### Eclipse Workspace Patch 1.0
#P org.eclipse.jdt.core
Index: model/org/eclipse/jdt/internal/core/builder/BatchImageBuilder.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/builder/BatchImageBuilder.java,v
retrieving revision 1.66
diff -u -r1.66 BatchImageBuilder.java
--- model/org/eclipse/jdt/internal/core/builder/BatchImageBuilder.java	22 Dec 2006 16:02:08 -0000	1.66
+++ model/org/eclipse/jdt/internal/core/builder/BatchImageBuilder.java	5 Jan 2007 16:52:30 -0000
@@ -131,13 +131,15 @@
 								if (org.eclipse.jdt.internal.compiler.util.Util.isClassFileName(proxy.getName())) {
 									IResource resource = proxy.requestResource();
 									if (exclusionPatterns != null || inclusionPatterns != null)
-										if (Util.isExcluded(resource, inclusionPatterns, exclusionPatterns)) return false;
+										if (Util.isExcluded(resource.getFullPath(), inclusionPatterns, exclusionPatterns, false))
+											return false;
 									resource.delete(IResource.FORCE, null);
 								}
 								return false;
 							}
 							if (exclusionPatterns != null && inclusionPatterns == null) // must walk children if inclusionPatterns != null
-								if (Util.isExcluded(proxy.requestResource(), inclusionPatterns, exclusionPatterns)) return false;
+								if (Util.isExcluded(proxy.requestFullPath(), null, exclusionPatterns, true))
+									return false;
 							notifier.checkCancel();
 							return true;
 						}
@@ -193,7 +195,7 @@
 						resource = proxy.requestResource();
 						if (javaBuilder.filterExtraResource(resource)) return false;
 						if (exclusionPatterns != null || inclusionPatterns != null)
-							if (Util.isExcluded(resource, inclusionPatterns, exclusionPatterns))
+							if (Util.isExcluded(resource.getFullPath(), inclusionPatterns, exclusionPatterns, false))
 								return false;
 
 						IPath partialPath = resource.getFullPath().removeFirstSegments(segmentCount);
@@ -220,7 +222,8 @@
 						if (javaBuilder.filterExtraResource(resource)) return false;
 						if (isAlsoProject && isExcludedFromProject(resource.getFullPath())) return false; // the sourceFolder == project
 						if (exclusionPatterns != null && inclusionPatterns == null) // must walk children if inclusionPatterns != null
-							if (Util.isExcluded(resource, inclusionPatterns, exclusionPatterns)) return false;
+							if (Util.isExcluded(resource.getFullPath(), null, exclusionPatterns, true))
+								return false;
 				}
 				return true;
 			}
Index: model/org/eclipse/jdt/internal/core/builder/IncrementalImageBuilder.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/builder/IncrementalImageBuilder.java,v
retrieving revision 1.90
diff -u -r1.90 IncrementalImageBuilder.java
--- model/org/eclipse/jdt/internal/core/builder/IncrementalImageBuilder.java	22 Dec 2006 16:02:08 -0000	1.90
+++ model/org/eclipse/jdt/internal/core/builder/IncrementalImageBuilder.java	5 Jan 2007 16:52:30 -0000
@@ -431,6 +431,18 @@
 	ArrayList visited = this.makeOutputFolderConsistent ? new ArrayList(sourceLocations.length) : null;
 	for (int i = 0, l = sourceLocations.length; i < l; i++) {
 		ClasspathMultiDirectory md = sourceLocations[i];
+		if (this.makeOutputFolderConsistent && md.hasIndependentOutputFolder && !visited.contains(md.binaryFolder)) {
+			// even a project which acts as its own source folder can have an independent/nested output folder
+			visited.add(md.binaryFolder);
+			IResourceDelta binaryDelta = delta.findMember(md.binaryFolder.getProjectRelativePath());
+			if (binaryDelta != null) {
+				int segmentCount = binaryDelta.getFullPath().segmentCount();
