### Eclipse Workspace Patch 1.0
#P org.eclipse.pde.api.tools.tests
Index: src/org/eclipse/pde/api/tools/builder/tests/usage/UnusedApiProblemFilterTests.java
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools.tests/src/org/eclipse/pde/api/tools/builder/tests/usage/UnusedApiProblemFilterTests.java,v
retrieving revision 1.9
diff -u -r1.9 UnusedApiProblemFilterTests.java
--- src/org/eclipse/pde/api/tools/builder/tests/usage/UnusedApiProblemFilterTests.java	20 Feb 2009 19:27:40 -0000	1.9
+++ src/org/eclipse/pde/api/tools/builder/tests/usage/UnusedApiProblemFilterTests.java	26 Feb 2009 20:37:20 -0000
@@ -161,11 +161,11 @@
 	}
 	
 	public void testUnusedFilter2F() {
-//		x2(false);
+		x2(false);
 	}
 	
 	public void testUnusedFilter2I() {
-//		x2(true);
+		x2(true);
 	}
 	
 	/**
@@ -173,19 +173,22 @@
 	 * problem filter
 	 * @param inc
 	 */
-//	private void x2(boolean inc) {
-//		String testname = "test2";
-//		String sourcename = "testUF2";
-//		setExpectedProblemIds(getDefaultProblemIdSet(1));
-//		setExpectedMessageArgs(new String[][] {{"testUF2.m1() has non-API return type internal"}});
-//		deployReplacementTest(
-//				getBeforePath(testname),
-//				null,
-//				getFilterFilePath(testname),
-//				sourcename,
-//				inc);
-//	}
+	private void x2(boolean inc) {
+		String testname = "test2";
+		String sourcename = "testUF2";
+		setExpectedProblemIds(getDefaultProblemIdSet(1));
+		setExpectedMessageArgs(new String[][] {{"testUF2.m1() has non-API return type internal"}});
+		deployReplacementTest(
+				getBeforePath(testname),
+				null,
+				getFilterFilePath(testname),
+				sourcename,
+				inc);
+	}
 
+	/**
+	 * 
+	 */
 	public void testUnusedFilter3F() {
 		x3(false);
 	}
#P org.eclipse.pde.api.tools
Index: src/org/eclipse/pde/api/tools/internal/builder/ApiAnalysisBuilder.java
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/builder/ApiAnalysisBuilder.java,v
retrieving revision 1.92
diff -u -r1.92 ApiAnalysisBuilder.java
--- src/org/eclipse/pde/api/tools/internal/builder/ApiAnalysisBuilder.java	24 Feb 2009 21:26:13 -0000	1.92
+++ src/org/eclipse/pde/api/tools/internal/builder/ApiAnalysisBuilder.java	26 Feb 2009 20:37:21 -0000
@@ -19,11 +19,11 @@
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Date;
 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 java.util.jar.JarFile;
@@ -87,12 +87,18 @@
 	 * - removal of the .api_filter file
 	 */
 	class ResourceDeltaVisitor implements IResourceDeltaVisitor {
-		IProject[] projects;
-		public ResourceDeltaVisitor(IProject[] projects) {
+		
+		private boolean fRequireFullBuild = false;
+		private Set projects;
+		
+		/**
+		 * Constructor
+		 * @param projects
+		 */
+		public ResourceDeltaVisitor(Set/*<IProject>*/ projects) {
 			this.projects = projects;
 		}
-		private boolean fRequireFullBuild = false;
-
+		
 		/**
 		 * Returns whether a full build should be run.
