12 files changed, 74 insertions, 56 deletions

diff --git a/subprojects/language/src/main/java/tools/refinery/language/GenerateProblem.mwe2 b/subprojects/language/src/main/java/tools/refinery/language/GenerateProblem.mwe2
index 59eba8f7..863e55d4 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/GenerateProblem.mwe2
+++ b/subprojects/language/src/main/java/tools/refinery/language/GenerateProblem.mwe2
@@ -51,7 +51,7 @@ Workflow {
 
                 language = StandardLanguage {
                         name = 'tools.refinery.language.Problem'
-                        fileExtensions = 'problem'
+                        fileExtensions = 'refinery,problem'
                         referencedResource = 'platform:/resource/tools.refinery.refinery-language-model/model/problem.genmodel'
                         serializer = {
                                 generateStub = false
diff --git a/subprojects/language/src/main/java/tools/refinery/language/Problem.xtext b/subprojects/language/src/main/java/tools/refinery/language/Problem.xtext
index 0fb96954..c5c42ebe 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/Problem.xtext
+++ b/subprojects/language/src/main/java/tools/refinery/language/Problem.xtext
@@ -9,13 +9,16 @@ import "http://www.eclipse.org/emf/2002/Ecore" as ecore
 import "https://refinery.tools/emf/2021/Problem"
 
 Problem:
-        ("problem" name=Identifier ".")?
+        (kind=ModuleKind name=QualifiedName? ".")?
         statements+=Statement*;
 
+enum ModuleKind:
+        PROBLEM="problem" | MODULE="module";
+
 Statement:
         Assertion | ClassDeclaration | EnumDeclaration |
         PredicateDefinition | /* FunctionDefinition | RuleDefinition | */
-        ScopeDeclaration | IndividualDeclaration;
+        ScopeDeclaration | NodeDeclaration;
 
 ClassDeclaration:
         abstract?="abstract"? "class"
@@ -252,8 +255,11 @@ RangeMultiplicity:
 ExactMultiplicity:
         exactValue=INT;
 
-IndividualDeclaration:
-        "indiv" nodes+=EnumLiteral ("," nodes+=EnumLiteral)* ".";
+NodeDeclaration:
+        kind=NodeKind nodes+=EnumLiteral ("," nodes+=EnumLiteral)* ".";
+
+enum NodeKind:
+        NODE="node" | ATOM="atom" | MULTI="multi";
 
 UpperBound returns ecore::EInt:
         INT | "*";
@@ -268,7 +274,8 @@ Identifier:
         NonContainmentIdentifier | "contains" | "container";
 
 NonContainmentIdentifier:
-        ID | "contained" | "sum" | "prod" | "min" | "max";
+        ID | "node" | "atom" | "multi" | "contained" |
+        "sum" | "prod" | "min" | "max" | "problem" | "module";
 
 Real returns ecore::EDouble:
         EXPONENTIAL | INT "." (INT | EXPONENTIAL);
diff --git a/subprojects/language/src/main/java/tools/refinery/language/formatting2/ProblemFormatter.java b/subprojects/language/src/main/java/tools/refinery/language/formatting2/ProblemFormatter.java
index 0f3bd3ee..0b87e8bb 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/formatting2/ProblemFormatter.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/formatting2/ProblemFormatter.java
@@ -23,7 +23,7 @@ public class ProblemFormatter extends AbstractJavaFormatter {
         protected void format(Problem problem, IFormattableDocument doc) {
                 doc.prepend(problem, this::noSpace);
                 var region = regionFor(problem);
-                doc.append(region.keyword("problem"), this::oneSpace);
+                doc.append(region.feature(ProblemPackage.Literals.PROBLEM__KIND), this::oneSpace);
                 doc.prepend(region.keyword("."), this::noSpace);
                 appendNewLines(doc, region.keyword("."), this::twoNewLines);
                 for (var statement : problem.getStatements()) {
@@ -132,10 +132,10 @@ public class ProblemFormatter extends AbstractJavaFormatter {
                 }
         }
 
