Repair inner class nesting when stripped by an obfuscator

enigma-swing/src/main/java/org/quiltmc/enigma/gui/Gui.java

@@ -367,7 +367,8 @@ public void closeEditor(EditorPanel editor) {
 	 * @param reference the reference
 	 */
 	public void showReference(EntryReference<Entry<?>, Entry<?>> reference) {
-		this.editorTabbedPane.openClass(reference.getLocationClassEntry().getOutermostClass()).showReference(reference);
+		ClassEntry sourceRoot = this.controller.getProject().getSourceRoot(reference.getLocationClassEntry());
+		this.editorTabbedPane.openClass(sourceRoot).showReference(reference);
 	}
 
 	public void setObfClasses(Collection<ClassEntry> obfClasses) {

enigma-swing/src/main/java/org/quiltmc/enigma/gui/GuiController.java

@@ -444,6 +444,10 @@ public void navigateTo(EntryReference<Entry<?>, Entry<?>> reference) {
 		this.openReference(reference);
 	}
 
+	public ClassEntry getSourceRoot(Entry<?> entry) {
+		return this.project.getSourceRoot(entry.getContainingClass());
+	}
+
 	public void refreshClasses() {
 		if (this.project == null) {
 			return;
@@ -461,7 +465,7 @@ public void addSeparatedClasses(List<ClassEntry> obfClasses, List<ClassEntry> de
 
 		Collection<ClassEntry> classes = this.project.getJarIndex().getIndex(EntryIndex.class).getClasses();
 		Stream<ClassEntry> visibleClasses = classes.stream()
-				.filter(entry -> !entry.isInnerClass());
+				.filter(entry -> !this.project.isNestedInSource(entry));
 
 		visibleClasses.forEach(entry -> {
 			TranslateResult<ClassEntry> result = mapper.extendedDeobfuscate(entry);
@@ -594,27 +598,27 @@ private void applyChange0(ValidationContext vc, EntryChange<?> change, boolean u
 
 				// local variable entries need to be propagated up the tree to update param names in javadoc
 				if (target instanceof LocalVariableEntry) {
-					this.chp.invalidateJavadoc(target.getTopLevelClass());
+					this.chp.invalidateJavadoc(this.getSourceRoot(target));
 
 					var children = this.project.getJarIndex().getIndex(InheritanceIndex.class).getChildren(target.getContainingClass());
 					for (ClassEntry child : children) {
-						this.chp.invalidateJavadoc(child.getTopLevelClass());
+						this.chp.invalidateJavadoc(this.getSourceRoot(child));
 					}
 				}
 			}
 
 			if (!Objects.equals(prev.javadoc(), mapping.javadoc())) {
-				this.chp.invalidateJavadoc(target.getTopLevelClass());
+				this.chp.invalidateJavadoc(this.getSourceRoot(target));
 			}
 
-			if (renamed && target instanceof ClassEntry classEntry && !classEntry.isInnerClass()) {
+			if (renamed && target instanceof ClassEntry classEntry && !this.project.isNestedInSource(classEntry)) {
 				boolean isOldOb = prev.targetName() == null;
 				boolean isNewOb = mapping.targetName() == null;
 				this.gui.moveClassTree(target.getContainingClass(), updateSwingState, isOldOb, isNewOb);
 			} else if (updateSwingState) {
 				// update stat icons for classes that could have had their mappings changed by this update
 				boolean propagate = target instanceof FieldEntry || target instanceof MethodEntry || target instanceof LocalVariableEntry;
-				this.gui.reloadStats(change.getTarget().getTopLevelClass(), propagate);
+				this.gui.reloadStats(this.getSourceRoot(change.getTarget()), propagate);
 			}
 		}
 	}

enigma-swing/src/main/java/org/quiltmc/enigma/gui/dialog/SearchDialog.java

@@ -229,7 +229,7 @@ public void show(boolean clear, Type... types) {
 
 			switch (searchedType) {
 				case CLASS -> entryIndex.getClasses().parallelStream()
-						.filter(e -> !e.isInnerClass())
+						.filter(e -> !this.gui.getController().getProject().isNestedInSource(e))
 						.map(e -> SearchEntryImpl.from(e, this.gui.getController()))
 						.map(SearchUtil.Entry::from)
 						.sequential()

enigma-swing/src/main/java/org/quiltmc/enigma/gui/node/ClassSelectorClassNode.java

