fix: don't visit inner classes twice in pre-processing

jadx-core/src/main/java/jadx/core/dex/nodes/ClassNode.java

@@ -450,15 +450,18 @@ public class ClassNode extends NotificationAttrNode implements ILoadable, ICodeN
 	}
 
 	public ClassNode getParentClass() {
-		if (parentClass == null) {
-			if (clsInfo.isInner()) {
-				ClassNode parent = root.resolveClass(clsInfo.getParentClass());
-				parentClass = parent == null ? this : parent;
-			} else {
-				parentClass = this;
+		return parentClass;
+	}
+
+	public void updateParentClass() {
+		if (clsInfo.isInner()) {
+			ClassNode parent = root.resolveClass(clsInfo.getParentClass());
+			if (parent != null) {
+				parentClass = parent;
+				return;
 			}
 		}
-		return parentClass;
+		parentClass = this;
 	}
 
 	public ClassNode getTopParentClass() {
@@ -548,7 +551,7 @@ public class ClassNode extends NotificationAttrNode implements ILoadable, ICodeN
 	}
 
 	public boolean isInner() {
-		return parentClass != null;
+		return parentClass != this;
 	}
 
 	@Nullable

jadx-core/src/main/java/jadx/core/dex/nodes/RootNode.java

@@ -100,14 +100,16 @@ public class RootNode {
 			markDuplicatedClasses(classes);
 		}
 		classes = new ArrayList<>(clsMap.values());
-		// sort classes by name, expect top classes before inner
-		classes.sort(Comparator.comparing(ClassNode::getFullName));
-		initInnerClasses();
 
 		// print stats for loaded classes
 		int mthCount = classes.stream().mapToInt(c -> c.getMethods().size()).sum();
 		int insnsCount = classes.stream().flatMap(c -> c.getMethods().stream()).mapToInt(MethodNode::getInsnsCount).sum();
 		LOG.info("Loaded classes: {}, methods: {}, instructions: {}", classes.size(), mthCount, insnsCount);
+
+		// sort classes by name, expect top classes before inner
+		classes.sort(Comparator.comparing(ClassNode::getFullName));
+		// move inner classes
+		initInnerClasses();
 	}
 
 	private void addDummyClass(IClassData classData, Exception exc) {
@@ -254,6 +256,7 @@ public class RootNode {
 				innerCls.getClassInfo().updateNames(this);
 			}
 		}
+		classes.forEach(ClassNode::updateParentClass);
 	}
 
 	public void runPreDecompileStage() {
@@ -266,6 +269,9 @@ public class RootNode {
 				LOG.error("Visitor init failed: {}", pass.getClass().getSimpleName(), e);
 			}
 			for (ClassNode cls : classes) {
+				if (cls.isInner()) {
+					continue;
+				}
 				DepthTraversal.visit(pass, cls);
 			}
 			if (debugEnabled) {