[BUG] [JSR-199] ECJ cannot resolve JPMS modules if using a user-provided

file manager

+ make ClasspathJsr199 capable of handling sources
+ consistently extract module and pass it into CUs and class readers
+ implement module extraction from JavaFileObject (src & class)
+ implement ClasspathJsr199.listPackages() using JavaFileObjects
+ detect initial / duplicate source files by JavaFileObject, not path
+ fix arg passing in ProblemReporter.invalidPackageReference()
+ implement package matching in InMemoryJavaFileManager.list() (test)

TODO:
+ exception handling
+ encoding? (currently hardcodes UTF-8)

Fixes #958

org.eclipse.jdt.compiler.tool.tests/src/org/eclipse/jdt/compiler/tool/tests/CompilerToolJava9Tests.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2017, 2021 IBM Corporation and others.
+ * Copyright (c) 2017, 2024 IBM Corporation and others.
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0

org.eclipse.jdt.compiler.tool.tests/src/org/eclipse/jdt/compiler/tool/tests/InMemoryCompilationTest.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021 IBM Corporation and others.
+ * Copyright (c) 2021, 2024 IBM Corporation and others.
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0
@@ -191,7 +191,16 @@ public Iterable<JavaFileObject> list(Location location, String packageName, Set<
 				throws IOException {
 			List<JavaFileObject> result = new ArrayList<>();
 			if (location == StandardLocation.SOURCE_PATH && kinds.contains(Kind.SOURCE)) {
-				result.addAll(sources);
+				for (InMemoryJavaSourceFileObject sourceFileObject : sources) {
+					String name = sourceFileObject.getAbsClassName();
+					int lastDot = name.lastIndexOf('.');
+					if (lastDot == -1)
+						continue;
+					String packName = name.substring(0, lastDot-1);
+					boolean match = recurse ? packName.startsWith(packageName) : packName.equals(packageName);
+					if (match)
+						result.add(sourceFileObject);
+				}
 			}
 			if (super.hasLocation(location)) {
 				Iterable<JavaFileObject> superResult = super.list(location, packageName, kinds, recurse);

org.eclipse.jdt.core.compiler.batch/src/org/eclipse/jdt/internal/compiler/apt/dispatch/BatchFilerImpl.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2006, 2018 BEA Systems, Inc.
+ * Copyright (c) 2006, 2024 BEA Systems, Inc.
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0
@@ -19,6 +19,7 @@
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.net.URI;
+import java.util.Collections;
 import java.util.HashSet;
 import javax.annotation.processing.Filer;
 import javax.annotation.processing.FilerException;
@@ -28,8 +29,12 @@
 import javax.tools.JavaFileManager;
 import javax.tools.JavaFileManager.Location;
 import javax.tools.JavaFileObject;
+import javax.tools.JavaFileObject.Kind;
 import javax.tools.StandardLocation;
+import org.eclipse.jdt.internal.compiler.batch.ClasspathJsr199;
+import org.eclipse.jdt.internal.compiler.batch.Main;
 import org.eclipse.jdt.internal.compiler.env.ICompilationUnit;
+import org.eclipse.jdt.internal.compiler.env.IModule;
 import org.eclipse.jdt.internal.compiler.lookup.ReferenceBinding;
 
 /**
@@ -43,13 +48,30 @@ public class BatchFilerImpl implements Filer {
 	protected final BatchProcessingEnvImpl _env;
 	protected final JavaFileManager _fileManager;
 	protected final HashSet<URI> _createdFiles;
+	protected String _moduleName;
 
-	public BatchFilerImpl(BaseAnnotationProcessorManager dispatchManager, BatchProcessingEnvImpl env)
+	public BatchFilerImpl(BaseAnnotationProcessorManager dispatchManager, BatchProcessingEnvImpl env, Main main)
 	{
 		this._dispatchManager = dispatchManager;
 		this._fileManager = env._fileManager;
 		this._env = env;
 		this._createdFiles = new HashSet<>();
+		if (this._fileManager.hasLocation(StandardLocation.SOURCE_PATH)) {
+			try {
+				for (JavaFileObject javaFileObject : this._fileManager.list(StandardLocation.SOURCE_PATH, "", //$NON-NLS-1$
+						Collections.singleton(Kind.SOURCE), false)) {
+					if (javaFileObject.getName().equals(IModule.MODULE_INFO_JAVA)) {
+						IModule module = ClasspathJsr199.extractModuleFromFileObject(javaFileObject, main::getNewParser, null);
+						if (module != null)
+							this._moduleName = String.valueOf(module.name());
+						break;
+					}
+				}
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			}
+		}
 	}
 
 	public void addNewUnit(ICompilationUnit unit) {
@@ -74,7 +96,7 @@ public JavaFileObject createClassFile(CharSequence name,
 		}
 
 		this._createdFiles.add(uri);
-		return new HookedJavaFileObject(jfo, jfo.getName(), name.toString(), this);
+		return new HookedJavaFileObject(jfo, jfo.getName(), name.toString(), this, this._moduleName);
 	}
 
