
-                                Arguments.of(IntTerms.mul(intA, intB)),
-                                Arguments.of(IntTerms.div(intA, intB)),
-                                Arguments.of(IntTerms.pow(intA, intB)),
-                                Arguments.of(IntTerms.min(intA, intB)),
-                                Arguments.of(IntTerms.max(intA, intB)),
-                                Arguments.of(IntTerms.eq(intA, intB)),
-                                Arguments.of(IntTerms.notEq(intA, intB)),
-                                Arguments.of(IntTerms.less(intA, intB)),
-                                Arguments.of(IntTerms.lessEq(intA, intB)),
-                                Arguments.of(IntTerms.greater(intA, intB)),
-                                Arguments.of(IntTerms.greaterEq(intA, intB)),
-                                Arguments.of(IntTerms.asInt(realA)),
-                                Arguments.of(RealTerms.plus(realA)),
-                                Arguments.of(RealTerms.minus(realA)),
-                                Arguments.of(RealTerms.add(realA, realB)),
-                                Arguments.of(RealTerms.sub(realA, realB)),
-                                Arguments.of(RealTerms.mul(realA, realB)),
-                                Arguments.of(RealTerms.div(realA, realB)),
-                                Arguments.of(RealTerms.pow(realA, realB)),
-                                Arguments.of(RealTerms.min(realA, realB)),
-                                Arguments.of(RealTerms.max(realA, realB)),
-                                Arguments.of(RealTerms.asReal(intA)),
-                                Arguments.of(BoolTerms.not(boolA)),
-                                Arguments.of(BoolTerms.and(boolA, boolB)),
-                                Arguments.of(BoolTerms.or(boolA, boolB)),
-                                Arguments.of(BoolTerms.xor(boolA, boolB)),
-                                Arguments.of(RealTerms.eq(realA, realB)),
-                                Arguments.of(UpperCardinalityTerms.add(upperCardinalityA, upperCardinalityB)),
-                                Arguments.of(UpperCardinalityTerms.mul(upperCardinalityA, upperCardinalityB)),
-                                Arguments.of(UpperCardinalityTerms.min(upperCardinalityA, upperCardinalityB)),
-                                Arguments.of(UpperCardinalityTerms.max(upperCardinalityA, upperCardinalityB))
-                );
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/bool/BoolTermsEvaluateTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/bool/BoolTermsEvaluateTest.java
deleted file mode 100644
index beff705e..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/bool/BoolTermsEvaluateTest.java
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.bool;
-
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.CsvSource;
-import tools.refinery.store.query.valuation.Valuation;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.is;
-
-class BoolTermsEvaluateTest {
-        @ParameterizedTest(name = "!{0} == {1}")
-        @CsvSource(value = {
-                        "false, true",
-                        "true, false",
-                        "null, null"
-        }, nullValues = "null")
-        void notTest(Boolean a, Boolean result) {
-                var term = BoolTerms.not(BoolTerms.constant(a));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "{0} && {1} == {2}")
-        @CsvSource(value = {
-                        "false, false, false",
-                        "false, true, false",
-                        "true, false, false",
-                        "true, true, true",
-                        "false, null, null",
-                        "null, false, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void andTest(Boolean a, Boolean b, Boolean result) {
-                var term = BoolTerms.and(BoolTerms.constant(a), BoolTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "{0} || {1} == {2}")
-        @CsvSource(value = {
-                        "false, false, false",
-                        "false, true, true",
-                        "true, false, true",
-                        "true, true, true",
-                        "true, null, null",
-                        "null, true, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void orTest(Boolean a, Boolean b, Boolean result) {
-                var term = BoolTerms.or(BoolTerms.constant(a), BoolTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "{0} ^^ {1} == {2}")
-        @CsvSource(value = {
-                        "false, false, false",
-                        "false, true, true",
-                        "true, false, true",
-                        "true, true, false",
-                        "false, null, null",
-                        "null, false, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void xorTest(Boolean a, Boolean b, Boolean result) {
-                var term = BoolTerms.xor(BoolTerms.constant(a), BoolTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/int_/IntTermsEvaluateTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/int_/IntTermsEvaluateTest.java
deleted file mode 100644
index abe50d75..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/int_/IntTermsEvaluateTest.java
+++ /dev/null
@@ -1,259 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.int_;
-
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.Arguments;
-import org.junit.jupiter.params.provider.CsvSource;
-import org.junit.jupiter.params.provider.MethodSource;
-import tools.refinery.store.query.term.real.RealTerms;
-import tools.refinery.store.query.valuation.Valuation;
-
-import java.util.stream.Stream;
-
-import static org.hamcrest.Matchers.is;
-import static org.hamcrest.MatcherAssert.assertThat;
-
-class IntTermsEvaluateTest {
-        @ParameterizedTest(name = "+{0} == {1}")
-        @CsvSource(value = {
-                        "2, 2",
-                        "null, null"
-        }, nullValues = "null")
-        void plusTest(Integer a, Integer result) {
-                var term = IntTerms.plus(IntTerms.constant(a));
-                assertThat(term.getType(), is(Integer.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "-{0} == {1}")
-        @CsvSource(value = {
-                        "2, -2",
-                        "null, null"
-        }, nullValues = "null")
-        void minusTest(Integer a, Integer result) {
-                var term = IntTerms.minus(IntTerms.constant(a));
-                assertThat(term.getType(), is(Integer.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "{0} + {1} == {2}")
-        @CsvSource(value = {
-                        "1, 2, 3",
-                        "null, 2, null",
-                        "1, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void addTest(Integer a, Integer b, Integer result) {
-                var term = IntTerms.add(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Integer.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "{0} - {1} == {2}")
-        @CsvSource(value = {