+				IResourceDelta[] children = binaryDelta.getAffectedChildren();
+				for (int j = 0, m = children.length; j < m; j++)
+					if (!checkForClassFileChanges(children[j], md, segmentCount))
+						return false;
+			}
+		}
 		if (md.sourceFolder.equals(javaBuilder.currentProject)) {
 			// skip nested source & output folders when the project is a source folder
 			int segmentCount = delta.getFullPath().segmentCount();
@@ -440,17 +452,6 @@
 					if (!findSourceFiles(children[j], md, segmentCount))
 						return false;
 		} else {
-			if (this.makeOutputFolderConsistent && md.hasIndependentOutputFolder && !visited.contains(md.binaryFolder)) {
-				visited.add(md.binaryFolder);
-				IResourceDelta binaryDelta = delta.findMember(md.binaryFolder.getProjectRelativePath());
-				if (binaryDelta != null) {
-					int segmentCount = binaryDelta.getFullPath().segmentCount();
-					IResourceDelta[] children = binaryDelta.getAffectedChildren();
-					for (int j = 0, m = children.length; j < m; j++)
-						if (!checkForClassFileChanges(children[j], md, segmentCount))
-							return false;
-				}
-			}
 			IResourceDelta sourceDelta = delta.findMember(md.sourceFolder.getProjectRelativePath());
 			if (sourceDelta != null) {
 				if (sourceDelta.getKind() == IResourceDelta.REMOVED) {
Index: model/org/eclipse/jdt/internal/core/builder/AbstractImageBuilder.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/builder/AbstractImageBuilder.java,v
retrieving revision 1.101
diff -u -r1.101 AbstractImageBuilder.java
--- model/org/eclipse/jdt/internal/core/builder/AbstractImageBuilder.java	22 Dec 2006 16:02:08 -0000	1.101
+++ model/org/eclipse/jdt/internal/core/builder/AbstractImageBuilder.java	5 Jan 2007 16:52:30 -0000
@@ -219,16 +219,25 @@
 							if (org.eclipse.jdt.internal.core.util.Util.isJavaLikeFileName(proxy.getName())) {
 								IResource resource = proxy.requestResource();
 								if (exclusionPatterns != null || inclusionPatterns != null)
-									if (Util.isExcluded(resource, inclusionPatterns, exclusionPatterns)) return false;
+									if (Util.isExcluded(resource.getFullPath(), inclusionPatterns, exclusionPatterns, false))
+										return false;
 								sourceFiles.add(new SourceFile((IFile) resource, sourceLocation));
 							}
 							return false;
 						case IResource.FOLDER :
-							if (exclusionPatterns != null && inclusionPatterns == null) // must walk children if inclusionPatterns != null
-								if (Util.isExcluded(proxy.requestResource(), inclusionPatterns, exclusionPatterns)) return false;
 							IPath folderPath = null;
 							if (isAlsoProject)
-								if (isExcludedFromProject(folderPath = proxy.requestFullPath())) return false;
+								if (isExcludedFromProject(folderPath = proxy.requestFullPath()))
+									return false;
+							if (exclusionPatterns != null) {
+								if (folderPath == null)
+									folderPath = proxy.requestFullPath();
+								if (Util.isExcluded(folderPath, inclusionPatterns, exclusionPatterns, true)) {
+									// must walk children if inclusionPatterns != null, can skip them if == null
+									// but folder is excluded so do not create it in the output folder
+									return inclusionPatterns != null;
+								}
+							}
 							if (!isOutputFolder) {
 								if (folderPath == null)
 									folderPath = proxy.requestFullPath();
#P org.eclipse.jdt.core.tests.builder
Index: src/org/eclipse/jdt/core/tests/builder/CopyResourceTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.builder/src/org/eclipse/jdt/core/tests/builder/CopyResourceTests.java,v
retrieving revision 1.19
diff -u -r1.19 CopyResourceTests.java