-        protected void format(IndividualDeclaration individualDeclaration, IFormattableDocument doc) {
-                surroundNewLines(doc, individualDeclaration, this::singleNewLine);
-                var region = regionFor(individualDeclaration);
-                doc.append(region.keyword("indiv"), this::oneSpace);
+        protected void format(NodeDeclaration nodeDeclaration, IFormattableDocument doc) {
+                surroundNewLines(doc, nodeDeclaration, this::singleNewLine);
+                var region = regionFor(nodeDeclaration);
+                doc.append(region.feature(ProblemPackage.Literals.NODE_DECLARATION__KIND), this::oneSpace);
                 formatList(region, ",", doc);
                 doc.prepend(region.keyword("."), this::noSpace);
         }
diff --git a/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemLocationInFileProvider.java b/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemLocationInFileProvider.java
index 29eaad84..c81431e5 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemLocationInFileProvider.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemLocationInFileProvider.java
@@ -25,10 +25,10 @@ public class ProblemLocationInFileProvider extends DefaultLocationInFileProvider
         }
 
         protected ITextRegion getNodeTextRegion(Node node, RegionDescription query) {
-                if (ProblemUtil.isIndividualNode(node)) {
+                if (ProblemUtil.isDeclaredNode(node)) {
                         return super.doGetTextRegion(node, query);
                 }
-                if (ProblemUtil.isNewNode(node)) {
+                if (ProblemUtil.isMultiNode(node)) {
                         EObject container = node.eContainer();
                         return doGetTextRegion(container, query);
                 }
diff --git a/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemResourceDescriptionStrategy.java b/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemResourceDescriptionStrategy.java
index c04c7d09..79dad6e7 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemResourceDescriptionStrategy.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/resource/ProblemResourceDescriptionStrategy.java
@@ -91,8 +91,7 @@ public class ProblemResourceDescriptionStrategy extends DefaultResourceDescripti
                         return false;
                 }
                 if (eObject instanceof Node node) {
-                        // Only enum literals and new nodes are visible across problem files.
-                        return ProblemUtil.isIndividualNode(node) || ProblemUtil.isNewNode(node);
+                        return !ProblemUtil.isImplicitNode(node);
                 }
                 return true;
         }
@@ -111,7 +110,7 @@ public class ProblemResourceDescriptionStrategy extends DefaultResourceDescripti
 
         protected boolean shouldExportSimpleName(EObject eObject) {
                 if (eObject instanceof Node node) {
-                        return !ProblemUtil.isNewNode(node);
+                        return !ProblemUtil.isMultiNode(node);
                 }
                 if (eObject instanceof PredicateDefinition predicateDefinition) {
                         return !ProblemUtil.isInvalidMultiplicityConstraint(predicateDefinition);
@@ -146,6 +145,5 @@ public class ProblemResourceDescriptionStrategy extends DefaultResourceDescripti
                         return false;
                 }
                 return eObject instanceof ClassDeclaration || eObject instanceof EnumDeclaration;
-
         }
 }
diff --git a/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemUtil.java b/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemUtil.java
index 7b6407e1..ee0e141d 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemUtil.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/utils/ProblemUtil.java
@@ -54,14 +54,24 @@ public final class ProblemUtil {
                 return eObject instanceof PredicateDefinition predicateDefinition && predicateDefinition.isError();
         }
 
-        public static boolean isIndividualNode(Node node) {
+        public static boolean isAtomNode(Node node) {
                 var containingFeature = node.eContainingFeature();
-                return containingFeature == ProblemPackage.Literals.INDIVIDUAL_DECLARATION__NODES
-                                || containingFeature == ProblemPackage.Literals.ENUM_DECLARATION__LITERALS;
+                if (containingFeature == ProblemPackage.Literals.NODE_DECLARATION__NODES) {
+                        return ((NodeDeclaration) node.eContainer()).getKind() == NodeKind.ATOM;
+                }
+                return containingFeature == ProblemPackage.Literals.ENUM_DECLARATION__LITERALS;
+        }
+
+        public static boolean isMultiNode(Node node) {
+                var containingFeature = node.eContainingFeature();
+                if (containingFeature == ProblemPackage.Literals.NODE_DECLARATION__NODES) {
+                        return ((NodeDeclaration) node.eContainer()).getKind() == NodeKind.MULTI;
+                }
+                return containingFeature == ProblemPackage.Literals.CLASS_DECLARATION__NEW_NODE;
         }
 
-        public static boolean isNewNode(Node node) {
-                return node.eContainingFeature() == ProblemPackage.Literals.CLASS_DECLARATION__NEW_NODE;
+        public static boolean isDeclaredNode(Node node) {
+                return node.eContainingFeature() == ProblemPackage.Literals.NODE_DECLARATION__NODES;
         }
 