-                        "1, 3, -2",
-                        "null, 3, null",
-                        "1, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void subTest(Integer a, Integer b, Integer result) {
-                var term = IntTerms.sub(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Integer.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "{0} * {1} == {2}")
-        @CsvSource(value = {
-                        "2, 3, 6",
-                        "null, 3, null",
-                        "2, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void mulTest(Integer a, Integer b, Integer result) {
-                var term = IntTerms.mul(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Integer.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "{0} * {1} == {2}")
-        @CsvSource(value = {
-                        "6, 3, 2",
-                        "7, 3, 2",
-                        "6, 0, null",
-                        "null, 3, null",
-                        "6, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void divTest(Integer a, Integer b, Integer result) {
-                var term = IntTerms.div(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Integer.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "{0} ** {1} == {2}")
-        @CsvSource(value = {
-                        "1, 0, 1",
-                        "1, 3, 1",
-                        "1, -3, null",
-                        "2, 0, 1",
-                        "2, 2, 4",
-                        "2, 3, 8",
-                        "2, 4, 16",
-                        "2, 5, 32",
-                        "2, 6, 64",
-                        "2, -3, null",
-                        "null, 3, null",
-                        "2, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void powTest(Integer a, Integer b, Integer result) {
-                var term = IntTerms.pow(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Integer.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "min({0}, {1}) == {2}")
-        @CsvSource(value = {
-                        "1, 2, 1",
-                        "2, 1, 1",
-                        "null, 2, null",
-                        "1, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void minTest(Integer a, Integer b, Integer result) {
-                var term = IntTerms.min(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Integer.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "max({0}, {1}) == {2}")
-        @CsvSource(value = {
-                        "1, 2, 2",
-                        "2, 1, 2",
-                        "null, 2, null",
-                        "1, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void maxTest(Integer a, Integer b, Integer result) {
-                var term = IntTerms.max(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Integer.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} == {1}) == {2}")
-        @CsvSource(value = {
-                        "1, 1, true",
-                        "1, 2, false",
-                        "null, 1, null",
-                        "1, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void eqTest(Integer a, Integer b, Boolean result) {
-                var term = IntTerms.eq(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} != {1}) == {2}")
-        @CsvSource(value = {
-                        "1, 1, false",
-                        "1, 2, true",
-                        "null, 1, null",
-                        "1, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void notEqTest(Integer a, Integer b, Boolean result) {
-                var term = IntTerms.notEq(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} < {1}) == {2}")
-        @CsvSource(value = {
-                        "1, -2, false",
-                        "1, 1, false",
-                        "1, 2, true",
-                        "null, 1, null",
-                        "1, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void lessTest(Integer a, Integer b, Boolean result) {
-                var term = IntTerms.less(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} <= {1}) == {2}")
-        @CsvSource(value = {
-                        "1, -2, false",
-                        "1, 1, true",
-                        "1, 2, true",
-                        "null, 1, null",
-                        "1, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void lessEqTest(Integer a, Integer b, Boolean result) {
-                var term = IntTerms.lessEq(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} > {1}) == {2}")
-        @CsvSource(value = {
-                        "1, -2, true",
-                        "1, 1, false",
-                        "1, 2, false",
-                        "null, 1, null",
-                        "1, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void greaterTest(Integer a, Integer b, Boolean result) {
-                var term = IntTerms.greater(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} >= {1}) == {2}")
-        @CsvSource(value = {
-                        "1, -2, true",
-                        "1, 1, true",
-                        "1, 2, false",
-                        "null, 1, null",
-                        "1, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void greaterEqTest(Integer a, Integer b, Boolean result) {
-                var term = IntTerms.greaterEq(IntTerms.constant(a), IntTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "{0} as int == {1}")
-        @MethodSource
-        void asIntTest(Double a, Integer result) {
-                var term = IntTerms.asInt(RealTerms.constant(a));
-                assertThat(term.getType(), is(Integer.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        static Stream<Arguments> asIntTest() {
-                return Stream.of(
-                                Arguments.of(2.0, 2),
-                                Arguments.of(2.1, 2),
-                                Arguments.of(2.9, 2),
-                                Arguments.of(-2.0, -2),
-                                Arguments.of(-2.1, -2),
-                                Arguments.of(-2.9, -2),
-                                Arguments.of(0.0, 0),
-                                Arguments.of(-0.0, 0),
-                                Arguments.of(Double.POSITIVE_INFINITY, Integer.MAX_VALUE),
-                                Arguments.of(Double.NEGATIVE_INFINITY, Integer.MIN_VALUE),
-                                Arguments.of(Double.NaN, null),
-                                Arguments.of(null, null)
-                );
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/real/RealTermEvaluateTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/real/RealTermEvaluateTest.java
deleted file mode 100644
index 6a8eebf1..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/real/RealTermEvaluateTest.java
+++ /dev/null
@@ -1,238 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.real;
-