@@ -122,7 +122,7 @@ public void done() {
 
 	@Override
 	public String toString() {
-		return this.deobfEntry.getSimpleName();
+		return this.deobfEntry.getContextualName();
 	}
 
 	@Override

enigma-swing/src/main/java/org/quiltmc/enigma/gui/panel/EntryTooltip.java

@@ -319,7 +319,7 @@ public void mousePressed(MouseEvent e) {
 
 		{
 			final ClassHandle targetTopClassHandle = this.gui.getController().getClassHandleProvider()
-					.openClass(target.getTopLevelClass());
+					.openClass(this.gui.getController().getSourceRoot(target));
 
 			if (targetTopClassHandle != null) {
 				this.declarationSnippet = new DeclarationSnippetPanel(this.gui, target, targetTopClassHandle);

enigma/src/main/java/org/quiltmc/enigma/api/EnigmaProject.java

@@ -8,6 +8,7 @@
 import org.quiltmc.enigma.api.analysis.EntryReference;
 import org.quiltmc.enigma.api.analysis.index.jar.EnclosingMethodIndex;
 import org.quiltmc.enigma.api.analysis.index.jar.EntryIndex;
+import org.quiltmc.enigma.api.analysis.index.jar.InnerClassIndex;
 import org.quiltmc.enigma.api.analysis.index.jar.JarIndex;
 import org.quiltmc.enigma.api.analysis.index.mapping.MappingsIndex;
 import org.quiltmc.enigma.api.service.ObfuscationTestService;
@@ -33,6 +34,7 @@
 import org.quiltmc.enigma.api.translation.representation.entry.LocalVariableEntry;
 import org.quiltmc.enigma.api.translation.representation.entry.MethodEntry;
 import org.quiltmc.enigma.impl.translation.mapping.MappingsChecker;
+import org.quiltmc.enigma.util.AsmUtil;
 import org.quiltmc.enigma.util.I18n;
 import org.tinylog.Logger;
 
@@ -306,6 +308,14 @@ public boolean isAnonymousOrLocal(ClassEntry classEntry) {
 		return enclosingMethodIndex.hasEnclosingMethod(classEntry);
 	}
 
+	public boolean isNestedInSource(ClassEntry classEntry) {
+		return this.jarIndex.getIndex(InnerClassIndex.class).isNestedInSource(classEntry);
+	}
+
+	public ClassEntry getSourceRoot(ClassEntry classEntry) {
+		return this.jarIndex.getIndex(InnerClassIndex.class).getSourceRoot(classEntry);
+	}
+
 	/**
 	 * Verifies that the provided {@code parameter} has a valid index for its parent method.
 	 * This method validates both the upper and lower bounds of the parent method's index range.
@@ -413,7 +423,7 @@ public SourceExport decompile(ProgressListener progress, DecompilerService decom
 
 		public Stream<ClassSource> decompileStream(ProgressListener progress, DecompilerService decompilerService, DecompileErrorStrategy errorStrategy) {
 			Collection<ClassNode> classes = this.compiled.values().stream()
-					.filter(classNode -> classNode.name.indexOf('$') == -1)
+					.filter(classNode -> !AsmUtil.isNestedInSource(classNode))
 					.toList();
 
 			progress.init(classes.size(), I18n.translate("progress.classes.decompiling"));

enigma/src/main/java/org/quiltmc/enigma/api/analysis/index/jar/InnerClassIndex.java

