refactor: move terms and DNF into logic subproject

14 files changed, 0 insertions, 795 deletions

diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/AbstractDomain.java b/subprojects/store/src/main/java/tools/refinery/store/representation/AbstractDomain.java
deleted file mode 100644
index dfdb43bd..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/AbstractDomain.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.representation;
-
-import java.util.Objects;
-import java.util.Optional;
-
-public non-sealed interface AbstractDomain<A, C> extends AnyAbstractDomain {
-        @Override
-        Class<A> abstractType();
-
-        @Override
-        Class<C> concreteType();
-
-        A toAbstract(C concreteValue);
-
-        Optional<C> toConcrete(A abstractValue);
-
-        default boolean isConcrete(A abstractValue) {
-                return toConcrete(abstractValue).isPresent();
-        }
-
-        default boolean isRefinement(A originalValue, A refinedValue) {
-                return Objects.equals(commonRefinement(originalValue, refinedValue), refinedValue);
-        }
-
-        A commonRefinement(A leftValue, A rightValue);
-
-        A commonAncestor(A leftValue, A rightValue);
-
-        A unknown();
-
-        boolean isError(A abstractValue);
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/AnyAbstractDomain.java b/subprojects/store/src/main/java/tools/refinery/store/representation/AnyAbstractDomain.java
deleted file mode 100644
index c354fab7..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/AnyAbstractDomain.java
+++ /dev/null
@@ -1,12 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.representation;
-
-public sealed interface AnyAbstractDomain permits AbstractDomain {
-        Class<?> abstractType();
-
-        Class<?> concreteType();
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValue.java b/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValue.java
deleted file mode 100644
index f81ee9a4..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValue.java
+++ /dev/null
@@ -1,76 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.representation;
-
-public enum TruthValue {
-        TRUE("true"),
-
-        FALSE("false"),
-
-        UNKNOWN("unknown"),
-
-        ERROR("error");
-
-        private final String name;
-
-        TruthValue(String name) {
-                this.name = name;
-        }
-
-        public String getName() {
-                return name;
-        }
-
-        public static TruthValue toTruthValue(boolean value) {
-                return value ? TRUE : FALSE;
-        }
-
-        public boolean isConsistent() {
-                return this != ERROR;
-        }
-
-        public boolean isComplete() {
-                return this != UNKNOWN;
-        }
-
-        public boolean isConcrete() {
-                return this == TRUE || this == FALSE;
-        }
-
-        public boolean must() {
-                return this == TRUE || this == ERROR;
-        }
-
-        public boolean may() {
-                return this == TRUE || this == UNKNOWN;
-        }
-
-        public TruthValue not() {
-                return switch (this) {
-                        case TRUE -> FALSE;
-                        case FALSE -> TRUE;
-                        default -> this;
-                };
-        }
-
-        public TruthValue merge(TruthValue other) {
-                return switch (this) {
-                        case TRUE -> other == UNKNOWN || other == TRUE ? TRUE : ERROR;
-                        case FALSE -> other == UNKNOWN || other == FALSE ? FALSE : ERROR;
-                        case UNKNOWN -> other;
-                        case ERROR -> ERROR;
-                };
-        }
-
-        public TruthValue join(TruthValue other) {
-                return switch (this) {
-                        case TRUE -> other == ERROR || other == TRUE ? TRUE : UNKNOWN;
-                        case FALSE -> other == ERROR || other == FALSE ? FALSE : UNKNOWN;
-                        case UNKNOWN -> UNKNOWN;
-                        case ERROR -> other;
-                };
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValueDomain.java b/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValueDomain.java
deleted file mode 100644
index 61696dca..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/TruthValueDomain.java
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.representation;
-
-import java.util.Optional;
-
-// Singleton pattern, because there is only one domain for truth values.