-import org.hamcrest.Matcher;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.CsvSource;
-import tools.refinery.store.query.term.int_.IntTerms;
-import tools.refinery.store.query.valuation.Valuation;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.*;
-
-class RealTermEvaluateTest {
-        public static final double TOLERANCE = 1e-6;
-
-        private static Matcher<Double> closeToOrNull(Double expected) {
-                return expected == null ? nullValue(Double.class) : closeTo(expected, TOLERANCE);
-        }
-
-        @ParameterizedTest(name = "+{0} == {1}")
-        @CsvSource(value = {
-                        "2.5, 2.5",
-                        "null, null"
-        }, nullValues = "null")
-        void plusTest(Double a, Double result) {
-                var term = RealTerms.plus(RealTerms.constant(a));
-                assertThat(term.getType(), is(Double.class));
-                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
-        }
-
-        @ParameterizedTest(name = "-{0} == {1}")
-        @CsvSource(value = {
-                        "2.5, -2.5",
-                        "null, null"
-        }, nullValues = "null")
-        void minusTest(Double a, Double result) {
-                var term = RealTerms.minus(RealTerms.constant(a));
-                assertThat(term.getType(), is(Double.class));
-                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
-        }
-
-        @ParameterizedTest(name = "{0} + {1} == {2}")
-        @CsvSource(value = {
-                        "1.2, 2.3, 3.5",
-                        "null, 2.3, null",
-                        "1.2, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void addTest(Double a, Double b, Double result) {
-                var term = RealTerms.add(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Double.class));
-                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
-        }
-
-        @ParameterizedTest(name = "{0} - {1} == {2}")
-        @CsvSource(value = {
-                        "1.2, 3.4, -2.2",
-                        "null, 3.4, null",
-                        "1.2, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void subTest(Double a, Double b, Double result) {
-                var term = RealTerms.sub(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Double.class));
-                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
-        }
-
-        @ParameterizedTest(name = "{0} * {1} == {2}")
-        @CsvSource(value = {
-                        "2.3, 3.4, 7.82",
-                        "null, 3.4, null",
-                        "2.3, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void mulTest(Double a, Double b, Double result) {
-                var term = RealTerms.mul(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Double.class));
-                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
-        }
-
-        @ParameterizedTest(name = "{0} * {1} == {2}")
-        @CsvSource(value = {
-                        "7.82, 3.4, 2.3",
-                        "null, 3.4, null",
-                        "7.82, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void divTest(Double a, Double b, Double result) {
-                var term = RealTerms.div(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Double.class));
-                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
-        }
-
-        @ParameterizedTest(name = "{0} ** {1} == {2}")
-        @CsvSource(value = {
-                        "2.0, 6.0, 64.0",
-                        "null, 6.0, null",
-                        "2.0, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void powTest(Double a, Double b, Double result) {
-                var term = RealTerms.pow(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Double.class));
-                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
-        }
-
-        @ParameterizedTest(name = "min({0}, {1}) == {2}")
-        @CsvSource(value = {
-                        "1.5, 2.7, 1.5",
-                        "2.7, 1.5, 1.5",
-                        "null, 2.7, null",
-                        "1.5, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void minTest(Double a, Double b, Double result) {
-                var term = RealTerms.min(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Double.class));
-                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
-        }
-
-        @ParameterizedTest(name = "max({0}, {1}) == {2}")
-        @CsvSource(value = {
-                        "1.5, 2.7, 2.7",
-                        "2.7, 1.7, 2.7",
-                        "null, 2.7, null",
-                        "1.5, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void maxTest(Double a, Double b, Double result) {
-                var term = RealTerms.max(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Double.class));
-                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
-        }
-
-        @ParameterizedTest(name = "({0} == {1}) == {2}")
-        @CsvSource(value = {
-                        "1.5, 1.5, true",
-                        "1.5, 2.7, false",
-                        "null, 1.5, null",
-                        "1.5, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void eqTest(Double a, Double b, Boolean result) {
-                var term = RealTerms.eq(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} != {1}) == {2}")
-        @CsvSource(value = {
-                        "1.5, 1.5, false",
-                        "1.5, 2.7, true",
-                        "null, 1.5, null",
-                        "1.5, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void notEqTest(Double a, Double b, Boolean result) {
-                var term = RealTerms.notEq(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} < {1}) == {2}")
-        @CsvSource(value = {
-                        "1.5, -2.7, false",
-                        "1.5, 1.5, false",
-                        "1.5, 2.7, true",
-                        "null, 1.5, null",
-                        "1.5, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void lessTest(Double a, Double b, Boolean result) {
-                var term = RealTerms.less(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} <= {1}) == {2}")
-        @CsvSource(value = {
-                        "1.5, -2.7, false",
-                        "1.5, 1.5, true",
-                        "1.5, 2.7, true",
-                        "null, 1.5, null",
-                        "1.5, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void lessEqTest(Double a, Double b, Boolean result) {
-                var term = RealTerms.lessEq(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} > {1}) == {2}")
-        @CsvSource(value = {
-                        "1.5, -2.7, true",
-                        "1.5, 1.5, false",
-                        "1.5, 2.7, false",
-                        "null, 1.5, null",
-                        "1.5, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void greaterTest(Double a, Double b, Boolean result) {