@@ -0,0 +1,61 @@
+package org.quiltmc.enigma.api.analysis.index.jar;
+
+import org.jspecify.annotations.NonNull;
+import org.quiltmc.enigma.api.translation.representation.entry.ClassDefEntry;
+import org.quiltmc.enigma.api.translation.representation.entry.ClassEntry;
+
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * An index of the classes a jar declares nested with the {@code InnerClasses} attribute.
+ *
+ * <p>Enigma takes nesting from class names, where {@code a/B$C} is an inner class of {@code a/B}.
+ * Decompilers take it from the {@code InnerClasses} attribute, and only put a class' source inside another
+ * class' source when that attribute says so. An obfuscator that strips the attribute without renaming makes
+ * the two disagree: the class still reads as nested, but it decompiles to a file of its own.
+ *
+ * <p>A class counts as {@linkplain #isNestedInSource nested in source} when any class in the jar declares
+ * an {@code InnerClasses} record naming it. The compiler writes that record in the nested class, in its
+ * enclosing class and in every class that references it, so one record anywhere in the jar is enough.
+ */
+public class InnerClassIndex implements JarIndexer {
+	private final Set<ClassEntry> nestedInSource = new HashSet<>();
+
+	@Override
+	public void indexInnerClass(ClassDefEntry classEntry, @NonNull InnerClassData innerClassData) {
+		this.nestedInSource.add(new ClassEntry(innerClassData.name()));
+	}
+
+	/**
+	 * Returns whether {@code entry}'s source is written inside another class' source, i.e. whether the jar
+	 * declares it nested with an {@code InnerClasses} record. A class whose name looks nested but that has no
+	 * such record decompiles to a file of its own, and this returns {@code false} for it.
+	 *
+	 * @param entry the class to check
+	 */
+	public boolean isNestedInSource(ClassEntry entry) {
+		return this.nestedInSource.contains(entry);
+	}
+
+	/**
+	 * Returns the class whose source contains {@code entry}'s, which is {@code entry} itself unless it is
+	 * {@linkplain #isNestedInSource nested in source}. This is the class to decompile, to open in an editor
+	 * and to index tokens against when navigating to {@code entry}.
+	 *
+	 * @param entry the class to find the source of
+	 */
+	public ClassEntry getSourceRoot(ClassEntry entry) {
+		ClassEntry root = entry;
+		while (root.getOuterClass() != null && this.isNestedInSource(root)) {
+			root = root.getOuterClass();
+		}
+
+		return root;
+	}
+
+	@Override
+	public String getTranslationKey() {
+		return "progress.jar.indexing.process.inner_classes";
+	}
+}

enigma/src/main/java/org/quiltmc/enigma/api/analysis/index/jar/JarIndexer.java

@@ -1,5 +1,6 @@
 package org.quiltmc.enigma.api.analysis.index.jar;
 
+import org.jspecify.annotations.Nullable;
 import org.quiltmc.enigma.api.analysis.ReferenceTargetType;
 import org.quiltmc.enigma.api.translation.representation.Lambda;
 import org.quiltmc.enigma.api.translation.representation.entry.ClassDefEntry;
@@ -34,6 +35,9 @@ default void indexLambda(MethodDefEntry callerEntry, Lambda lambda, ReferenceTar
 	default void indexEnclosingMethod(ClassDefEntry classEntry, EnclosingMethodData enclosingMethodData) {
 	}
 
+	default void indexInnerClass(ClassDefEntry classEntry, InnerClassData innerClassData) {
+	}
+
 	default void processIndex(JarIndex index) {
 	}
 
@@ -51,6 +55,10 @@ default Class<? extends JarIndexer> getType() {
 		return this.getClass();
 	}
 
+	// https://docs.oracle.com/javase/specs/jvms/se7/html/jvms-4.html#jvms-4.7.6
+	record InnerClassData(String name, @Nullable String outerName, @Nullable String innerName, int access) {
+	}
+
 	record EnclosingMethodData(String owner, String name, String descriptor) {
 		public MethodEntry getMethod() {
 			return MethodEntry.parse(this.owner, this.name, this.descriptor);