--- src/org/eclipse/jdt/core/tests/builder/CopyResourceTests.java	28 Jun 2006 19:38:47 -0000	1.19
+++ src/org/eclipse/jdt/core/tests/builder/CopyResourceTests.java	5 Jan 2007 16:52:32 -0000
@@ -31,33 +31,57 @@
 	// https://bugs.eclipse.org/bugs/show_bug.cgi?id=117302
 	public void testFilteredResources() throws JavaModelException {
 		IPath projectPath = env.addProject("P"); //$NON-NLS-1$
-		IPath src = env.getPackageFragmentRootPath(projectPath, ""); //$NON-NLS-1$
-		env.setOutputFolder(projectPath, "bin"); //$NON-NLS-1$
+		env.removePackageFragmentRoot(projectPath, ""); //$NON-NLS-1$
+		IPath src = env.addPackageFragmentRoot(
+			projectPath,
+			"", //$NON-NLS-1$
+			new IPath[] {new org.eclipse.core.runtime.Path("foo/;bar/")}, //$NON-NLS-1$
+			new IPath[] {new org.eclipse.core.runtime.Path("foo/ignored/")}, //$NON-NLS-1$
+			"bin"); //$NON-NLS-1$
 		env.addExternalJars(projectPath, Util.getJavaClassLibs());
 
-		env.addClass(src, "x", "A", //$NON-NLS-1$ //$NON-NLS-2$
-			"package x;"+ //$NON-NLS-1$
-			"public class A extends q.B {}" //$NON-NLS-1$
+		env.addClass(src, "foo", "A", //$NON-NLS-1$ //$NON-NLS-2$
+			"package foo;"+ //$NON-NLS-1$
+			"public class A extends bar.B {}" //$NON-NLS-1$
 		);
-		env.addClass(src, "q", "B", //$NON-NLS-1$ //$NON-NLS-2$
-			"package q;"+ //$NON-NLS-1$
+		env.addClass(src, "bar", "B", //$NON-NLS-1$ //$NON-NLS-2$
+			"package bar;"+ //$NON-NLS-1$
 			"public class B {}" //$NON-NLS-1$
 		);
-		env.addFile(src.append("q"), "test.txt", "test file"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+		env.addFolder(src, "foo/skip"); //$NON-NLS-1$
+		IPath ignored = env.addFolder(src, "foo/ignored"); //$NON-NLS-1$
+		env.addFile(ignored, "test.txt", "test file"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+		env.addFile(src.append("bar"), "test.txt", "test file"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+
 		org.eclipse.jdt.core.IJavaProject p = env.getJavaProject("P");
 		java.util.Map options = p.getOptions(true);
-		options.put(org.eclipse.jdt.core.JavaCore.CORE_JAVA_BUILD_RESOURCE_COPY_FILTER, "q*"); //$NON-NLS-1$
+		options.put(org.eclipse.jdt.core.JavaCore.CORE_JAVA_BUILD_RESOURCE_COPY_FILTER, "bar*"); //$NON-NLS-1$
+		options.put(org.eclipse.jdt.core.JavaCore.CORE_JAVA_BUILD_RECREATE_MODIFIED_CLASS_FILES_IN_OUTPUT_FOLDER, "enabled"); //$NON-NLS-1$
 		p.setOptions(options);
 
 		int max = org.eclipse.jdt.internal.core.builder.AbstractImageBuilder.MAX_AT_ONCE;
 		try {
 			org.eclipse.jdt.internal.core.builder.AbstractImageBuilder.MAX_AT_ONCE = 1;
 			fullBuild();
+			expectingNoProblems();
+			expectingNoPresenceOf(projectPath.append("bin/foo/skip/")); //$NON-NLS-1$
+			expectingNoPresenceOf(projectPath.append("bin/foo/ignored/")); //$NON-NLS-1$
+			expectingNoPresenceOf(projectPath.append("bin/bar/test.txt")); //$NON-NLS-1$
+
+			env.removeFolder(projectPath.append("bin/bar")); //$NON-NLS-1$
+			env.addClass(src, "x", "A", //$NON-NLS-1$ //$NON-NLS-2$
+				"package x;"+ //$NON-NLS-1$
+				"public class A extends bar.B {}" //$NON-NLS-1$
+			);
+			env.addFile(src.append("bar"), "test.txt", "changed test file"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+			incrementalBuild();
+			expectingNoProblems();
+			expectingNoPresenceOf(projectPath.append("bin/foo/skip/")); //$NON-NLS-1$
+			expectingNoPresenceOf(projectPath.append("bin/foo/ignored/")); //$NON-NLS-1$
+			expectingNoPresenceOf(projectPath.append("bin/bar/test.txt")); //$NON-NLS-1$
 		} finally {
 			org.eclipse.jdt.internal.core.builder.AbstractImageBuilder.MAX_AT_ONCE = max;
 		}
-		expectingNoProblems();
-		expectingNoPresenceOf(projectPath.append("bin/q/test.txt")); //$NON-NLS-1$