 		 * 
@@ -125,16 +131,11 @@
 						IProject project = resource.getProject();
 						if (fCurrentProject.equals(project)) {
 							if (delta.getKind() == IResourceDelta.ADDED) {
-								fAddedRemovedDeltas.add(delta);
-							}
-							fTypesToCheck.add(resource);
-						} else if (this.projects != null) {
-							loop: for (int i = 0, max = this.projects.length; i < max; i++) {
-								if (this.projects[i].equals(project)) {
-									fTypesToCheck.add(resource);
-									break loop;
-								}
+								fAddedDeltas.add(delta);
 							}
+							fChangedTypesToCheck.add(resource);
+						} else if (this.projects.contains(project)) {
+							fChangedTypesToCheck.add(resource);
 						}
 					} else if (!fRequireFullBuild && IApiCoreConstants.API_FILTERS_XML_NAME.equals(fileName)) {
 						switch(delta.getKind()) {
@@ -202,13 +203,22 @@
 	private StringSet fPackages = new StringSet(3);
 	
 	/**
-	 * The type that we want to check for API problems
+	 * The changed types that we want to check for API problems
+	 */
+	private HashSet fChangedTypesToCheck = new HashSet();
+	/**
+	 * The computed dependent types we also want to check for API problems 
+	 */
+	private HashSet fDependentTypesToCheck = new HashSet();
+	/**
+	 * The set of added deltas that come directly from the builder resource delta 
 	 */
-	private HashSet fTypesToCheck = new HashSet();
+	private HashSet fAddedDeltas = new HashSet(4);
+	
 	/**
-	 * The set of added/removed deltas that come directly from the builder resource delta 
+	 * The set of removed deltas that come directly from the builder {@link IResourceDelta}
 	 */
-	private HashSet fAddedRemovedDeltas = new HashSet(5);
+	private HashSet fRemovedDeltas = new HashSet(4);
 	
 	/**
 	 * Current build state
@@ -331,11 +341,10 @@
 					if (fBuildState == null) {
 						buildAll(baseline, localMonitor.newChild(1));
 					} else {
-						IProject[] reexportedProjects = null;
+						HashSet reexportedProjects = new HashSet();
 						String[] projectNames = this.fBuildState.getReexportedComponents();
 						int length = projectNames.length;
 						if (length != 0) {
-							List allProjects = new ArrayList();
 							IWorkspaceRoot root = ResourcesPlugin.getWorkspace().getRoot();
 							for (int i = 0, max = projectNames.length; i < max; i++) {
 								String projectName = projectNames[i];
@@ -343,14 +352,10 @@
 								if (project.isAccessible()) {
 									// select only projects that don't exist in the reference baseline
 									if (baseline != null && baseline.getApiComponent(projectName) == null) {
-										allProjects.add(project);
+										reexportedProjects.add(project);
 									}
 								}
 							}
-							if (allProjects.size() != 0) {
-								reexportedProjects = new IProject[allProjects.size()];
-								allProjects.toArray(reexportedProjects);
-							}
 						}
 						ResourceDeltaVisitor visitor = new ResourceDeltaVisitor(reexportedProjects);
 						for (int i = 0; i < deltas.length; i++) {
@@ -392,8 +397,9 @@
 		} finally {
 			fTypes.clear();
 			fPackages.clear();
-			fTypesToCheck.clear();
-			fAddedRemovedDeltas.clear();
+			fChangedTypesToCheck.clear();
+			fDependentTypesToCheck.clear();
+			fAddedDeltas.clear();
 			fProjectToOutputLocations.clear();
 			updateMonitor(monitor, 0);
 			fAnalyzer.dispose();
@@ -647,11 +653,11 @@
 		IApiBaseline wsprofile = null;
 		try {
 			clearLastState(); // so if the build fails, a full build will be triggered
-			int typesToCheckSize = fTypesToCheck.size();
-			SubMonitor localMonitor = SubMonitor.convert(monitor, BuilderMessages.api_analysis_on_0, 2 + (typesToCheckSize != 0 ? 3 : 0));
+			int typesToCheckSize = fChangedTypesToCheck.size();
+			SubMonitor localMonitor = SubMonitor.convert(monitor, BuilderMessages.api_analysis_on_0, 3 + (typesToCheckSize != 0 ? 3 : 0));