-                var term = RealTerms.greater(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "({0} >= {1}) == {2}")
-        @CsvSource(value = {
-                        "1.5, -2.7, true",
-                        "1.5, 1.5, true",
-                        "1.5, 2.7, false",
-                        "null, 1.5, null",
-                        "1.5, null, null",
-                        "null, null, null"
-        }, nullValues = "null")
-        void greaterEqTest(Double a, Double b, Boolean result) {
-                var term = RealTerms.greaterEq(RealTerms.constant(a), RealTerms.constant(b));
-                assertThat(term.getType(), is(Boolean.class));
-                assertThat(term.evaluate(Valuation.empty()), is(result));
-        }
-
-        @ParameterizedTest(name = "{0} as real == {1}")
-        @CsvSource(value = {
-                        "0, 0.0",
-                        "5, 5.0",
-                        "null, null"
-        }, nullValues = "null")
-        void asRealTest(Integer a, Double result) {
-                var term = RealTerms.asReal(IntTerms.constant(a));
-                assertThat(term.getType(), is(Double.class));
-                assertThat(term.evaluate(Valuation.empty()), closeToOrNull(result));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorStreamTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorStreamTest.java
deleted file mode 100644
index 31baf36e..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorStreamTest.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.uppercardinality;
-
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.Arguments;
-import org.junit.jupiter.params.provider.MethodSource;
-import tools.refinery.store.representation.cardinality.UpperCardinalities;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-import java.util.List;
-import java.util.stream.Stream;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.is;
-
-class UpperCardinalitySumAggregatorStreamTest {
-        @ParameterizedTest
-        @MethodSource
-        void testStream(List<UpperCardinality> list, UpperCardinality expected) {
-                var result = UpperCardinalitySumAggregator.INSTANCE.aggregateStream(list.stream());
-                assertThat(result, is(expected));
-        }
-
-        static Stream<Arguments> testStream() {
-                return Stream.of(
-                                Arguments.of(List.of(), UpperCardinalities.ZERO),
-                                Arguments.of(List.of(UpperCardinality.of(3)), UpperCardinality.of(3)),
-                                Arguments.of(
-                                                List.of(
-                                                                UpperCardinality.of(2),
-                                                                UpperCardinality.of(3)
-                                                ),
-                                                UpperCardinality.of(5)
-                                ),
-                                Arguments.of(List.of(UpperCardinalities.UNBOUNDED), UpperCardinalities.UNBOUNDED),
-                                Arguments.of(
-                                                List.of(
-                                                                UpperCardinalities.UNBOUNDED,
-                                                                UpperCardinalities.UNBOUNDED
-                                                ),
-                                                UpperCardinalities.UNBOUNDED
-                                ),
-                                Arguments.of(
-                                                List.of(
-                                                                UpperCardinalities.UNBOUNDED,
-                                                                UpperCardinality.of(3)
-                                                ),
-                                                UpperCardinalities.UNBOUNDED
-                                )
-                );
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorTest.java
deleted file mode 100644
index 780cd0ab..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalitySumAggregatorTest.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.uppercardinality;
-
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.term.StatefulAggregate;
-import tools.refinery.store.representation.cardinality.UpperCardinalities;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.is;
-
-class UpperCardinalitySumAggregatorTest {
-        private StatefulAggregate<UpperCardinality, UpperCardinality> accumulator;
-
-        @BeforeEach
-        void beforeEach() {
-                accumulator = UpperCardinalitySumAggregator.INSTANCE.createEmptyAggregate();
-        }
-
-        @Test
-        void emptyAggregationTest() {
-                assertThat(accumulator.getResult(), is(UpperCardinality.of(0)));
-        }
-
-        @Test
-        void singleBoundedTest() {
-                accumulator.add(UpperCardinality.of(3));
-                assertThat(accumulator.getResult(), is(UpperCardinality.of(3)));
-        }
-
-        @Test
-        void multipleBoundedTest() {
-                accumulator.add(UpperCardinality.of(2));
-                accumulator.add(UpperCardinality.of(3));
-                assertThat(accumulator.getResult(), is(UpperCardinality.of(5)));
-        }
-
-        @Test
-        void singleUnboundedTest() {
-                accumulator.add(UpperCardinalities.UNBOUNDED);
-                assertThat(accumulator.getResult(), is(UpperCardinalities.UNBOUNDED));
-        }
-
-        @Test
-        void multipleUnboundedTest() {
-                accumulator.add(UpperCardinalities.UNBOUNDED);
-                accumulator.add(UpperCardinalities.UNBOUNDED);
-                assertThat(accumulator.getResult(), is(UpperCardinalities.UNBOUNDED));
-        }
-
-        @Test
-        void removeBoundedTest() {
-                accumulator.add(UpperCardinality.of(2));
-                accumulator.add(UpperCardinality.of(3));
-                accumulator.remove(UpperCardinality.of(2));
-                assertThat(accumulator.getResult(), is(UpperCardinality.of(3)));
-        }
-
-        @Test
-        void removeAllUnboundedTest() {
-                accumulator.add(UpperCardinalities.UNBOUNDED);
-                accumulator.add(UpperCardinality.of(3));
-                accumulator.remove(UpperCardinalities.UNBOUNDED);
-                assertThat(accumulator.getResult(), is(UpperCardinality.of(3)));
-        }
-
-        @Test
-        void removeSomeUnboundedTest() {
-                accumulator.add(UpperCardinalities.UNBOUNDED);
-                accumulator.add(UpperCardinalities.UNBOUNDED);
-                accumulator.add(UpperCardinality.of(3));
-                accumulator.remove(UpperCardinalities.UNBOUNDED);
-                assertThat(accumulator.getResult(), is(UpperCardinalities.UNBOUNDED));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTermsEvaluateTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTermsEvaluateTest.java
