fix(smali-input): use synced list for threaded processing, improve inner classes handling

jadx-core/src/main/java/jadx/api/JadxDecompiler.java

@@ -435,7 +435,7 @@ public final class JadxDecompiler implements Closeable {
 		return list;
 	}
 
-	public List<JavaClass> getClasses() {
+	public synchronized List<JavaClass> getClasses() {
 		if (root == null) {
 			return Collections.emptyList();
 		}
@@ -443,10 +443,7 @@ public final class JadxDecompiler implements Closeable {
 			List<ClassNode> classNodeList = root.getClasses();
 			List<JavaClass> clsList = new ArrayList<>(classNodeList.size());
 			for (ClassNode classNode : classNodeList) {
-				if (classNode.contains(AFlag.DONT_GENERATE)) {
-					continue;
-				}
-				if (!classNode.getClassInfo().isInner()) {
+				if (!classNode.contains(AFlag.DONT_GENERATE) && !classNode.isInner()) {
 					clsList.add(convertClassNode(classNode));
 				}
 			}

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

@@ -612,17 +612,9 @@ public class ClassNode extends NotificationAttrNode
 		return parentClass;
 	}
 
-	public void updateParentClass() {
-		if (clsInfo.isInner()) {
-			ClassNode parent = root.resolveClass(clsInfo.getParentClass());
-			if (parent != null) {
-				parentClass = parent;
-				return;
-			}
-			// undo inner mark in class info
-			clsInfo.notInner(root);
-		}
-		parentClass = this;
+	public void notInner() {
+		this.clsInfo.notInner(root);
+		this.parentClass = this;
 	}
 
 	/**

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

@@ -159,7 +159,7 @@ public class RootNode {
 		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));
+		classes.sort(Comparator.comparing(ClassNode::getRawName));
 
 		if (args.isMoveInnerClasses()) {
 			// detect and move inner classes
@@ -309,10 +309,8 @@ public class RootNode {
 			ClassInfo clsInfo = cls.getClassInfo();
 			ClassNode parent = resolveParentClass(clsInfo);
 			if (parent == null) {
-				clsMap.remove(clsInfo);
-				clsInfo.notInner(this);
-				clsMap.put(clsInfo, cls);
 				updated.add(cls);
+				cls.notInner();
 			} else {
 				parent.addInnerClass(cls);
 			}
@@ -323,7 +321,6 @@ public class RootNode {
 				innerCls.getClassInfo().updateNames(this);
 			}
 		}
-		classes.forEach(ClassNode::updateParentClass);
 		for (PackageNode pkg : packages) {
 			pkg.getClasses().removeIf(cls -> cls.getClassInfo().isInner());
 		}

jadx-core/src/test/java/jadx/tests/api/IntegrationTest.java

@@ -221,8 +221,7 @@ public abstract class IntegrationTest extends TestUtils {
 		} else {
 			LOG.info("Convert back to top level: {}", cls);
 			cls.getTopParentClass().decompile(); // keep correct process order
-			cls.getClassInfo().notInner(root);
-			cls.updateParentClass();
+			cls.notInner();
 		}
 		decompileAndCheck(cls);
 		return cls;

jadx-plugins/jadx-smali-input/src/main/java/jadx/plugins/input/smali/SmaliConvert.java

@@ -1,11 +1,11 @@
 package jadx.plugins.input.smali;
 
-import java.io.OutputStream;
-import java.io.PrintStream;
 import java.nio.file.FileSystems;
 import java.nio.file.Path;
 import java.nio.file.PathMatcher;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.List;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
@@ -51,16 +51,18 @@ public class SmaliConvert {
 		long start = System.currentTimeMillis();
 		if (threads == 1 || inputFiles.size() == 1) {
 			for (Path inputFile : inputFiles) {
-				assemble(inputFile, smaliOptions);
+				assemble(dexData, inputFile, smaliOptions);
 			}
 		} else {
 			try {
 				ExecutorService executor = Executors.newFixedThreadPool(threads);
+				List<IDexData> syncList = Collections.synchronizedList(dexData);
 				for (Path inputFile : inputFiles) {
-					executor.execute(() -> assemble(inputFile, smaliOptions));
+					executor.execute(() -> assemble(syncList, inputFile, smaliOptions));
 				}
 				executor.shutdown();
-				executor.awaitTermination(1, TimeUnit.DAYS);
+				executor.awaitTermination(1, TimeUnit.HOURS);
+				dexData.sort(Comparator.comparing(IDexData::getFileName));
 			} catch (InterruptedException e) {
 				LOG.error("Smali compile interrupted", e);
 			}
@@ -70,30 +72,16 @@ public class SmaliConvert {
 		}
 	}
 
-	private void assemble(Path inputFile, SmaliOptions smaliOptions) {
+	private void assemble(List<IDexData> results, Path inputFile, SmaliOptions smaliOptions) {
 		Path path = inputFile.toAbsolutePath();
 		try {
 			byte[] dexContent = SmaliUtils.assemble(path.toFile(), smaliOptions);
-			dexData.add(new SimpleDexData(path.toString(), dexContent));
+			results.add(new SimpleDexData(path.toString(), dexContent));
 		} catch (Exception e) {
 			LOG.error("Failed to assemble smali file: {}", path, e);
 		}
 	}
 
-	private static void collectSystemErrors(OutputStream out, Runnable exec) {
-		PrintStream systemErr = System.err;
-		try (PrintStream err = new PrintStream(out)) {
-			System.setErr(err);
-			try {
-				exec.run();
-			} catch (Exception e) {
-				e.printStackTrace(err);
-			}
-		} finally {
-			System.setErr(systemErr);
-		}
-	}
-
 	private List<Path> filterSmaliFiles(List<Path> input) {
 		PathMatcher matcher = FileSystems.getDefault().getPathMatcher("glob:**.smali");
 		return input.stream()