### Eclipse Workspace Patch 1.0
#P org.eclipse.jdt.core
Index: batch/org/eclipse/jdt/internal/compiler/batch/ClasspathDirectory.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/batch/org/eclipse/jdt/internal/compiler/batch/ClasspathDirectory.java,v
retrieving revision 1.57
diff -u -r1.57 ClasspathDirectory.java
--- batch/org/eclipse/jdt/internal/compiler/batch/ClasspathDirectory.java	19 Aug 2010 06:26:31 -0000	1.57
+++ batch/org/eclipse/jdt/internal/compiler/batch/ClasspathDirectory.java	30 Aug 2010 15:20:34 -0000
@@ -86,7 +86,7 @@
 			return true;
 	return false;
 }
-public List fetchLinkedJars(FileSystem.ClasspathSectionProblemReporter problemReporter) {
+public List fetchLinkedJars(FileSystem.ClasspathProblemReporter problemReporter) {
 	return null;
 }
 public NameEnvironmentAnswer findClass(char[] typeName, String qualifiedPackageName, String qualifiedBinaryFileName) {
Index: batch/org/eclipse/jdt/internal/compiler/batch/ClasspathJar.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/batch/org/eclipse/jdt/internal/compiler/batch/ClasspathJar.java,v
retrieving revision 1.52
diff -u -r1.52 ClasspathJar.java
--- batch/org/eclipse/jdt/internal/compiler/batch/ClasspathJar.java	21 Jul 2009 19:54:06 -0000	1.52
+++ batch/org/eclipse/jdt/internal/compiler/batch/ClasspathJar.java	30 Aug 2010 15:20:34 -0000
@@ -43,7 +43,7 @@
 	this.closeZipFileAtEnd = closeZipFileAtEnd;
 }
 
-public List fetchLinkedJars(FileSystem.ClasspathSectionProblemReporter problemReporter) {
+public List fetchLinkedJars(FileSystem.ClasspathProblemReporter problemReporter) {
 	// expected to be called once only - if multiple calls desired, consider
 	// using a cache
 	InputStream inputStream = null;
Index: batch/org/eclipse/jdt/internal/compiler/batch/FileSystem.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/batch/org/eclipse/jdt/internal/compiler/batch/FileSystem.java,v
retrieving revision 1.55
diff -u -r1.55 FileSystem.java
--- batch/org/eclipse/jdt/internal/compiler/batch/FileSystem.java	21 Feb 2010 03:35:52 -0000	1.55
+++ batch/org/eclipse/jdt/internal/compiler/batch/FileSystem.java	30 Aug 2010 15:20:34 -0000
@@ -13,9 +13,11 @@
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import org.eclipse.jdt.core.compiler.CharOperation;
@@ -40,7 +42,7 @@
 		 * @return a list of the jar file names defined in the Class-Path
 		 *         section of the jar file manifest if any
 		 */
-		List fetchLinkedJars(ClasspathSectionProblemReporter problemReporter);
+		List fetchLinkedJars(ClasspathProblemReporter problemReporter);
 		/**
 		 * This method resets the environment. The resulting state is equivalent to
 		 * a new name environment without creating a new object.
@@ -68,9 +70,10 @@
 		 */
 		void initialize() throws IOException;
 	}
-	public interface ClasspathSectionProblemReporter {
+	public interface ClasspathProblemReporter {
 		void invalidClasspathSection(String jarFilePath);
 		void multipleClasspathSections(String jarFilePath);
+		void nestedClasspath(String classpathOne, String classpathTwo);
 	}
 
 	/**
@@ -103,14 +106,20 @@
 
 	Classpath[] classpaths;
 	Set knownFileNames;
+	private ClasspathProblemReporter problemReporter;
 