deleted file mode 100644
index 9d0f3bde..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/term/uppercardinality/UpperCardinalityTermsEvaluateTest.java
+++ /dev/null
@@ -1,104 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.term.uppercardinality;
-
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.Arguments;
-import org.junit.jupiter.params.provider.MethodSource;
-import tools.refinery.store.query.valuation.Valuation;
-import tools.refinery.store.representation.cardinality.UpperCardinalities;
-import tools.refinery.store.representation.cardinality.UpperCardinality;
-
-import java.util.stream.Stream;
-
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.is;
-
-class UpperCardinalityTermsEvaluateTest {
-        @ParameterizedTest(name = "min({0}, {1}) == {2}")
-        @MethodSource
-        void minTest(UpperCardinality a, UpperCardinality b, UpperCardinality expected) {
-                var term = UpperCardinalityTerms.min(UpperCardinalityTerms.constant(a), UpperCardinalityTerms.constant(b));
-                assertThat(term.getType(), is(UpperCardinality.class));
-                assertThat(term.evaluate(Valuation.empty()), is(expected));
-        }
-
-        static Stream<Arguments> minTest() {
-                return Stream.of(
-                                Arguments.of(UpperCardinality.of(0), UpperCardinality.of(0), UpperCardinality.of(0)),
-                                Arguments.of(UpperCardinality.of(0), UpperCardinality.of(1), UpperCardinality.of(0)),
-                                Arguments.of(UpperCardinality.of(1), UpperCardinality.of(0), UpperCardinality.of(0)),
-                                Arguments.of(UpperCardinality.of(0), UpperCardinalities.UNBOUNDED, UpperCardinality.of(0)),
-                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinality.of(0), UpperCardinality.of(0)),
-                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
-                                Arguments.of(UpperCardinality.of(1), null, null),
-                                Arguments.of(null, UpperCardinality.of(1), null),
-                                Arguments.of(null, null, null)
-                );
-        }
-
-        @ParameterizedTest(name = "max({0}, {1}) == {2}")
-        @MethodSource
-        void maxTest(UpperCardinality a, UpperCardinality b, UpperCardinality expected) {
-                var term = UpperCardinalityTerms.max(UpperCardinalityTerms.constant(a), UpperCardinalityTerms.constant(b));
-                assertThat(term.getType(), is(UpperCardinality.class));
-                assertThat(term.evaluate(Valuation.empty()), is(expected));
-        }
-
-        static Stream<Arguments> maxTest() {
-                return Stream.of(
-                                Arguments.of(UpperCardinality.of(0), UpperCardinality.of(0), UpperCardinality.of(0)),
-                                Arguments.of(UpperCardinality.of(0), UpperCardinality.of(1), UpperCardinality.of(1)),
-                                Arguments.of(UpperCardinality.of(1), UpperCardinality.of(0), UpperCardinality.of(1)),
-                                Arguments.of(UpperCardinality.of(0), UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
-                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinality.of(0), UpperCardinalities.UNBOUNDED),
-                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
-                                Arguments.of(UpperCardinality.of(1), null, null),
-                                Arguments.of(null, UpperCardinality.of(1), null),
-                                Arguments.of(null, null, null)
-                );
-        }
-
-        @ParameterizedTest(name = "{0} + {1} == {2}")
-        @MethodSource
-        void addTest(UpperCardinality a, UpperCardinality b, UpperCardinality expected) {
-                var term = UpperCardinalityTerms.add(UpperCardinalityTerms.constant(a), UpperCardinalityTerms.constant(b));
-                assertThat(term.getType(), is(UpperCardinality.class));
-                assertThat(term.evaluate(Valuation.empty()), is(expected));
-        }
-
-        static Stream<Arguments> addTest() {
-                return Stream.of(
-                                Arguments.of(UpperCardinality.of(2), UpperCardinality.of(3), UpperCardinality.of(5)),
-                                Arguments.of(UpperCardinality.of(2), UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
-                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinality.of(2), UpperCardinalities.UNBOUNDED),
-                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
-                                Arguments.of(UpperCardinality.of(1), null, null),
-                                Arguments.of(null, UpperCardinality.of(1), null),
-                                Arguments.of(null, null, null)
-                );
-        }
-
-        @ParameterizedTest(name = "{0} * {1} == {2}")
-        @MethodSource
-        void mulTest(UpperCardinality a, UpperCardinality b, UpperCardinality expected) {
-                var term = UpperCardinalityTerms.mul(UpperCardinalityTerms.constant(a), UpperCardinalityTerms.constant(b));
-                assertThat(term.getType(), is(UpperCardinality.class));
-                assertThat(term.evaluate(Valuation.empty()), is(expected));
-        }
-
-        static Stream<Arguments> mulTest() {
-                return Stream.of(
-                                Arguments.of(UpperCardinality.of(2), UpperCardinality.of(3), UpperCardinality.of(6)),
-                                Arguments.of(UpperCardinality.of(2), UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
-                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinality.of(2), UpperCardinalities.UNBOUNDED),
-                                Arguments.of(UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED, UpperCardinalities.UNBOUNDED),
-                                Arguments.of(UpperCardinality.of(1), null, null),
-                                Arguments.of(null, UpperCardinality.of(1), null),
-                                Arguments.of(null, null, null)
-                );
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToRawTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToRawTest.java
deleted file mode 100644
index d447e99c..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToRawTest.java
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.tests;
-
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.SymbolicParameter;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.view.AnySymbolView;
-import tools.refinery.store.query.view.KeyOnlyView;
-import tools.refinery.store.representation.Symbol;
-
-import java.util.List;
-
-import static org.hamcrest.CoreMatchers.containsString;
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.hamcrest.Matchers.allOf;
-import static org.junit.jupiter.api.Assertions.assertThrows;
-import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
-