-@SuppressWarnings("squid:S6548")
-public final class TruthValueDomain implements AbstractDomain<TruthValue, Boolean> {
-        public static final TruthValueDomain INSTANCE = new TruthValueDomain();
-
-        private TruthValueDomain() {
-        }
-
-        @Override
-        public Class<TruthValue> abstractType() {
-                return TruthValue.class;
-        }
-
-        @Override
-        public Class<Boolean> concreteType() {
-                return Boolean.class;
-        }
-
-        @Override
-        public TruthValue toAbstract(Boolean concreteValue) {
-                return TruthValue.toTruthValue(concreteValue);
-        }
-
-        @Override
-        public Optional<Boolean> toConcrete(TruthValue abstractValue) {
-                return switch (abstractValue) {
-                        case TRUE -> Optional.of(true);
-                        case FALSE -> Optional.of(false);
-                        default -> Optional.empty();
-                };
-        }
-
-        @Override
-        public boolean isConcrete(TruthValue abstractValue) {
-                return abstractValue.isConcrete();
-        }
-
-        @Override
-        public TruthValue commonRefinement(TruthValue leftValue, TruthValue rightValue) {
-                return leftValue.merge(rightValue);
-        }
-
-        @Override
-        public TruthValue commonAncestor(TruthValue leftValue, TruthValue rightValue) {
-                return leftValue.join(rightValue);
-        }
-
-        @Override
-        public TruthValue unknown() {
-                return TruthValue.UNKNOWN;
-        }
-
-        @Override
-        public boolean isError(TruthValue abstractValue) {
-                return !abstractValue.isConsistent();
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityDomain.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityDomain.java
deleted file mode 100644
index 7ae2d935..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityDomain.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.representation.cardinality;
-
-import tools.refinery.store.representation.AbstractDomain;
-
-import java.util.Optional;
-
-// Singleton pattern, because there is only one domain for truth values.
-@SuppressWarnings("squid:S6548")
-public class CardinalityDomain implements AbstractDomain<CardinalityInterval, Integer> {
-        public static final CardinalityDomain INSTANCE = new CardinalityDomain();
-
-        private CardinalityDomain() {
-        }
-
-        @Override
-        public Class<CardinalityInterval> abstractType() {
-                return CardinalityInterval.class;
-        }
-
-        @Override
-        public Class<Integer> concreteType() {
-                return Integer.class;
-        }
-
-        @Override
-        public CardinalityInterval toAbstract(Integer concreteValue) {
-                return CardinalityIntervals.exactly(concreteValue);
-        }
-
-        @Override
-        public Optional<Integer> toConcrete(CardinalityInterval abstractValue) {
-                return isConcrete(abstractValue) ? Optional.of(abstractValue.lowerBound()) : Optional.empty();
-        }
-
-        @Override
-        public boolean isConcrete(CardinalityInterval abstractValue) {
-                if (!(abstractValue instanceof NonEmptyCardinalityInterval nonEmptyValue) ||
-                                !((nonEmptyValue.upperBound()) instanceof FiniteUpperCardinality finiteUpperCardinality)) {
-                        return false;
-                }
-                return nonEmptyValue.lowerBound() == finiteUpperCardinality.finiteUpperBound();
-        }
-
-        @Override
-        public CardinalityInterval commonRefinement(CardinalityInterval leftValue, CardinalityInterval rightValue) {
-                return leftValue.meet(rightValue);
-        }
-
-        @Override
-        public CardinalityInterval commonAncestor(CardinalityInterval leftValue, CardinalityInterval rightValue) {
-                return leftValue.join(rightValue);
-        }
-
-        @Override
-        public CardinalityInterval unknown() {
-                return CardinalityIntervals.SET;
-        }
-
-        @Override
-        public boolean isError(CardinalityInterval abstractValue) {
-                return abstractValue.isEmpty();
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityInterval.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityInterval.java
deleted file mode 100644
index b20c685a..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityInterval.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.representation.cardinality;
-