 	/* (non-Javadoc)
@@ -146,7 +168,13 @@ public JavaFileObject createSourceFile(CharSequence name,
 		if (typeElement != null) {
 			throw new FilerException("Source file already exists : " + moduleAndPkgString); //$NON-NLS-1$
 		}
-		Location location = mod == null ? StandardLocation.SOURCE_OUTPUT : this._fileManager.getLocationForModule(StandardLocation.SOURCE_OUTPUT, mod);
+		Location location;
+		if (mod == null) {
+			location = StandardLocation.SOURCE_OUTPUT;
+			mod = this._moduleName;
+		} else {
+			location = this._fileManager.getLocationForModule(StandardLocation.SOURCE_OUTPUT, mod);
+		}
 		JavaFileObject jfo = this._fileManager.getJavaFileForOutput(location, name.toString(), JavaFileObject.Kind.SOURCE, null);
 		URI uri = jfo.toUri();
 		if (this._createdFiles.contains(uri)) {
@@ -155,7 +183,7 @@ public JavaFileObject createSourceFile(CharSequence name,
 
 		this._createdFiles.add(uri);
 		// hook the file object's writers to create compilation unit and add to addedUnits()
-		return new HookedJavaFileObject(jfo, jfo.getName(), name.toString(), this);
+		return new HookedJavaFileObject(jfo, jfo.getName(), name.toString(), this, mod);
 	}
 
 	/* (non-Javadoc)

org.eclipse.jdt.core.compiler.batch/src/org/eclipse/jdt/internal/compiler/apt/dispatch/BatchProcessingEnvImpl.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2006, 2023 BEA Systems, Inc.
+ * Copyright (c) 2006, 2024 BEA Systems, Inc.
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0
@@ -89,7 +89,7 @@ public BatchProcessingEnvImpl(BaseAnnotationProcessorManager dispatchManager, Ma
 			this._fileManager = manager;
 		}
 		this._processorOptions = Collections.unmodifiableMap(parseProcessorOptions(commandLineArguments));
-		this._filer = new BatchFilerImpl(this._dispatchManager, this);
+		this._filer = new BatchFilerImpl(this._dispatchManager, this, this._compilerOwner);
 		this._messager = new BatchMessagerImpl(this, this._compilerOwner);
 	}
 

org.eclipse.jdt.core.compiler.batch/src/org/eclipse/jdt/internal/compiler/apt/dispatch/HookedJavaFileObject.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2006, 2023 BEA Systems, Inc. and others
+ * Copyright (c) 2006, 2024 BEA Systems, Inc. and others
  *
  * This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License 2.0
@@ -200,11 +200,14 @@ public String toString() {
 
 	private final String _typeName;
 
-	public HookedJavaFileObject(JavaFileObject fileObject, String fileName, String typeName, BatchFilerImpl filer) {
+	private final String _moduleName;
+
+	public HookedJavaFileObject(JavaFileObject fileObject, String fileName, String typeName, BatchFilerImpl filer, String module) {
 		super(fileObject);
 		this._filer = filer;
 		this._fileName = fileName;
 		this._typeName = typeName;
+		this._moduleName = module;
 	}
 
 	@SuppressWarnings("resource") // ForwardingOutputStream forwards close() too
@@ -225,8 +228,19 @@ protected void closed() {
 			//TODO: support encoding
 			switch(this.getKind()) {
 				case SOURCE :
-					CompilationUnit unit = new CompilationUnit(null, this._fileName, null /* encoding */, null, this._filer._env.shouldIgnoreOptionalProblems(this._fileName.toCharArray()), null);
-					this._filer.addNewUnit(unit);
+					try {
+						CompilationUnit unit = new CompilationUnit(
+								getCharContent(false).toString().toCharArray(),
+								this._fileName,
+								null /* encoding */,
+								null /* destination path */,
+								this._filer._env.shouldIgnoreOptionalProblems(this._fileName.toCharArray()),
+								this._moduleName);
+						this._filer.addNewUnit(unit);
+					} catch (IOException e) {
+						// TODO Auto-generated catch block
+						e.printStackTrace();
+					}
 					break;
 				case CLASS :
 					IBinaryType binaryType = null;