         public static boolean isInvalidMultiplicityConstraint(PredicateDefinition predicateDefinition) {
diff --git a/subprojects/language/src/main/java/tools/refinery/language/validation/ProblemValidator.java b/subprojects/language/src/main/java/tools/refinery/language/validation/ProblemValidator.java
index 8bda4b95..a95e8b3c 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/validation/ProblemValidator.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/validation/ProblemValidator.java
@@ -84,7 +84,7 @@ public class ProblemValidator extends AbstractProblemValidator {
         @Check
         public void checkNodeConstants(VariableOrNodeExpr expr) {
                 var variableOrNode = expr.getVariableOrNode();
-                if (variableOrNode instanceof Node node && !ProblemUtil.isIndividualNode(node)) {
+                if (variableOrNode instanceof Node node && !ProblemUtil.isAtomNode(node)) {
                         var name = node.getName();
                         var message = ("Only individuals can be referenced in predicates. " +
                                         "Mark '%s' as individual with the declaration 'indiv %s.'").formatted(name, name);
@@ -96,16 +96,16 @@ public class ProblemValidator extends AbstractProblemValidator {
         @Check
         public void checkUniqueDeclarations(Problem problem) {
                 var relations = new ArrayList<Relation>();
-                var individuals = new ArrayList<Node>();
+                var nodes = new ArrayList<Node>();
                 for (var statement : problem.getStatements()) {
                         if (statement instanceof Relation relation) {
                                 relations.add(relation);
-                        } else if (statement instanceof IndividualDeclaration individualDeclaration) {
-                                individuals.addAll(individualDeclaration.getNodes());
+                        } else if (statement instanceof NodeDeclaration nodeDeclaration) {
+                                nodes.addAll(nodeDeclaration.getNodes());
                         }
                 }
                 checkUniqueSimpleNames(relations);
-                checkUniqueSimpleNames(individuals);
+                checkUniqueSimpleNames(nodes);
         }
 
         @Check
@@ -362,7 +362,7 @@ public class ProblemValidator extends AbstractProblemValidator {
                         return;
                 }
                 var node = getNodeArgumentForMultiObjectAssertion(arguments.get(0));
-                if (node != null && !node.eIsProxy() && ProblemUtil.isIndividualNode(node)) {
+                if (node != null && !node.eIsProxy() && ProblemUtil.isAtomNode(node)) {
                         acceptError("Individual nodes must exist.", assertion, null, 0, UNSUPPORTED_ASSERTION_ISSUE);
                 }
         }
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java
index 72d57f54..17ae5fbb 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/ProblemParsingTest.java
@@ -42,7 +42,7 @@ class ProblemParsingTest {
                                 error invalidTaxStatus(Person p) <->
                                         taxStatus(p, CHILD), children(p, _q).
 
-                                indiv family.
+                                atom family.
                                 Family(family).
                                 members(family, anne): true.
                                 members(family, bob).
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java
index f688d970..4a15f9de 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/formatting2/ProblemFormatterTest.java
@@ -183,8 +183,8 @@ class ProblemFormatterTest {
         }
 
         @Test
-        void individualDeclarationTest() {
-                testFormatter("  indiv  a  ,  b  .  ", "indiv a, b.\n");
+        void atomDeclarationTest() {
+                testFormatter("  atom  a  ,  b  .  ", "atom a, b.\n");
         }
 
         @Test
@@ -194,7 +194,7 @@ class ProblemFormatterTest {
                                 pred foo(node a).
                                 class Foo.
                                 foo(n1, n2).
-                                indiv i1.
+                                atom i1.
                                 !foo(i1, n1).
                                 pred bar(node a, node b).
                                 pred quux().
@@ -207,7 +207,7 @@ class ProblemFormatterTest {
                                 class Foo.
 
                                 foo(n1, n2).
-                                indiv i1.
+                                atom i1.
                                 !foo(i1, n1).
 
                                 pred bar(node a, node b).
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java
index e76d2993..bc0320a6 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/scoping/NodeScopingTest.java
@@ -69,35 +69,35 @@ class NodeScopingTest {
         }
 
         @ParameterizedTest
-        @MethodSource("individualNodeReferenceSource")
-        void individualNodeInAssertionTest(String qualifiedNamePrefix, boolean namedProblem) {
+        @MethodSource("atomNodeReferenceSource")
+        void atomNodeInAssertionTest(String qualifiedNamePrefix, boolean namedProblem) {
                 var problem = parse("""
-                                indiv a, b.
+                                atom a, b.
                                 pred predicate(node x, node y) <-> node(x).
                                 predicate({PARAM}a, {PARAM}a).
                                 ?predicate({PARAM}a, {PARAM}b).
                                 """, qualifiedNamePrefix, namedProblem);
                 assertThat(problem.getResourceErrors(), empty());
                 assertThat(problem.nodeNames(), empty());
-                assertThat(problem.assertion(0).arg(0).node(), equalTo(problem.individualNode("a")));
-                assertThat(problem.assertion(0).arg(1).node(), equalTo(problem.individualNode("a")));
-                assertThat(problem.assertion(1).arg(0).node(), equalTo(problem.individualNode("a")));
-                assertThat(problem.assertion(1).arg(1).node(), equalTo(problem.individualNode("b")));
+                assertThat(problem.assertion(0).arg(0).node(), equalTo(problem.atomNode("a")));
+                assertThat(problem.assertion(0).arg(1).node(), equalTo(problem.atomNode("a")));
+                assertThat(problem.assertion(1).arg(0).node(), equalTo(problem.atomNode("a")));
+                assertThat(problem.assertion(1).arg(1).node(), equalTo(problem.atomNode("b")));
         }
 