-public sealed interface CardinalityInterval permits NonEmptyCardinalityInterval, EmptyCardinalityInterval {
-        int lowerBound();
-
-        UpperCardinality upperBound();
-
-        boolean isEmpty();
-
-        CardinalityInterval min(CardinalityInterval other);
-
-        CardinalityInterval max(CardinalityInterval other);
-
-        CardinalityInterval add(CardinalityInterval other);
-
-        CardinalityInterval take(int count);
-
-        CardinalityInterval multiply(CardinalityInterval other);
-
-        CardinalityInterval meet(CardinalityInterval other);
-
-        CardinalityInterval join(CardinalityInterval other);
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityIntervals.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityIntervals.java
deleted file mode 100644
index 855fd248..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/CardinalityIntervals.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.representation.cardinality;
-
-public final class CardinalityIntervals {
-        public static final CardinalityInterval NONE = exactly(0);
-
-        public static final CardinalityInterval ONE = exactly(1);
-
-        public static final CardinalityInterval LONE = atMost(1);
-
-        public static final CardinalityInterval SET = atLeast(0);
-
-        public static final CardinalityInterval SOME = atLeast(1);
-
-        public static final CardinalityInterval ERROR = EmptyCardinalityInterval.INSTANCE;
-
-        private CardinalityIntervals() {
-                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
-        }
-
-        public static CardinalityInterval between(int lowerBound, UpperCardinality upperBound) {
-                if (upperBound.compareToInt(lowerBound) < 0) {
-                        return ERROR;
-                }
-                return new NonEmptyCardinalityInterval(lowerBound, upperBound);
-        }
-
-        public static CardinalityInterval between(int lowerBound, int upperBound) {
-                return between(lowerBound, UpperCardinalities.atMost(upperBound));
-        }
-
-        public static CardinalityInterval atMost(UpperCardinality upperBound) {
-                return new NonEmptyCardinalityInterval(0, upperBound);
-        }
-
-        public static CardinalityInterval atMost(int upperBound) {
-                return atMost(UpperCardinalities.atMost(upperBound));
-        }
-
-        public static CardinalityInterval atLeast(int lowerBound) {
-                return new NonEmptyCardinalityInterval(lowerBound, UpperCardinalities.UNBOUNDED);
-        }
-
-        public static CardinalityInterval exactly(int lowerBound) {
-                return new NonEmptyCardinalityInterval(lowerBound, UpperCardinalities.atMost(lowerBound));
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/EmptyCardinalityInterval.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/EmptyCardinalityInterval.java
deleted file mode 100644
index 9e371e21..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/EmptyCardinalityInterval.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.representation.cardinality;
-
-// Singleton implementation, because there is only a single empty interval.
-@SuppressWarnings("squid:S6548")
-public final class EmptyCardinalityInterval implements CardinalityInterval {
-        static final EmptyCardinalityInterval INSTANCE = new EmptyCardinalityInterval();
-
-        private EmptyCardinalityInterval() {
-                // Singleton constructor.
-        }
-
-        @Override
-        public int lowerBound() {
-                return 1;
-        }
-
-        @Override
-        public boolean isEmpty() {
-                return true;
-        }
-
-        @Override
-        public UpperCardinality upperBound() {
-                return UpperCardinalities.ZERO;
-        }
-
-        @Override
-        public CardinalityInterval min(CardinalityInterval other) {
-                return this;
-        }
-
-        @Override
-        public CardinalityInterval max(CardinalityInterval other) {
-                return this;
-        }
-
-        @Override
-        public CardinalityInterval add(CardinalityInterval other) {
-                return this;
-        }
-
-        @Override
-        public CardinalityInterval take(int count) {
-                return this;
-        }
-
-        @Override
-        public CardinalityInterval multiply(CardinalityInterval other) {
-                return this;
-        }
-
-        @Override
-        public CardinalityInterval meet(CardinalityInterval other) {
-                return this;
-        }
-
-        @Override