 			localMonitor.subTask(NLS.bind(BuilderMessages.ApiAnalysisBuilder_finding_affected_source_files, fCurrentProject.getName()));
 			updateMonitor(localMonitor, 0);
-			collectAffectedSourceFiles(state, fTypesToCheck);
+			collectAffectedSourceFiles(state, fDependentTypesToCheck);
 			updateMonitor(localMonitor, 1);
 			if (typesToCheckSize != 0) {
 				IPluginModelBase currentModel = getCurrentModel();
@@ -668,10 +674,34 @@
 					if(apiComponent == null) {
 						return;
 					}
-					List tnames = new ArrayList(typesToCheckSize),
-						 cnames = new ArrayList(typesToCheckSize);
-					collectAllQualifiedNames(fTypesToCheck, tnames, cnames, localMonitor.newChild(1));
+					HashSet tnames = new HashSet(typesToCheckSize),
+						 	cnames = new HashSet(typesToCheckSize);
+					//collect changed type qualified names
+					collectAllQualifiedNames(fChangedTypesToCheck, tnames, cnames, false, localMonitor.newChild(1));
+					//collect dependent type qualified names
+					collectAllQualifiedNames(fDependentTypesToCheck, tnames, cnames, true, localMonitor.newChild(1));
+					//make sure a type only appears in one place
+					fDependentTypesToCheck.removeAll(fChangedTypesToCheck);
+					IPath path = null;
+					for(Iterator iter = fRemovedDeltas.iterator(); iter.hasNext();) {
+						path = resolveJavaPathFromResource(((IResourceDelta) iter.next()).getResource());
+						if(path != null) {
+							cnames.add(path.toString().replace('/', '.'));
+						}
+					}
 					updateMonitor(localMonitor, 1);
+					//clean up markers on the manifest
+					IResource manifestFile = Util.getManifestFile(this.fCurrentProject);
+					if (manifestFile != null) {
+						try {
+							IMarker[] markers = manifestFile.findMarkers(IApiMarkerConstants.COMPATIBILITY_PROBLEM_MARKER, false, IResource.DEPTH_ZERO);
+							cleanMarkersWithTypeNames(markers, tnames);
+							cleanMarkersWithTypeNames(markers, getTypeNamesFromDeltas(this.fAddedDeltas, IResourceDelta.ADDED, true));
+							cleanMarkersWithTypeNames(manifestFile.findMarkers(IApiMarkerConstants.SINCE_TAGS_PROBLEM_MARKER, false, IResource.DEPTH_ZERO), tnames);
+						} catch (CoreException e) {
+							ApiPlugin.log(e.getStatus());
+						}
+					}
 					fAnalyzer.analyzeComponent(fBuildState, 
 							null, 
 							null, 
@@ -704,146 +734,122 @@
 	 * @param cnames the list to collect the changed type names into
 	 * @param monitor
 	 */
-	private void collectAllQualifiedNames(final HashSet alltypes, List tnames, List cnames, final IProgressMonitor monitor) {
+	private void collectAllQualifiedNames(final HashSet alltypes, Set tnames, Set cnames, boolean dependenttypes, final IProgressMonitor monitor) {
 		IType[] types = null;
 		IFile file = null;
 		for (Iterator iterator = alltypes.iterator(); iterator.hasNext(); ) {
 			file = (IFile) iterator.next();
-			ICompilationUnit unit = (ICompilationUnit) JavaCore.create(file);
-			if(!unit.exists()) {
-				continue;
-			}
-			IType type = unit.findPrimaryType();
+			IType type = getTypeFromResource(file);
 			if(type == null) {
 				continue;
 			}
+			if(dependenttypes) {
+				tnames.add(type.getFullyQualifiedName());
+			}
+			else {
+				cnames.add(type.getFullyQualifiedName());
+			}
 			updateMonitor(monitor, 0);
+			
 			cleanupUnsupportedTagMarkers(file);
 			updateMonitor(monitor, 0);
 			cleanupCompatibilityMarkers(file);
 			updateMonitor(monitor, 0);
-			cnames.add(type.getFullyQualifiedName());
+			cleanupUsageMarkers(file);
+			updateMonitor(monitor, 0);
+			
 			try {
-				cleanupUsageMarkers(file);
-				updateMonitor(monitor, 0);
-				types = unit.getAllTypes();
-				String tname = null;
+				types = type.getCompilationUnit().getAllTypes();