enigma/src/main/java/org/quiltmc/enigma/api/analysis/index/jar/MainJarIndex.java

@@ -27,10 +27,11 @@ public static MainJarIndex empty() {
 		BridgeMethodIndex bridgeMethodIndex = new IndependentBridgeMethodIndex(entryIndex, inheritanceIndex, referenceIndex);
 		PackageVisibilityIndex packageVisibilityIndex = new PackageVisibilityIndex();
 		EnclosingMethodIndex enclosingMethodIndex = new EnclosingMethodIndex();
+		InnerClassIndex innerClassIndex = new InnerClassIndex();
 		LambdaIndex lambdaIndex = new LambdaIndex();
 		return new MainJarIndex(
 				entryIndex, inheritanceIndex, referenceIndex, bridgeMethodIndex,
-				packageVisibilityIndex, enclosingMethodIndex, lambdaIndex
+				packageVisibilityIndex, enclosingMethodIndex, innerClassIndex, lambdaIndex
 		);
 	}
 

enigma/src/main/java/org/quiltmc/enigma/api/class_handle/ClassHandleProvider.java

@@ -143,7 +143,8 @@ public void invalidateJavadoc(ClassEntry entry) {
 				e.invalidateJavadoc();
 			}
 
-			if (entry.isInnerClass()) {
+			// only a class written inside another class' source affects that class' text
+			if (entry.isInnerClass() && this.project.isNestedInSource(entry)) {
 				this.invalidateJavadoc(entry.getOuterClass());
 			}
 		});

enigma/src/main/java/org/quiltmc/enigma/api/stats/StatsGenerator.java

@@ -128,7 +128,7 @@ public ProjectStatsResult generate(ProgressListener progress, @Nullable ClassEnt
 				this.generationLatch = new CountDownLatch(1);
 
 				List<ClassEntry> classes = this.entryIndex.getClasses()
-						.stream().filter(entry -> !entry.isInnerClass()).toList();
+						.stream().filter(entry -> !this.project.isNestedInSource(entry)).toList();
 
 				int done = 0;
 				progress.init(classes.size() - 1, I18n.translate("progress.stats"));
@@ -162,7 +162,7 @@ public ProjectStatsResult generate(ProgressListener progress, @Nullable ClassEnt
 
 	private void addChildrenRecursively(List<Entry<?>> entries, Entry<?> toCheck) {
 		if (toCheck instanceof ClassEntry innerClassEntry) {
-			List<ParentedEntry<?>> classChildren = this.project.getJarIndex().getChildrenByClass().get(innerClassEntry);
+			List<ParentedEntry<?>> classChildren = this.ownChildren(innerClassEntry);
 			if (!classChildren.isEmpty()) {
 				entries.addAll(classChildren);
 				for (Entry<?> entry : classChildren) {
@@ -174,6 +174,16 @@ private void addChildrenRecursively(List<Entry<?>> entries, Entry<?> toCheck) {
 		}
 	}
 
+	/**
+	 * Returns the members of {@code classEntry} and the classes written inside its source. A class that is
+	 * not nested in source has its own stats, so including it here would count its members twice.
+	 */
+	private List<ParentedEntry<?>> ownChildren(ClassEntry classEntry) {
+		return this.project.getJarIndex().getChildrenByClass().get(classEntry).stream()
+				.filter(child -> !(child instanceof ClassEntry childClass) || this.project.isNestedInSource(childClass))
+				.toList();
+	}
+
 	/**
 	 * Generates stats for the provided class.
 	 * @param classEntry the class to generate stats for
@@ -192,7 +202,7 @@ private StatsResult generate(ClassEntry classEntry, GenerationParameters paramet
 		Map<StatType, Integer> mappableCounts = new EnumMap<>(StatType.class);
 		Map<StatType, Map<String, Integer>> unmappedCounts = new EnumMap<>(StatType.class);
 