-        public CardinalityInterval join(CardinalityInterval other) {
-                return other;
-        }
-
-        @Override
-        public String toString() {
-                return "error";
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinality.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinality.java
deleted file mode 100644
index b63a8637..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/FiniteUpperCardinality.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.representation.cardinality;
-
-import org.jetbrains.annotations.NotNull;
-import org.jetbrains.annotations.Nullable;
-
-import java.util.function.IntBinaryOperator;
-
-public record FiniteUpperCardinality(int finiteUpperBound) implements UpperCardinality {
-        public FiniteUpperCardinality {
-                if (finiteUpperBound < 0) {
-                        throw new IllegalArgumentException("finiteUpperBound must not be negative");
-                }
-        }
-
-        @Override
-        public UpperCardinality add(UpperCardinality other) {
-                return lift(other, Integer::sum);
-        }
-
-        @Override
-        @Nullable
-        public UpperCardinality take(int count) {
-                if (finiteUpperBound < count) {
-                        return null;
-                }
-                return new FiniteUpperCardinality(finiteUpperBound - count);
-        }
-
-        @Override
-        public UpperCardinality multiply(UpperCardinality other) {
-                return lift(other, (a, b) -> a * b);
-        }
-
-        @Override
-        public int compareTo(@NotNull UpperCardinality upperCardinality) {
-                if (upperCardinality instanceof FiniteUpperCardinality finiteUpperCardinality) {
-                        return compareToInt(finiteUpperCardinality.finiteUpperBound);
-                }
-                if (upperCardinality instanceof UnboundedUpperCardinality) {
-                        return -1;
-                }
-                throw new IllegalArgumentException("Unknown UpperCardinality: " + upperCardinality);
-        }
-
-        @Override
-        public int compareToInt(int value) {
-                return Integer.compare(finiteUpperBound, value);
-        }
-
-        @Override
-        public String toString() {
-                return Integer.toString(finiteUpperBound);
-        }
-
-        private UpperCardinality lift(@NotNull UpperCardinality other, IntBinaryOperator operator) {
-                if (other instanceof FiniteUpperCardinality finiteUpperCardinality) {
-                        return UpperCardinalities.atMost(operator.applyAsInt(finiteUpperBound,
-                                        finiteUpperCardinality.finiteUpperBound));
-                }
-                if (other instanceof UnboundedUpperCardinality) {
-                        return UpperCardinalities.UNBOUNDED;
-                }
-                throw new IllegalArgumentException("Unknown UpperCardinality: " + other);
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                FiniteUpperCardinality that = (FiniteUpperCardinality) o;
-                return finiteUpperBound == that.finiteUpperBound;
-        }
-
-        @Override
-        public int hashCode() {
-                return finiteUpperBound;
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/NonEmptyCardinalityInterval.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/NonEmptyCardinalityInterval.java
deleted file mode 100644
index 6bd66df7..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/NonEmptyCardinalityInterval.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.representation.cardinality;
-
-import java.util.Objects;
-import java.util.function.BinaryOperator;
-import java.util.function.IntBinaryOperator;
-
-public record NonEmptyCardinalityInterval(int lowerBound, UpperCardinality upperBound) implements CardinalityInterval {
-        public NonEmptyCardinalityInterval {
-                if (lowerBound < 0) {
-                        throw new IllegalArgumentException("lowerBound must not be negative");
-                }
-                if (upperBound.compareToInt(lowerBound) < 0) {
-                        throw new IllegalArgumentException("lowerBound must not be larger than upperBound");
-                }
-        }
-
-        @Override
-        public boolean isEmpty() {
-                return false;
-        }
-
-        @Override
-        public CardinalityInterval min(CardinalityInterval other) {
-                return lift(other, Math::min, UpperCardinality::min);
-        }
-
-        @Override