 				for (int i = 0; i < types.length; i++) {
 					IType type2 = types[i];
 					if (type2.isMember()) {
-						tname = type2.getFullyQualifiedName('$');
+						tnames.add(type2.getFullyQualifiedName('$'));
 					} else {
-						tname = type2.getFullyQualifiedName();
+						tnames.add(type2.getFullyQualifiedName());
 					}
-					tnames.add(tname);
 				}
 			} catch (JavaModelException e) {
 				ApiPlugin.log(e.getStatus());
 			}
 			updateMonitor(monitor, 0);
 		}
-		// inject removed types inside changed type names so that we can properly detect type removal
-		for (Iterator iterator = this.fAddedRemovedDeltas.iterator(); iterator.hasNext(); ) {
-			IResourceDelta delta = (IResourceDelta) iterator.next();
-			if (delta.getKind() != IResourceDelta.REMOVED) continue;
-			IResource resource = delta.getResource();
-			IPath typePath = resolveJavaPathFromResource(resource);
-			if(typePath == null) {
+	}
+	
+	/**
+	 * Returns the primary {@link IType} for the {@link IJavaElement} represented by the 
+	 * given {@link IResource}, or <code>null</code> if the element does not exist
+	 * 
+	 * @param resource
+	 * @return
+	 */
+	private IType getTypeFromResource(IResource resource) {
+		ICompilationUnit unit = (ICompilationUnit) JavaCore.create(resource);
+		if(unit.exists()) {
+			return unit.findPrimaryType();
+		}
+		return null;
+	}
+	
+	/**
+	 * Collects the fully qualified type names from the elements in the collection 
+	 * of {@link IResourceDelta}s.
+	 * 
+	 * @param deltas the collection of deltas
+	 * @param deltakind the kind of delta we should care about
+	 * @param includesubstypes if we should include sub-types for a root type from the delta
+	 * @return a list of fully qualified type names
+	 * @throws CoreException
+	 */
+	private Set/*<String>*/ getTypeNamesFromDeltas(Collection/*<IResourceDelta>*/ deltas, int deltakind, boolean includesubstypes) throws CoreException {
+		HashSet names = new HashSet(deltas.size());
+		IResourceDelta delta = null;
+		IType type = null;
+		IType[] types = null;
+		for (Iterator iterator = deltas.iterator(); iterator.hasNext();) {
+			delta = (IResourceDelta) iterator.next();
+			if(delta.getKind() != deltakind) {
 				continue;
 			}
-			// record removed type names (package + type)
-			StringBuffer buffer = new StringBuffer();
-			String[] segments = typePath.segments();
-			for (int i = 0, max = segments.length; i < max; i++) {
-				if (i > 0) {
-					buffer.append('.');
-				}
-				buffer.append(segments[i]);
+			type = getTypeFromResource(delta.getResource());
+			if(type == null) {
+				continue;
 			}
-			cnames.add(String.valueOf(buffer));
-		}
-		// clean up markers on added deltas
-		if (!this.fAddedRemovedDeltas.isEmpty()) {
-			IResource manifestFile = Util.getManifestFile(this.fCurrentProject);
-			if (manifestFile != null) {
-				try {
-					IMarker[] markers = manifestFile.findMarkers(IApiMarkerConstants.COMPATIBILITY_PROBLEM_MARKER, false, IResource.DEPTH_INFINITE);
-					for (int i = 0, max = markers.length; i < max; i++) {
-						IMarker marker = markers[i];
-						String typeName = marker.getAttribute(IApiMarkerConstants.MARKER_ATTR_PROBLEM_TYPE_NAME, null);
-						if (typeName != null) {
-							for (Iterator iterator = this.fAddedRemovedDeltas.iterator(); iterator.hasNext(); ) {
-								IResourceDelta delta = (IResourceDelta) iterator.next();
-								if (delta.getKind() != IResourceDelta.ADDED) continue;
-								ICompilationUnit unit = (ICompilationUnit) JavaCore.create(delta.getResource());
-								if(!unit.exists()) {
-									continue;
-								}
-								IType type = unit.findPrimaryType();
-								if(type == null) {
-									continue;
-								}
-								if (typeName.equals(type.getFullyQualifiedName())) {
-									marker.delete();