-class StructurallyEqualToRawTest {
-        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
-        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
-        private static final AnySymbolView personView = new KeyOnlyView<>(person);
-        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
-        private static final NodeVariable p = Variable.of("p");
-        private static final NodeVariable q = Variable.of("q");
-
-        @Test
-        void flatEqualsTest() {
-                var actual = Dnf.builder("Actual").parameters(p).clause(personView.call(p)).build();
-
-                assertThat(actual, structurallyEqualTo(
-                                List.of(new SymbolicParameter(q, ParameterDirection.OUT)),
-                                List.of(List.of(personView.call(q)))
-                ));
-        }
-
-        @Test
-        void flatNotEqualsTest() {
-                var actual = Dnf.builder("Actual").parameters(p).clause(friendView.call(p, q)).build();
-
-                var assertion = structurallyEqualTo(
-                                List.of(new SymbolicParameter(q, ParameterDirection.OUT)),
-                                List.of(List.of(friendView.call(q, q)))
-                );
-                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-        }
-
-        @Test
-        void deepEqualsTest() {
-                var actual = Dnf.builder("Actual").parameters(q).clause(
-                                Dnf.builder("Actual2").parameters(p).clause(personView.call(p)).build().call(q)
-                ).build();
-
-                assertThat(actual, structurallyEqualTo(
-                                List.of(new SymbolicParameter(q, ParameterDirection.OUT)),
-                                List.of(
-                                                List.of(
-                                                                Dnf.builder("Expected2").parameters(p).clause(personView.call(p)).build().call(q)
-                                                )
-                                )
-                ));
-        }
-
-        @Test
-        void deepNotEqualsTest() {
-                var actual = Dnf.builder("Actual").parameter(q).clause(
-                                Dnf.builder("Actual2").parameters(p).clause(friendView.call(p, q)).build().call(q)
-                ).build();
-
-                var assertion = structurallyEqualTo(
-                                List.of(new SymbolicParameter(q, ParameterDirection.OUT)),
-                                List.of(
-                                                List.of(
-                                                                Dnf.builder("Expected2")
-                                                                                .parameters(p)
-                                                                                .clause(friendView.call(p, p))
-                                                                                .build()
-                                                                                .call(q)
-                                                )
-                                )
-                );
-                var error = assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-                assertThat(error.getMessage(), allOf(containsString("Expected2"), containsString("Actual2")));
-        }
-
-        @Test
-        void parameterListLengthMismatchTest() {
-                var actual = Dnf.builder("Actual").parameters(p, q).clause(
-                                friendView.call(p, q)
-                ).build();
-
-                var assertion = structurallyEqualTo(
-                                List.of(new SymbolicParameter(p, ParameterDirection.OUT)),
-                                List.of(List.of(friendView.call(p, p)))
-                );
-
-                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-        }
-
-        @Test
-        void parameterDirectionMismatchTest() {
-                var actual = Dnf.builder("Actual").parameter(p, ParameterDirection.IN).clause(
-                                personView.call(p)
-                ).build();
-
-                var assertion = structurallyEqualTo(
-                                List.of(new SymbolicParameter(p, ParameterDirection.OUT)),
-                                List.of(List.of(personView.call(p)))
-                );
-
-                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-        }
-
-        @Test
-        void clauseCountMismatchTest() {
-                var actual = Dnf.builder("Actual").parameters(p, q).clause(
-                                friendView.call(p, q)
-                ).build();
-
-                var assertion = structurallyEqualTo(
-                                List.of(
-                                                new SymbolicParameter(p, ParameterDirection.OUT),
-                                                new SymbolicParameter(q, ParameterDirection.OUT)
-                                ),
-                                List.of(
-                                                List.of(friendView.call(p, q)),
-                                                List.of(friendView.call(q, p))
-                                )
-                );
-
-                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-        }
-
-        @Test
-        void literalCountMismatchTest() {
-                var actual = Dnf.builder("Actual").parameters(p, q).clause(
-                                friendView.call(p, q)
-                ).build();
-
-                var assertion = structurallyEqualTo(
-                                List.of(
-                                                new SymbolicParameter(p, ParameterDirection.OUT),
-                                                new SymbolicParameter(q, ParameterDirection.OUT)
-                                ),
-                                List.of(
-                                                List.of(friendView.call(p, q), friendView.call(q, p))
-                                )
-                );
-
-                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-        }
-}
diff --git a/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToTest.java b/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToTest.java
deleted file mode 100644
index f716b805..00000000
--- a/subprojects/store-query/src/test/java/tools/refinery/store/query/tests/StructurallyEqualToTest.java
+++ /dev/null
@@ -1,127 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.tests;
-
-import org.junit.jupiter.api.Test;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.term.NodeVariable;
-import tools.refinery.store.query.term.ParameterDirection;
-import tools.refinery.store.query.term.Variable;
-import tools.refinery.store.query.view.AnySymbolView;
-import tools.refinery.store.query.view.KeyOnlyView;
-import tools.refinery.store.representation.Symbol;
-
-import static org.hamcrest.CoreMatchers.containsString;
-import static org.hamcrest.MatcherAssert.assertThat;