-		List<ParentedEntry<?>> children = this.project.getJarIndex().getChildrenByClass().get(classEntry);
+		List<ParentedEntry<?>> children = this.ownChildren(classEntry);
 		List<Entry<?>> entries = new ArrayList<>(children);
 
 		for (Entry<?> entry : children) {
@@ -311,7 +321,8 @@ private void update(StatType type, Map<StatType, Integer> mappable, Map<StatType
 		if (this.project.isRenamable(entry)) {
 			if (this.project.isObfuscated(entry)
 					|| (!parameters.countFallback() && this.fallbackNameProposerIdCache.contains(this.project.getRemapper().getMapping(entry).sourcePluginId()))) { // fallback proposed mappings don't count
-				String parent = this.project.getRemapper().deobfuscate(entry.getTopLevelClass()).getName().replace('/', '.');
+				ClassEntry statsClass = this.project.getSourceRoot(entry.getContainingClass());
+				String parent = this.project.getRemapper().deobfuscate(statsClass).getFullName().replace('/', '.');
 
 				unmapped.computeIfAbsent(type, t -> new HashMap<>());
 				unmapped.get(type).put(parent, unmapped.get(type).getOrDefault(parent, 0) + 1);

enigma/src/main/java/org/quiltmc/enigma/impl/analysis/index/AbstractJarIndex.java

@@ -228,6 +228,11 @@ public void indexLambda(MethodDefEntry callerEntry, Lambda lambda, ReferenceTarg
 		this.indexers.forEach((key, indexer) -> indexer.indexLambda(callerEntry, lambda, targetType));
 	}
 
+	@Override
+	public void indexInnerClass(ClassDefEntry classEntry, InnerClassData innerClassData) {
+		this.indexers.forEach((key, indexer) -> indexer.indexInnerClass(classEntry, innerClassData));
+	}
+
 	@Override
 	public void indexEnclosingMethod(ClassDefEntry classEntry, EnclosingMethodData enclosingMethodData) {
 		this.indexers.forEach((key, indexer) -> indexer.indexEnclosingMethod(classEntry, enclosingMethodData));

enigma/src/main/java/org/quiltmc/enigma/impl/analysis/index/IndexClassVisitor.java

@@ -35,6 +35,13 @@ public void visitOuterClass(String owner, String name, String descriptor) {
 		super.visitOuterClass(owner, name, descriptor);
 	}
 
+	@Override
+	public void visitInnerClass(String name, String outerName, String innerName, int access) {
+		this.indexer.indexInnerClass(this.classEntry, new JarIndexer.InnerClassData(name, outerName, innerName, access));
+
+		super.visitInnerClass(name, outerName, innerName, access);
+	}
+
 	@Override
 	public FieldVisitor visitField(int access, String name, String desc, String signature, Object value) {
 		this.indexer.indexField(FieldDefEntry.parse(this.classEntry, access, name, desc, signature));

enigma/src/main/java/org/quiltmc/enigma/impl/source/vineflower/EnigmaContextSource.java

@@ -29,6 +29,11 @@ public IContextSource getExternalSource() {
 		return this.external;
 	}
 
+	/** The internal name of the class this source was created for. */
+	public String getClassName() {
+		return this.name;
+	}
+
 	@Override
 	public String getName() {
 		return "class " + this.name;
@@ -40,14 +45,30 @@ private void collectClassNames() {
 		}
 
 		this.classNames = new ArrayList<>();
-		String root = this.name.contains("$") ? this.name.substring(0, this.name.indexOf("$")) : this.name;
+		String root = this.sourceRoot(this.name);
 		this.classNames.add(root);
 
 		Map<String, Object> options = VineflowerPreferences.getEffectiveOptions();
 		if (!options.containsKey(IFernflowerPreferences.DECOMPILE_INNER)
 				|| "1".equals(options.get(IFernflowerPreferences.DECOMPILE_INNER))) {
-			this.classNames.addAll(this.classProvider.getClasses(root).stream().filter(s -> s.contains("$")).toList());
+			this.classNames.addAll(this.classProvider.getClasses(root).stream()
+					.filter(s -> !s.equals(root) && this.isNestedInSource(s))
+					.toList());
+		}
+	}
+
+	private String sourceRoot(String className) {
+		String root = className;
+		while (root.lastIndexOf('$') > 0 && this.isNestedInSource(root)) {
+			root = root.substring(0, root.lastIndexOf('$'));
 		}
+
+		return root;
+	}
+
+	private boolean isNestedInSource(String className) {
+		ClassNode node = this.classProvider.get(className);
+		return node != null && AsmUtil.isNestedInSource(node);
 	}
 
 	@Override