-									return;
-								} else {
-									// check secondary types
-									try {
-										types = unit.getAllTypes();
-										for (int j = 0; j < types.length; j++) {
-											IType type2 = types[i];
-											String fullyQualifiedName = null;
-											if (type2.isMember()) {
-												fullyQualifiedName = type2.getFullyQualifiedName('$');
-											} else {
-												fullyQualifiedName = type2.getFullyQualifiedName();
-											}
-											if (typeName.equals(fullyQualifiedName)) {
-												marker.delete();
-												return;
-											}
-										}
-									} catch (JavaModelException e) {
-										ApiPlugin.log(e.getStatus());
-									}
-								}
-							}
-						}
+			names.add(type.getFullyQualifiedName());
+			if(includesubstypes) {
+				types = type.getCompilationUnit().getAllTypes();
+				for (int j = 0; j < types.length; j++) {
+					IType type2 = types[j];
+					if (type2.isMember()) {
+						names.add(type2.getFullyQualifiedName('$'));
+					} else {
+						names.add(type2.getFullyQualifiedName());
 					}
-				} catch (CoreException e) {
-					ApiPlugin.log(e.getStatus());
 				}
 			}
 		}
-		IResource resource = fCurrentProject.findMember(MANIFEST_PATH);
-		if (resource != null) {
-			try {
-				IMarker[] markers = resource.findMarkers(IApiMarkerConstants.COMPATIBILITY_PROBLEM_MARKER, false, IResource.DEPTH_ZERO);
-				loop: for (int i = 0, max = markers.length; i < max; i++) {
-					IMarker marker = markers[i];
-					String typeNameFromMarker = Util.getTypeNameFromMarker(marker);
-					for (Iterator iterator = tnames.iterator(); iterator.hasNext(); ) {
-						String typeName = (String) iterator.next();
-						if (typeName.equals(typeNameFromMarker)) {
-							marker.delete();
-							continue loop;
-						}
-					}
-				}
-				markers = resource.findMarkers(IApiMarkerConstants.SINCE_TAGS_PROBLEM_MARKER, false, IResource.DEPTH_ZERO);
-				loop: for (int i = 0, max = markers.length; i < max; i++) {
-					IMarker marker = markers[i];
-					String typeNameFromMarker = Util.getTypeNameFromMarker(marker);
-					for (Iterator iterator = tnames.iterator(); iterator.hasNext(); ) {
-						String typeName = (String) iterator.next();
-						if (typeName.equals(typeNameFromMarker)) {
-							marker.delete();
-							continue loop;
-						}
+		return names;
+	}
+	
+	/**
+	 * Deletes markers from the workspace that have a type name that is in the given listing
+	 * of type names.
+	 * 
+	 * @param markers the list of markers to examine
+	 * @param typenames the list of type names to check for in the listing of markers
+	 * @throws CoreException
+	 */
+	private void cleanMarkersWithTypeNames(IMarker[] markers, final Set/*<String>*/ typenames) throws CoreException {
+		if((markers != null && markers.length > 0) && (typenames != null && typenames.size() > 0)) {
+			loop: for (int i = 0, max = markers.length; i < max; i++) {
+				IMarker marker = markers[i];
+				String typeNameFromMarker = Util.getTypeNameFromMarker(marker);
+				for (Iterator iterator = typenames.iterator(); iterator.hasNext(); ) {
+					String typeName = (String) iterator.next();
+					if (typeName.equals(typeNameFromMarker)) {
+						marker.delete();
+						continue loop;
 					}
 				}
-			} catch (CoreException e) {
-				ApiPlugin.log(e);
 			}
 		}
 	}
@@ -928,9 +934,9 @@
 			if (Util.isClassFile(resource.getName())) {
 				switch (binaryDelta.getKind()) {
 					case IResourceDelta.REMOVED :
-						fAddedRemovedDeltas.add(binaryDelta);
+						fRemovedDeltas.add(binaryDelta);
 						//$FALL-THROUGH$
-					case IResourceDelta.ADDED : {
+				case IResourceDelta.ADDED : {
 						IPath typePath = resolveJavaPathFromResource(resource);
 						if(typePath == null) {
 							return;