-import static org.junit.jupiter.api.Assertions.assertThrows;
-import static tools.refinery.store.query.tests.QueryMatchers.structurallyEqualTo;
-
-class StructurallyEqualToTest {
-        private static final Symbol<Boolean> person = Symbol.of("Person", 1);
-        private static final Symbol<Boolean> friend = Symbol.of("friend", 2);
-        private static final AnySymbolView personView = new KeyOnlyView<>(person);
-        private static final AnySymbolView friendView = new KeyOnlyView<>(friend);
-        private static final NodeVariable p = Variable.of("p");
-        private static final NodeVariable q = Variable.of("q");
-
-        @Test
-        void flatEqualsTest() {
-                var expected = Dnf.builder("Expected").parameters(q).clause(personView.call(q)).build();
-                var actual = Dnf.builder("Actual").parameters(p).clause(personView.call(p)).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void flatNotEqualsTest() {
-                var expected = Dnf.builder("Expected").parameters(q).clause(friendView.call(q, q)).build();
-                var actual = Dnf.builder("Actual").parameters(p).clause(friendView.call(p, q)).build();
-
-                var assertion = structurallyEqualTo(expected);
-                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-        }
-
-        @Test
-        void deepEqualsTest() {
-                var expected = Dnf.builder("Expected").parameters(q).clause(
-                                Dnf.builder("Expected2").parameters(p).clause(personView.call(p)).build().call(q)
-                ).build();
-                var actual = Dnf.builder("Actual").parameters(q).clause(
-                                Dnf.builder("Actual2").parameters(p).clause(personView.call(p)).build().call(q)
-                ).build();
-
-                assertThat(actual, structurallyEqualTo(expected));
-        }
-
-        @Test
-        void deepNotEqualsTest() {
-                var expected = Dnf.builder("Expected").parameters(q).clause(
-                                Dnf.builder("Expected2").parameters(p).clause(friendView.call(p, p)).build().call(q)
-                ).build();
-                var actual = Dnf.builder("Actual").parameter(q).clause(
-                                Dnf.builder("Actual2").parameters(p).clause(friendView.call(p, q)).build().call(q)
-                ).build();
-
-                var assertion = structurallyEqualTo(expected);
-                var error = assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-                assertThat(error.getMessage(), containsString(" called from Expected/1 "));
-        }
-
-        @Test
-        void parameterListLengthMismatchTest() {
-                var expected = Dnf.builder("Expected").parameter(p).clause(
-                                friendView.call(p, p)
-                ).build();
-                var actual = Dnf.builder("Actual").parameters(p, q).clause(
-                                friendView.call(p, q)
-                ).build();
-
-                var assertion = structurallyEqualTo(expected);
-                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-        }
-
-        @Test
-        void parameterDirectionMismatchTest() {
-                var expected = Dnf.builder("Expected").parameter(p, ParameterDirection.OUT).clause(
-                                personView.call(p)
-                ).build();
-                var actual = Dnf.builder("Actual").parameter(p, ParameterDirection.IN).clause(
-                                personView.call(p)
-                ).build();
-
-                var assertion = structurallyEqualTo(expected);
-                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-        }
-
-        @Test
-        void clauseCountMismatchTest() {
-                var expected = Dnf.builder("Expected")
-                                .parameters(p, q)
-                                .clause(friendView.call(p, q))
-                                .clause(friendView.call(q, p))
-                                .build();
-                var actual = Dnf.builder("Actual").parameters(p, q).clause(
-                                friendView.call(p, q)
-                ).build();
-
-                var assertion = structurallyEqualTo(expected);
-                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-        }
-
-        @Test
-        void literalCountMismatchTest() {
-                var expected = Dnf.builder("Expected").parameters(p, q).clause(
-                                friendView.call(p, q),
-                                friendView.call(q, p)
-                ).build();
-                var actual = Dnf.builder("Actual").parameters(p, q).clause(
-                                friendView.call(p, q)
-                ).build();
-
-                var assertion = structurallyEqualTo(expected);
-                assertThrows(AssertionError.class, () -> assertThat(actual, assertion));
-        }
-}
diff --git a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/MismatchDescribingDnfEqualityChecker.java b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/MismatchDescribingDnfEqualityChecker.java
deleted file mode 100644
index 6a3301b3..00000000
--- a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/MismatchDescribingDnfEqualityChecker.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.tests;
-
-import org.hamcrest.Description;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.SymbolicParameter;
-import tools.refinery.store.query.equality.DeepDnfEqualityChecker;
-import tools.refinery.store.query.literal.Literal;
-
-import java.util.List;
-
-class MismatchDescribingDnfEqualityChecker extends DeepDnfEqualityChecker {
-        private final Description description;
-        private boolean raw;
-        private boolean needsDescription = true;
-
-        MismatchDescribingDnfEqualityChecker(Description description) {
-                this.description = description;
-        }
-
-        public boolean needsDescription() {
-                return needsDescription;
-        }
-
-        @Override
-        public boolean dnfEqualRaw(List<SymbolicParameter> symbolicParameters, List<? extends List<? extends Literal>> clauses, Dnf other) {
-                try {
-                        raw = true;
-                        boolean result = super.dnfEqualRaw(symbolicParameters, clauses, other);
-                        if (!result && needsDescription) {
-                                description.appendText("was ").appendText(other.toDefinitionString());
-                        }
-                        return false;
-                } finally {
-                        raw = false;
-                }
-        }
-
-        @Override
-        protected boolean doCheckEqual(Pair pair) {
-                boolean result = super.doCheckEqual(pair);
-                if (!result && needsDescription) {
-                        describeMismatch(pair);
-                        // Only describe the first found (innermost) mismatch.