 /*
 	classPathNames is a collection is Strings representing the full path of each class path
 	initialFileNames is a collection is Strings, the trailing '.java' will be removed if its not already.
 */
 public FileSystem(String[] classpathNames, String[] initialFileNames, String encoding) {
+	this(classpathNames, initialFileNames, encoding, null);
+}	
+
+public FileSystem(String[] classpathNames, String[] initialFileNames, String encoding, ClasspathProblemReporter problemReporter) {
 	final int classpathSize = classpathNames.length;
 	this.classpaths = new Classpath[classpathSize];
+	this.problemReporter = problemReporter;
 	int counter = 0;
 	for (int i = 0; i < classpathSize; i++) {
 		Classpath classpath = getClasspath(classpathNames[i], encoding, null);
@@ -126,10 +135,11 @@
 	}
 	initializeKnownFileNames(initialFileNames);
 }
-protected FileSystem(Classpath[] paths, String[] initialFileNames) {
+protected FileSystem(Classpath[] paths, String[] initialFileNames, ClasspathProblemReporter problemReporter) {
 	final int length = paths.length;
 	int counter = 0;
 	this.classpaths = new FileSystem.Classpath[length];
+	this.problemReporter = problemReporter;
 	for (int i = 0; i < length; i++) {
 		final Classpath classpath = paths[i];
 		try {
@@ -145,6 +155,9 @@
 	}
 	initializeKnownFileNames(initialFileNames);
 }
+protected FileSystem(Classpath[] paths, String[] initialFileNames) {
+	this(paths, initialFileNames, null);
+}
 public static Classpath getClasspath(String classpathName, String encoding, AccessRuleSet accessRuleSet) {
 	return getClasspath(classpathName, encoding, false, accessRuleSet, null);
 }
@@ -185,7 +198,24 @@
 		this.knownFileNames = new HashSet(0);
 		return;
 	}
+	if (this.problemReporter == null) {
+		this.problemReporter = new ClasspathProblemReporter() {
+			public void nestedClasspath(String classpathOne, String classpathTwo) {
+				System.err.println("Nested classpath " + classpathOne + " and " + classpathTwo); //$NON-NLS-1$ //$NON-NLS-2$
+			}
+			public void multipleClasspathSections(String jarFilePath) {
+				System.err.println("Multiple classpath sections in " + jarFilePath); //$NON-NLS-1$
+			}
+			public void invalidClasspathSection(String jarFilePath) {
+				System.err.println("Invalid classpath section in " + jarFilePath); //$NON-NLS-1$
+			}
+		};
+	}
+	
 	this.knownFileNames = new HashSet(initialFileNames.length * 2);
+	
+	Map conflictingClasspath = new HashMap();
+	
 	for (int i = initialFileNames.length; --i >= 0;) {
 		File compilationUnitFile = new File(initialFileNames[i]);
 		char[] fileName = null;
@@ -204,16 +234,19 @@
 		for (int j = 0, max = this.classpaths.length; j < max; j++) {
 			char[] matchCandidate = this.classpaths[j].normalizedPath();
 			if (this.classpaths[j] instanceof  ClasspathDirectory &&
-					CharOperation.prefixEquals(matchCandidate, fileName) &&
-					(matchingPathName == null ||
-							matchCandidate.length < matchingPathName.length)) {
-				matchingPathName = matchCandidate;
+					CharOperation.prefixEquals(matchCandidate, fileName)) {
+					this.knownFileNames.add(new String(CharOperation.subarray(fileName, matchCandidate.length, fileName.length)));
+					if (matchingPathName != null && matchingPathName.length != matchCandidate.length) {
+						if (!conflictingClasspath.containsKey(matchCandidate)) {
+							conflictingClasspath.put(matchCandidate, matchingPathName);
+							this.problemReporter.nestedClasspath(new String(matchCandidate), new String(matchingPathName));
+						}
+					}
+					matchingPathName = matchCandidate;
 			}
 		}
 		if (matchingPathName == null) {
 			this.knownFileNames.add(new String(fileName)); // leave as is...
-		} else {
-			this.knownFileNames.add(new String(CharOperation.subarray(fileName, matchingPathName.length, fileName.length)));
 		}
 		matchingPathName = null;
 	}
Index: batch/org/eclipse/jdt/internal/compiler/batch/Main.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/batch/org/eclipse/jdt/internal/compiler/batch/Main.java,v
retrieving revision 1.353
diff -u -r1.353 Main.java
--- batch/org/eclipse/jdt/internal/compiler/batch/Main.java	25 Apr 2010 20:10:08 -0000	1.353
+++ batch/org/eclipse/jdt/internal/compiler/batch/Main.java	30 Aug 2010 15:20:34 -0000
@@ -62,6 +62,7 @@
 import org.eclipse.jdt.internal.compiler.IErrorHandlingPolicy;
 import org.eclipse.jdt.internal.compiler.IProblemFactory;
 import org.eclipse.jdt.internal.compiler.batch.FileSystem.Classpath;
+import org.eclipse.jdt.internal.compiler.batch.FileSystem.ClasspathProblemReporter;
 import org.eclipse.jdt.internal.compiler.classfmt.ClassFileConstants;
 import org.eclipse.jdt.internal.compiler.env.AccessRestriction;
 import org.eclipse.jdt.internal.compiler.env.AccessRule;
@@ -1329,6 +1330,7 @@
 	private PrintWriter err;
 
