### Eclipse Workspace Patch 1.0
#P org.eclipse.pde.api.tools
Index: src/org/eclipse/pde/api/tools/internal/builder/IncrementalApiBuilder.java
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/builder/IncrementalApiBuilder.java,v
retrieving revision 1.3
diff -u -r1.3 IncrementalApiBuilder.java
--- src/org/eclipse/pde/api/tools/internal/builder/IncrementalApiBuilder.java	2 Apr 2009 18:38:41 -0000	1.3
+++ src/org/eclipse/pde/api/tools/internal/builder/IncrementalApiBuilder.java	3 Apr 2009 17:16:58 -0000
@@ -349,12 +349,7 @@
 			if(type == null) {
 				continue;
 			}
-			this.builder.updateMonitor(monitor, 0);
-			this.builder.cleanupUnsupportedTagMarkers(file);
-			this.builder.updateMonitor(monitor, 0);
-			this.builder.cleanupCompatibilityMarkers(file);
-			this.builder.updateMonitor(monitor, 0);
-			this.builder.cleanupUsageMarkers(file);
+			this.builder.cleanupMarkers(file);
 			this.builder.updateMonitor(monitor, 0);
 			cnames.add(type.getFullyQualifiedName());
 			try {
@@ -376,15 +371,31 @@
 		IResource resource = project.findMember(ApiAnalysisBuilder.MANIFEST_PATH);
 		if (resource != null) {
 			try {
+				//TODO we should find a way to cache markers to type names, that way to get all
+				//the manifest markers for a given type name is time of O(1)
 				IMarker[] markers = resource.findMarkers(IApiMarkerConstants.COMPATIBILITY_PROBLEM_MARKER, false, IResource.DEPTH_ZERO);
+				String tname = null; 
 				for (int i = 0; i < markers.length; i++) {
-					if(tnames.contains(Util.getTypeNameFromMarker(markers[i]))) {
+					tname = Util.getTypeNameFromMarker(markers[i]);
+					if(tnames.contains(tname) || cnames.contains(tname)) {
 						markers[i].delete();
 					}
 				}
+				//TODO we should find a way to cache markers to type names, that way to get all
+				//the manifest markers for a given type name is time of O(1)
 				markers = resource.findMarkers(IApiMarkerConstants.SINCE_TAGS_PROBLEM_MARKER, false, IResource.DEPTH_ZERO);
 				for (int i = 0; i < markers.length; i++) {
-					if(tnames.contains(Util.getTypeNameFromMarker(markers[i]))) {
+					tname = Util.getTypeNameFromMarker(markers[i]);
+					if(tnames.contains(tname) || cnames.contains(tname)) {
+						markers[i].delete();
+					}
+				}
+				//TODO we should find a way to cache markers to type names, that way to get all
+				//the manifest markers for a given type name is time of O(1)
+				markers = resource.findMarkers(IApiMarkerConstants.UNUSED_FILTER_PROBLEM_MARKER, false, IResource.DEPTH_ZERO);
+				for (int i = 0; i < markers.length; i++) {
+					tname = Util.getTypeNameFromMarker(markers[i]);
+					if(tnames.contains(tname) || cnames.contains(tname)) {
 						markers[i].delete();
 					}
 				}
Index: src/org/eclipse/pde/api/tools/internal/builder/BaseApiAnalyzer.java
===================================================================
RCS file: /cvsroot/eclipse/pde/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/builder/BaseApiAnalyzer.java,v
retrieving revision 1.92
diff -u -r1.92 BaseApiAnalyzer.java
--- src/org/eclipse/pde/api/tools/internal/builder/BaseApiAnalyzer.java	31 Mar 2009 13:21:02 -0000	1.92
+++ src/org/eclipse/pde/api/tools/internal/builder/BaseApiAnalyzer.java	3 Apr 2009 17:16:58 -0000
@@ -27,7 +27,6 @@
 import java.util.jar.JarFile;
 
 import org.eclipse.core.resources.IFile;
-import org.eclipse.core.resources.IMarker;
 import org.eclipse.core.resources.IProject;
 import org.eclipse.core.resources.IResource;
 import org.eclipse.core.runtime.CoreException;
@@ -292,26 +291,30 @@
 			if(typenames != null || changedTypes != null) {
 				//incremental
 				Set typeNamesSet = null;
+				IResource resource = null;
 				if (typenames != null) {
 					typeNamesSet = new HashSet();
 					for (int i = 0; i < typenames.length; i++) {
-						String typeName = typenames[i];
-						typeNamesSet.add(typeName);
-						checkUnusedProblemFilters(store, project, typeName);
+						typeNamesSet.add(typenames[i]);
+						resource = Util.getResource(project, fJavaProject.findType(typenames[i]));
+						if(resource != null) {
+							createUnusedApiFilterProblems(store.getUnusedFilters(resource, typenames[i]));
+						}
 					}
 				}
 				if (changedTypes != null) {
 					// check the ones not already checked as part of type names check
 					for (int i = 0; i < changedTypes.length; i++) {
-						String typeName = changedTypes[i];
-						if (typeNamesSet == null || !typeNamesSet.remove(typeName)) {
-							checkUnusedProblemFilters(store, project, typeName);
+						if (typeNamesSet == null || !typeNamesSet.remove(changedTypes[i])) {
+							resource = Util.getResource(project, fJavaProject.findType(changedTypes[i]));
+							if(resource != null) {
+								createUnusedApiFilterProblems(store.getUnusedFilters(resource, changedTypes[i]));
+							}
 						}
 					}
 				}
 			} else {
 				//full build, clean up all old markers
-				project.deleteMarkers(IApiMarkerConstants.UNUSED_FILTER_PROBLEM_MARKER, false, IResource.DEPTH_INFINITE);
 				createUnusedApiFilterProblems(store.getUnusedFilters(null, null));
 			}
 		}
@@ -323,49 +326,6 @@
 		}
 	}
 