         @ParameterizedTest
-        @MethodSource("individualNodeReferenceSource")
-        void individualNodeInPredicateTest(String qualifiedNamePrefix, boolean namedProblem) {
+        @MethodSource("atomNodeReferenceSource")
+        void atomNodeInPredicateTest(String qualifiedNamePrefix, boolean namedProblem) {
                 var problem = parse("""
-                                indiv b.
+                                atom b.
                                 pred predicate(node a) <-> node({PARAM}b).
-                                """);
+                                """, qualifiedNamePrefix, namedProblem);
                 assertThat(problem.getResourceErrors(), empty());
                 assertThat(problem.nodeNames(), empty());
-                assertThat(problem.pred("predicate").conj(0).lit(0).arg(0).node(), equalTo(problem.individualNode("b")));
+                assertThat(problem.pred("predicate").conj(0).lit(0).arg(0).node(), equalTo(problem.atomNode("b")));
         }
 
-        static Stream<Arguments> individualNodeReferenceSource() {
+        static Stream<Arguments> atomNodeReferenceSource() {
                 return Stream.of(Arguments.of("", false), Arguments.of("", true), Arguments.of("test::", true));
         }
 
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java
index 65675b6b..ad583f8e 100644
--- a/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/serializer/ProblemSerializerTest.java
@@ -56,15 +56,16 @@ class ProblemSerializerTest {
                 var pred = createPred();
                 var node = ProblemFactory.eINSTANCE.createNode();
                 node.setName("a");
-                var individualDeclaration = ProblemFactory.eINSTANCE.createIndividualDeclaration();
-                individualDeclaration.getNodes().add(node);
-                problem.getStatements().add(individualDeclaration);
+                var atomDeclaration = ProblemFactory.eINSTANCE.createNodeDeclaration();
+                atomDeclaration.setKind(NodeKind.ATOM);
+                atomDeclaration.getNodes().add(node);
+                problem.getStatements().add(atomDeclaration);
                 createAssertion(pred, node, value);
 
                 assertSerializedResult("""
                                 pred foo(node p).
 
-                                indiv a.
+                                atom a.
                                 """ + serializedAssertion + "\n");
         }
 
@@ -79,15 +80,16 @@ class ProblemSerializerTest {
                 var pred = createPred();
                 var node = ProblemFactory.eINSTANCE.createNode();
                 node.setName("a");
-                var individualDeclaration = ProblemFactory.eINSTANCE.createIndividualDeclaration();
-                individualDeclaration.getNodes().add(node);
-                problem.getStatements().add(individualDeclaration);
+                var atomDeclaration = ProblemFactory.eINSTANCE.createNodeDeclaration();
+                atomDeclaration.setKind(NodeKind.ATOM);
+                atomDeclaration.getNodes().add(node);
+                problem.getStatements().add(atomDeclaration);
                 createAssertion(pred, node, value, true);
 
                 assertSerializedResult("""
                                 pred foo(node p).
 
-                                indiv a.
+                                atom a.
                                 default\040""" + serializedAssertion + "\n");
         }
 
diff --git a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedProblem.java b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedProblem.java
index fc51ff57..58bfce44 100644
--- a/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedProblem.java
+++ b/subprojects/language/src/testFixtures/java/tools/refinery/language/model/tests/utils/WrappedProblem.java
@@ -67,8 +67,9 @@ public record WrappedProblem(Problem problem) {
                 return ProblemNavigationUtil.named(problem.getNodes(), name);
         }
 
-        public Node individualNode(String name) {
-                var uniqueNodes = statementsOfType(IndividualDeclaration.class)
+        public Node atomNode(String name) {
+                var uniqueNodes = statementsOfType(NodeDeclaration.class)
+                                .filter(declaration -> declaration.getKind() == NodeKind.ATOM)
                                 .flatMap(declaration -> declaration.getNodes().stream());
                 return ProblemNavigationUtil.named(uniqueNodes, name);
         }