 	ArrayList extraProblems;
+	ClasspathProblemReporter problemReporter = null;
 	public final static String bundleName = "org.eclipse.jdt.internal.compiler.batch.messages"; //$NON-NLS-1$
 	// two uses: recognize 'none' in options; code the singleton none
 	// for the '-d none' option (wherever it may be found)
@@ -1452,6 +1454,17 @@
 public Main(PrintWriter outWriter, PrintWriter errWriter, boolean systemExitWhenFinished, Map customDefaultOptions, CompilationProgress compilationProgress) {
 	this.initialize(outWriter, errWriter, systemExitWhenFinished, customDefaultOptions, compilationProgress);
 	this.relocalize();
+	this.problemReporter = 	new FileSystem.ClasspathProblemReporter() {
+		public void invalidClasspathSection(String jarFilePath) {
+			addPendingErrors(bind("configure.invalidClasspathSection", jarFilePath)); //$NON-NLS-1$
+		}
+		public void multipleClasspathSections(String jarFilePath) {
+			addPendingErrors(bind("configure.multipleClasspathSections", jarFilePath)); //$NON-NLS-1$
+		}
+		public void nestedClasspath(String classpathOne, String classpathTwo) {
+			Main.this.logger.logWarning(bind("configure.nestedClasspathEntries", classpathOne, classpathTwo)); //$NON-NLS-1$
+		}
+	};
 }
 
 public void addExtraProblems(CategorizedProblem problem) {
@@ -2935,7 +2948,7 @@
 }
 
 public FileSystem getLibraryAccess() {
-	return new FileSystem(this.checkedClasspaths, this.filenames);
+	return new FileSystem(this.checkedClasspaths, this.filenames, this.problemReporter);
 }
 