-        public CardinalityInterval max(CardinalityInterval other) {
-                return lift(other, Math::max, UpperCardinality::max);
-        }
-
-        @Override
-        public CardinalityInterval add(CardinalityInterval other) {
-                return lift(other, Integer::sum, UpperCardinality::add);
-        }
-
-        @Override
-        public CardinalityInterval multiply(CardinalityInterval other) {
-                return lift(other, (a, b) -> a * b, UpperCardinality::multiply);
-        }
-
-        @Override
-        public CardinalityInterval meet(CardinalityInterval other) {
-                return lift(other, Math::max, UpperCardinality::min);
-        }
-
-        @Override
-        public CardinalityInterval join(CardinalityInterval other) {
-                return lift(other, Math::min, UpperCardinality::max, this);
-        }
-
-        @Override
-        public CardinalityInterval take(int count) {
-                int newLowerBound = Math.max(lowerBound - count, 0);
-                var newUpperBound = upperBound.take(count);
-                if (newUpperBound == null) {
-                        return CardinalityIntervals.ERROR;
-                }
-                return CardinalityIntervals.between(newLowerBound, newUpperBound);
-        }
-
-        private CardinalityInterval lift(CardinalityInterval other, IntBinaryOperator lowerOperator,
-                                                                         BinaryOperator<UpperCardinality> upperOperator,
-                                                                         CardinalityInterval whenEmpty) {
-                if (other instanceof NonEmptyCardinalityInterval nonEmptyOther) {
-                        return CardinalityIntervals.between(lowerOperator.applyAsInt(lowerBound, nonEmptyOther.lowerBound),
-                                        upperOperator.apply(upperBound, nonEmptyOther.upperBound));
-                }
-                if (other instanceof EmptyCardinalityInterval) {
-                        return whenEmpty;
-                }
-                throw new IllegalArgumentException("Unknown CardinalityInterval: " + other);
-        }
-
-        private CardinalityInterval lift(CardinalityInterval other, IntBinaryOperator lowerOperator,
-                                                                         BinaryOperator<UpperCardinality> upperOperator) {
-                return lift(other, lowerOperator, upperOperator, CardinalityIntervals.ERROR);
-        }
-
-        @Override
-        public String toString() {
-                if (upperBound instanceof FiniteUpperCardinality finiteUpperCardinality &&
-                                finiteUpperCardinality.finiteUpperBound() == lowerBound) {
-                        return "[%d]".formatted(lowerBound);
-                }
-                return "[%d..%s]".formatted(lowerBound, upperBound);
-        }
-
-        @Override
-        public boolean equals(Object o) {
-                if (this == o) return true;
-                if (o == null || getClass() != o.getClass()) return false;
-                NonEmptyCardinalityInterval that = (NonEmptyCardinalityInterval) o;
-                return lowerBound == that.lowerBound && Objects.equals(upperBound, that.upperBound);
-        }
-
-        @Override
-        public int hashCode() {
-                return lowerBound * 31 + upperBound.hashCode();
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UnboundedUpperCardinality.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UnboundedUpperCardinality.java
deleted file mode 100644
index 03c701ae..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UnboundedUpperCardinality.java
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.representation.cardinality;
-
-import org.jetbrains.annotations.NotNull;
-
-// Singleton implementation, because there is only a single countable infinity.
-@SuppressWarnings("squid:S6548")
-public final class UnboundedUpperCardinality implements UpperCardinality {
-        static final UnboundedUpperCardinality INSTANCE = new UnboundedUpperCardinality();
-
-        private UnboundedUpperCardinality() {
-                // Singleton constructor.
-        }
-
-        @Override
-        public UpperCardinality add(UpperCardinality other) {
-                return this;
-        }
-
-        @Override
-        public UpperCardinality take(int count) {
-                return this;
-        }
-
-        @Override
-        public UpperCardinality multiply(UpperCardinality other) {
-                return this;
-        }
-
-        // This should always be greater than any finite cardinality.