 	}
 
 	public void testSimpleProject() throws JavaModelException {
Index: src/org/eclipse/jdt/core/tests/builder/MultiSourceFolderAndOutputFolderTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.builder/src/org/eclipse/jdt/core/tests/builder/MultiSourceFolderAndOutputFolderTests.java,v
retrieving revision 1.17
diff -u -r1.17 MultiSourceFolderAndOutputFolderTests.java
--- src/org/eclipse/jdt/core/tests/builder/MultiSourceFolderAndOutputFolderTests.java	29 Mar 2006 03:16:23 -0000	1.17
+++ src/org/eclipse/jdt/core/tests/builder/MultiSourceFolderAndOutputFolderTests.java	5 Jan 2007 16:52:32 -0000
@@ -289,7 +289,7 @@
 	public void test0012() throws JavaModelException {
 		IPath projectPath = env.addProject("P");
 		env.removePackageFragmentRoot(projectPath, "");
-		IPath src = env.addPackageFragmentRoot(projectPath, "", new IPath[] {new Path("p1/p2/p3/X.java"), new Path("Y.java")}, false/*inclusion*/, "");
+		IPath src = env.addPackageFragmentRoot(projectPath, "", new IPath[] {new Path("p1/p2/p3/X.java"), new Path("Y.java")}, null, "");
 		env.addExternalJars(projectPath, Util.getJavaClassLibs());
 		
 		env.addClass(src, "p1.p2.p3", "X", 
Index: src/org/eclipse/jdt/core/tests/builder/TestingEnvironment.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.builder/src/org/eclipse/jdt/core/tests/builder/TestingEnvironment.java,v
retrieving revision 1.49
diff -u -r1.49 TestingEnvironment.java
--- src/org/eclipse/jdt/core/tests/builder/TestingEnvironment.java	20 Dec 2006 16:11:41 -0000	1.49
+++ src/org/eclipse/jdt/core/tests/builder/TestingEnvironment.java	5 Jan 2007 16:52:32 -0000
@@ -142,7 +142,7 @@
 	 * Returns the path of the added package fragment root.
 	 */
 	public IPath addPackageFragmentRoot(IPath projectPath, String sourceFolderName, IPath[] exclusionPatterns, String specificOutputLocation) throws JavaModelException {
-		return addPackageFragmentRoot(projectPath, sourceFolderName, exclusionPatterns, true/*exclusion patterns*/, specificOutputLocation);
+		return addPackageFragmentRoot(projectPath, sourceFolderName, null, exclusionPatterns, specificOutputLocation);
 	}
 	
 	/** Adds a package fragment root to the workspace.  If
@@ -150,7 +150,7 @@
 	 * exists, it is not replaced.  A workspace must be open.
 	 * Returns the path of the added package fragment root.
 	 */
-	public IPath addPackageFragmentRoot(IPath projectPath, String sourceFolderName, IPath[] patterns, boolean areExclusionPatterns, String specificOutputLocation) throws JavaModelException {
+	public IPath addPackageFragmentRoot(IPath projectPath, String sourceFolderName, IPath[] inclusionPatterns, IPath[] exclusionPatterns, String specificOutputLocation) throws JavaModelException {
 		checkAssertion("a workspace must be open", fIsOpen); //$NON-NLS-1$
 		IPath path = getPackageFragmentRootPath(projectPath, sourceFolderName);
 		createFolder(path);
@@ -159,13 +159,11 @@
 			outputPath = getPackageFragmentRootPath(projectPath, specificOutputLocation);
 			createFolder(outputPath);
 		}
-		IClasspathEntry entry;
-		if (areExclusionPatterns)
-			// exclusion patterns
-			entry = JavaCore.newSourceEntry(path, patterns == null ? new Path[0] : patterns, outputPath);
-		else
-			// inclusion patterns
-			entry = JavaCore.newSourceEntry(path, patterns == null ? new Path[0] : patterns, new Path[0], outputPath);
+		IClasspathEntry entry = JavaCore.newSourceEntry(
+			path,
+			inclusionPatterns == null ? new Path[0] : inclusionPatterns,
+			exclusionPatterns == null ? new Path[0] : exclusionPatterns,
+			outputPath);
 		addEntry(projectPath, entry);
 		return path;
 	}