-                        needsDescription = false;
-                }
-                return result;
-        }
-
-        private void describeMismatch(Pair pair) {
-                var inProgress = getInProgress();
-                int size = inProgress.size();
-                if (size <= 1 && !raw) {
-                        description.appendText("was ").appendText(pair.right().toDefinitionString());
-                        return;
-                }
-                var last = inProgress.get(size - 1);
-                description.appendText("expected ").appendText(last.left().toDefinitionString());
-                for (int i = size - 2; i >= 0; i--) {
-                        description.appendText(" called from ").appendText(inProgress.get(i).left().toString());
-                }
-                description.appendText(" was not structurally equal to ").appendText(last.right().toDefinitionString());
-        }
-}
diff --git a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/QueryMatchers.java b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/QueryMatchers.java
deleted file mode 100644
index cd449a6a..00000000
--- a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/QueryMatchers.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.tests;
-
-import org.hamcrest.Matcher;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.SymbolicParameter;
-import tools.refinery.store.query.literal.Literal;
-
-import java.util.List;
-
-public final class QueryMatchers {
-        private QueryMatchers() {
-                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
-        }
-
-        /**
-         * Compare two {@link Dnf} instances up to renaming of variables.
-         *
-         * @param expected The expected {@link Dnf} instance.
-         * @return A Hamcrest matcher for equality up to renaming of variables.
-         */
-        public static Matcher<Dnf> structurallyEqualTo(Dnf expected) {
-                return new StructurallyEqualTo(expected);
-        }
-
-        /**
-         * Compare a {@link Dnf} instance to another predicate in DNF form without constructing it.
-         * <p>
-         * This matcher should be used instead of {@link #structurallyEqualTo(Dnf)} when the validation and
-         * pre-processing associated with the {@link Dnf} constructor, i.e., validation of parameter directions,
-         * topological sorting of literals, and the reduction of trivial predicates is not desired. In particular, this
-         * matcher can be used to test for exact order of literal after pre-processing.
-         *
-         * @param expectedSymbolicParameters The expected list of symbolic parameters.
-         * @param expectedLiterals The expected clauses. Each clause is represented by a list of literals.
-         * @return A Hamcrest matcher for equality up to renaming of variables.
-         */
-        public static Matcher<Dnf> structurallyEqualTo(List<SymbolicParameter> expectedSymbolicParameters,
-                                                                                                   List<? extends List<? extends Literal>> expectedLiterals) {
-                return new StructurallyEqualToRaw(expectedSymbolicParameters, expectedLiterals);
-        }
-}
diff --git a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualTo.java b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualTo.java
deleted file mode 100644
index 86149141..00000000
--- a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualTo.java
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.tests;
-
-import org.hamcrest.Description;
-import org.hamcrest.TypeSafeMatcher;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.equality.DeepDnfEqualityChecker;
-
-public class StructurallyEqualTo extends TypeSafeMatcher<Dnf> {
-        private final Dnf expected;
-
-        public StructurallyEqualTo(Dnf expected) {
-                this.expected = expected;
-        }
-
-        @Override
-        protected boolean matchesSafely(Dnf item) {
-                var checker = new DeepDnfEqualityChecker();
-                return checker.dnfEqual(expected, item);
-        }
-
-        @Override
-        protected void describeMismatchSafely(Dnf item, Description mismatchDescription) {
-                var describingChecker = new MismatchDescribingDnfEqualityChecker(mismatchDescription);
-                if (describingChecker.dnfEqual(expected, item)) {
-                        throw new IllegalStateException("Mismatched Dnf was matching on repeated comparison");
-                }
-                if (describingChecker.needsDescription()) {
-                        super.describeMismatchSafely(item, mismatchDescription);
-                }
-        }
-
-        @Override
-        public void describeTo(Description description) {
-                description.appendText("structurally equal to ").appendText(expected.toDefinitionString());
-        }
-}
diff --git a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualToRaw.java b/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualToRaw.java
deleted file mode 100644
index 2f8c2944..00000000
--- a/subprojects/store-query/src/testFixtures/java/tools/refinery/store/query/tests/StructurallyEqualToRaw.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.query.tests;
-
-import org.hamcrest.Description;
-import org.hamcrest.TypeSafeMatcher;
-import tools.refinery.store.query.dnf.Dnf;
-import tools.refinery.store.query.dnf.SymbolicParameter;
-import tools.refinery.store.query.equality.DeepDnfEqualityChecker;
-import tools.refinery.store.query.literal.Literal;
-
-import java.util.List;
-
-public class StructurallyEqualToRaw extends TypeSafeMatcher<Dnf> {
-        private final List<SymbolicParameter> expectedSymbolicParameters;
-        private final List<? extends List<? extends Literal>> expectedClauses;
-
-        public StructurallyEqualToRaw(List<SymbolicParameter> expectedSymbolicParameters,
-                                                                  List<? extends List<? extends Literal>> expectedClauses) {
-                this.expectedSymbolicParameters = expectedSymbolicParameters;
-                this.expectedClauses = expectedClauses;
-        }
-
-        @Override
-        protected boolean matchesSafely(Dnf item) {
-                var checker = new DeepDnfEqualityChecker();
-                return checker.dnfEqualRaw(expectedSymbolicParameters, expectedClauses, item);
-        }
-
-        @Override
-        protected void describeMismatchSafely(Dnf item, Description mismatchDescription) {
-                var describingChecker = new MismatchDescribingDnfEqualityChecker(mismatchDescription);
-                if (describingChecker.dnfEqualRaw(expectedSymbolicParameters, expectedClauses, item)) {
-                        throw new IllegalStateException("Mismatched Dnf was matching on repeated comparison");
-                }
-                if (describingChecker.needsDescription()) {
-                        super.describeMismatchSafely(item, mismatchDescription);
-                }
-        }
-
-        @Override
-        public void describeTo(Description description) {
-                description.appendText("structurally equal to ")
-                                .appendValueList("(", ", ", ")", expectedSymbolicParameters)
-                                .appendText(" <-> ")
-                                .appendValueList("", ", ", ".", expectedClauses);
-        }
-}