-        @SuppressWarnings("ComparatorMethodParameterNotUsed")
-        @Override
-        public int compareTo(@NotNull UpperCardinality upperCardinality) {
-                if (upperCardinality instanceof FiniteUpperCardinality) {
-                        return 1;
-                }
-                if (upperCardinality instanceof UnboundedUpperCardinality) {
-                        return 0;
-                }
-                throw new IllegalArgumentException("Unknown UpperCardinality: " + upperCardinality);
-        }
-
-        @Override
-        public int compareToInt(int value) {
-                return 1;
-        }
-
-        @Override
-        public String toString() {
-                return "*";
-        }
-
-        @Override
-        public boolean equals(Object obj) {
-                return this == obj || (obj != null && getClass() == obj.getClass());
-        }
-
-        @Override
-        public int hashCode() {
-                return -1;
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinalities.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinalities.java
deleted file mode 100644
index 17d1b292..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinalities.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.representation.cardinality;
-
-public final class UpperCardinalities {
-        public static final UpperCardinality UNBOUNDED = UnboundedUpperCardinality.INSTANCE;
-
-        public static final UpperCardinality ZERO;
-
-        public static final UpperCardinality ONE;
-
-        private static final FiniteUpperCardinality[] cache = new FiniteUpperCardinality[256];
-
-        static {
-                for (int i = 0; i < cache.length; i++) {
-                        cache[i] = new FiniteUpperCardinality(i);
-                }
-                ZERO = cache[0];
-                ONE = cache[1];
-        }
-
-        private UpperCardinalities() {
-                throw new IllegalStateException("This is a static utility class and should not be instantiated directly");
-        }
-
-        public static UpperCardinality atMost(int upperBound) {
-                if (upperBound < 0) {
-                        return UNBOUNDED;
-                }
-                if (upperBound < cache.length) {
-                        return cache[upperBound];
-                }
-                return new FiniteUpperCardinality(upperBound);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinality.java b/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinality.java
deleted file mode 100644
index 3f0db028..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/representation/cardinality/UpperCardinality.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.representation.cardinality;
-
-import org.jetbrains.annotations.Nullable;
-
-public sealed interface UpperCardinality extends Comparable<UpperCardinality> permits FiniteUpperCardinality,
-                UnboundedUpperCardinality {
-        default UpperCardinality min(UpperCardinality other) {
-                return this.compareTo(other) <= 0 ? this : other;
-        }
-
-        default UpperCardinality max(UpperCardinality other) {
-                return this.compareTo(other) >= 0 ? this : other;
-        }
-
-        UpperCardinality add(UpperCardinality other);
-
-        @Nullable
-        UpperCardinality take(int count);
-
-        UpperCardinality multiply(UpperCardinality other);
-
-        int compareToInt(int value);
-
-        static UpperCardinality of(int upperBound) {
-                return UpperCardinalities.atMost(upperBound);
-        }
-}
diff --git a/subprojects/store/src/main/java/tools/refinery/store/util/CycleDetectingMapper.java b/subprojects/store/src/main/java/tools/refinery/store/util/CycleDetectingMapper.java
deleted file mode 100644
index 2e302663..00000000
--- a/subprojects/store/src/main/java/tools/refinery/store/util/CycleDetectingMapper.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * SPDX-FileCopyrightText: 2021-2023 The Refinery Authors <https://refinery.tools/>
- *
- * SPDX-License-Identifier: EPL-2.0
- */
-package tools.refinery.store.util;
-
-import java.util.*;
-import java.util.function.Function;
-import java.util.stream.Collectors;
-
-public class CycleDetectingMapper<T, R> {
-        private static final String SEPARATOR = " -> ";
-
-        private final Function<T, String> getName;
-
-        private final Function<T, R> doMap;
-
-        private final Set<T> inProgress = new LinkedHashSet<>();
-
-        private final Map<T, R> results = new HashMap<>();
-
-        public CycleDetectingMapper(Function<T, R> doMap) {
-                this(Objects::toString, doMap);
-        }
-
-        public CycleDetectingMapper(Function<T, String> getName, Function<T, R> doMap) {
-                this.getName = getName;
-                this.doMap = doMap;
-        }
-
-        public R map(T input) {
-                if (inProgress.contains(input)) {
-                        var path = inProgress.stream().map(getName).collect(Collectors.joining(SEPARATOR));
-                        throw new IllegalArgumentException("Circular reference %s%s%s detected".formatted(path, SEPARATOR,
-                                        getName.apply(input)));
-                }
-                // We can't use computeIfAbsent here, because translating referenced queries calls this method in a reentrant
-                // way, which would cause a ConcurrentModificationException with computeIfAbsent.
-                @SuppressWarnings("squid:S3824")
-                var result = results.get(input);
-                if (result == null) {
-                        inProgress.add(input);
-                        try {
-                                result = doMap.apply(input);
-                                results.put(input, result);
-                        } finally {
-                                inProgress.remove(input);
-                        }
-                }
-                return result;
-        }
-
-        public List<T> getInProgress() {
-                return List.copyOf(inProgress);
-        }
-
-        public R getAlreadyMapped(T input) {
-                return results.get(input);
-        }
-}