-	private void checkUnusedProblemFilters(ApiFilterStore store,
-			IProject project, String typeName) throws JavaModelException,
-			CoreException {
-		IType element = fJavaProject.findType(typeName);
-		IResource resource = Util.getResource(project, element);
-		if(resource != null) {
-			if (!Util.isManifest(resource.getProjectRelativePath())) {
-				resource.deleteMarkers(IApiMarkerConstants.UNUSED_FILTER_PROBLEM_MARKER, false, IResource.DEPTH_INFINITE);
-				IResource manifestFile = project.findMember(Util.MANIFEST_PROJECT_RELATIVE_PATH);
-				if (manifestFile != null) {
-					try {
-						IMarker[] markers = manifestFile.findMarkers(IApiMarkerConstants.UNUSED_FILTER_PROBLEM_MARKER, false, IResource.DEPTH_ZERO);
-						loop: for (int j = 0, max = markers.length; j < max; j++) {
-							IMarker marker = markers[j];
-							String typeNameFromMarker = Util.getTypeNameFromMarker(marker);
-							if (typeName.equals(typeNameFromMarker)) {
-								marker.delete();
-								continue loop;
-							}
-						}
-					} catch (CoreException e) {
-						ApiPlugin.log(e.getStatus());
-					}
-				}
-			} else {
-				try {
-					IMarker[] markers = resource.findMarkers(IApiMarkerConstants.UNUSED_FILTER_PROBLEM_MARKER, false, IResource.DEPTH_ZERO);
-					loop: for (int j = 0, max = markers.length; j < max; j++) {
-						IMarker marker = markers[j];
-						String typeNameFromMarker = Util.getTypeNameFromMarker(marker);
-						if (typeName.equals(typeNameFromMarker)) {
-							marker.delete();
-							continue loop;
-						}
-					}
-				} catch (CoreException e) {
-					ApiPlugin.log(e.getStatus());
-				}
-			}
-			createUnusedApiFilterProblems(store.getUnusedFilters(resource, typeName));
-		}
-	}
-
 	/**
 	 * Creates a new unused {@link IApiProblemFilter} problem
 	 * @param filters the filters to create the problems for
@@ -376,9 +336,10 @@
 			return;
 		}
 		IApiProblemFilter filter = null;
+		IApiProblem problem = null;
 		for (int i = 0; i < filters.length; i++) {
 			filter = filters[i];
-			IApiProblem problem = filter.getUnderlyingProblem();
+			problem = filter.getUnderlyingProblem();
 			if(problem == null) {
 				return;
 			}
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 1.98
diff -u -r1.98 ApiAnalysisBuilder.java
--- src/org/eclipse/pde/api/tools/internal/builder/ApiAnalysisBuilder.java	31 Mar 2009 13:21:02 -0000	1.98
+++ src/org/eclipse/pde/api/tools/internal/builder/ApiAnalysisBuilder.java	3 Apr 2009 17:16:58 -0000
@@ -128,6 +128,7 @@
 	 * @param resource
 	 */
 	void cleanupMarkers(IResource resource) {
+		cleanUnusedFilterMarkers(resource);
 		cleanupUsageMarkers(resource);
 		cleanupCompatibilityMarkers(resource);
 		cleanupUnsupportedTagMarkers(resource);
@@ -183,6 +184,21 @@
 		}
 	}
 	
+	/**
+	 * Cleans up the unused API filter problems from the given resource
+	 * @param resource
+	 */
+	void cleanUnusedFilterMarkers(IResource resource) {
+		try {
+			if(resource != null && resource.isAccessible()) {
+				resource.deleteMarkers(IApiMarkerConstants.UNUSED_FILTER_PROBLEM_MARKER, false, IResource.DEPTH_INFINITE);
+			}
+		}
+		catch(CoreException ce) {
+			ApiPlugin.log(ce.getStatus());
+		}
+	}
+	
 	/* (non-Javadoc)
 	 * @see org.eclipse.core.resources.IncrementalProjectBuilder#build(int, java.util.Map, org.eclipse.core.runtime.IProgressMonitor)
 	 */
#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 1.12
diff -u -r1.12 UnusedApiProblemFilterTests.java
--- src/org/eclipse/pde/api/tools/builder/tests/usage/UnusedApiProblemFilterTests.java	28 Mar 2009 17:50:02 -0000	1.12
+++ src/org/eclipse/pde/api/tools/builder/tests/usage/UnusedApiProblemFilterTests.java	3 Apr 2009 17:16:59 -0000
@@ -209,13 +209,13 @@
 				inc);
 	}
 	
-//	public void testUnusedFilter2F() throws Exception {
-//		x2(false);
-//	}
-//	
-//	public void testUnusedFilter2I() throws Exception {
-//		x2(true);
-//	}
+	public void testUnusedFilter2F() throws Exception {
+		x2(false);
+	}
+	
+	public void testUnusedFilter2I() throws Exception {
+		x2(true);
+	}
 	
 	/**
 	 * Tests that there is no problem reported for a compilation unit that has been deleted, which has an api