 /*
@@ -3011,22 +3024,13 @@
 	}
 	ArrayList result = new ArrayList();
 	HashMap knownNames = new HashMap();
-	FileSystem.ClasspathSectionProblemReporter problemReporter =
-		new FileSystem.ClasspathSectionProblemReporter() {
-			public void invalidClasspathSection(String jarFilePath) {
-				addPendingErrors(bind("configure.invalidClasspathSection", jarFilePath)); //$NON-NLS-1$
-			}
-			public void multipleClasspathSections(String jarFilePath) {
-				addPendingErrors(bind("configure.multipleClasspathSections", jarFilePath)); //$NON-NLS-1$
-			}
-		};
 	while (! classpaths.isEmpty()) {
 		Classpath current = (Classpath) classpaths.remove(0);
 		String currentPath = current.getPath();
 		if (knownNames.get(currentPath) == null) {
 			knownNames.put(currentPath, current);
 			result.add(current);
-			List linkedJars = current.fetchLinkedJars(problemReporter);
+			List linkedJars = current.fetchLinkedJars(this.problemReporter);
 			if (linkedJars != null) {
 				classpaths.addAll(0, linkedJars);
 			}
Index: batch/org/eclipse/jdt/internal/compiler/batch/messages.properties
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/batch/org/eclipse/jdt/internal/compiler/batch/messages.properties,v
retrieving revision 1.918
diff -u -r1.918 messages.properties
--- batch/org/eclipse/jdt/internal/compiler/batch/messages.properties	25 Aug 2010 10:53:58 -0000	1.918
+++ batch/org/eclipse/jdt/internal/compiler/batch/messages.properties	30 Aug 2010 15:20:34 -0000
@@ -95,6 +95,7 @@
 configure.incompatibleComplianceForCldcTarget=Target level ''{0}'' is incompatible with compliance level ''{1}''. A compliance level ''1.4''or lower is required
 configure.invalidClasspathSection = invalid Class-Path header in manifest of jar file: {0}
 configure.multipleClasspathSections = multiple Class-Path headers in manifest of jar file: {0}
+configure.nestedClasspathEntries = Nested classpath entries found: {0} and {1}
 configure.missingwarningspropertiesfile=properties file {0} does not exist
 configure.ioexceptionwarningspropertiesfile=An IOException occurred while reading the properties file {0}
 configure.multipleencodings=Multiple encoding specified: {1}. The default encoding has been set to {0}
#P org.eclipse.jdt.core.tests.compiler
Index: src/org/eclipse/jdt/core/tests/compiler/regression/BatchCompilerTest.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.compiler/src/org/eclipse/jdt/core/tests/compiler/regression/BatchCompilerTest.java,v
retrieving revision 1.210
diff -u -r1.210 BatchCompilerTest.java
--- src/org/eclipse/jdt/core/tests/compiler/regression/BatchCompilerTest.java	25 Aug 2010 11:11:58 -0000	1.210
+++ src/org/eclipse/jdt/core/tests/compiler/regression/BatchCompilerTest.java	30 Aug 2010 15:20:44 -0000
@@ -11789,4 +11789,58 @@
 		System.setProperty("user.dir", javaUserDir);
 	}
 }
+//https://bugs.eclipse.org/bugs/show_bug.cgi?id=322789
+public void test322789() throws IOException {
+	final String javaClassspath = System.getProperty("java.class.path");
+	final String javaUserDir = System.getProperty("user.dir");
+	try {
+		
+		File outputDir = new File(OUTPUT_DIR);
+		File srcDir = new File(outputDir, "src");
+		srcDir.mkdirs();
+
+		System.setProperty("user.dir", OUTPUT_DIR);
+		System.setProperty("java.class.path", srcDir.getCanonicalPath()+";"+outputDir.getCanonicalPath());
+		char[] srcPath = srcDir.getCanonicalPath().toCharArray();
+		char[] outputPath = outputDir.getCanonicalPath().toCharArray();
+		if (File.separatorChar == '\\') {
+			CharOperation.replace(srcPath, '\\', '/');
+			CharOperation.replace(outputPath, '\\', '/');
+		}
+		
+		this.runConformTest(
+				new String[] {
+					"src/p/AbstractJavaSourceClassLoader.java",
+					"package p;\n" +
+					"public abstract class AbstractJavaSourceClassLoader {\n" +
+					"	public interface ProtectionDomainFactory {}\n" +
+					"}\n",
+					"src/p/" + PACKAGE_INFO_NAME + ".java",
+					"/*  \n" +
+					" * Package information : p  \n" +
+					" */ \n" +
+					"package p;\n",					
+				},
+				"\"" + OUTPUT_DIR + File.separator + "src" + File.separator + "p" + File.separator + "AbstractJavaSourceClassLoader.java\""
+				+ " \"" + OUTPUT_DIR + File.separator + "src" + File.separator + "p" + File.separator + PACKAGE_INFO_NAME + ".java\""
+		        + " -1.5 -g -preserveAllLocals"
+		        + " -proceedOnError -referenceInfo"
+		        + " -d \"" + OUTPUT_DIR + "\"",
+				"Nested classpath entries found: "+ new String(outputPath) +"/ and "+ new String(srcPath) +"/\r\n",
+		        "",
+		        true);
+		final String userDir = System.getProperty("user.dir");
+		File f = new File(userDir, "p" + File.separator + "AbstractJavaSourceClassLoader.java");
+		if (!Util.delete(f)) {
+			System.out.println("Could not delete AbstractJavaSourceClassLoader.java");
+		}
+		f = new File(userDir, "p" + File.separator + "package-info.java");
+		if (!Util.delete(f)) {
+			System.out.println("Could not delete package-info.java");
+		}
+	} finally {
+		System.setProperty("java.class.path", javaClassspath);
+		System.setProperty("user.dir", javaUserDir);
+	}
+}
 }