Delete orphan files that are copied/generated by bnd automatic manifest

Currently we copy everything that would normally go to the jar into the
output folder, but if on the next build the resource is not put anymore
we have some orphan files.

This records what resources are created as part of the project build and
finally deletes any orphans on close.

Fix #587

ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/bnd/FileResource.java

@@ -112,7 +112,7 @@ private static void addResources(Jar jar, IContainer container, String prefix, P
 			return;
 		}
 		for (IResource resource : container.members()) {
-			if (filter == null || filter.test(container)) {
+			if (filter == null || filter.test(resource)) {
 				if (resource instanceof IFile) {
 					IPath projectRelativePath = resource.getProjectRelativePath();
 					String relativePath = projectRelativePath.toString();

ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/bnd/ProjectJar.java

@@ -14,6 +14,8 @@
 package org.eclipse.pde.internal.core.bnd;
 
 import java.io.InputStream;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.function.Predicate;
 import java.util.jar.JarFile;
 import java.util.jar.Manifest;
@@ -27,9 +29,11 @@
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
 import org.eclipse.core.runtime.NullProgressMonitor;
+import org.eclipse.core.runtime.QualifiedName;
 import org.eclipse.jdt.core.IClasspathEntry;
 import org.eclipse.jdt.core.IJavaProject;
 import org.eclipse.jdt.core.JavaCore;
+import org.eclipse.pde.internal.core.PDECore;
 import org.eclipse.pde.internal.core.project.PDEProject;
 
 import aQute.bnd.osgi.Jar;
@@ -38,13 +42,29 @@
 
 public class ProjectJar extends Jar {
 
+	public static final QualifiedName GENERATED_PROPERTY = new QualifiedName(PDECore.PLUGIN_ID, "bndgenerated"); //$NON-NLS-1$
+
 	private final IContainer outputFolder;
 	private IFile manifestFile;
+	private final Map<String, IFile> orphanFilesMap = new HashMap<>();
 
 	public ProjectJar(IProject project, Predicate<IResource> filter) throws CoreException {
 		super(project.getName());
 		outputFolder = PDEProject.getJavaOutputFolder(project);
-		FileResource.addResources(this, outputFolder, filter);
+		Predicate<IResource> resourceScanner = r -> {
+			if (r instanceof IFile f) {
+				try {
+					String path = r.getPersistentProperty(GENERATED_PROPERTY);
+					if (path != null) {
+						orphanFilesMap.put(path, f);
+					}
+				} catch (CoreException e) {
+					// can't use that the ...
+				}
+			}
+			return filter.test(r);
+		};
+		FileResource.addResources(this, outputFolder, resourceScanner);
 		if (project.hasNature(JavaCore.NATURE_ID)) {
 			IJavaProject javaProject = JavaCore.create(project);
 			IWorkspaceRoot workspaceRoot = project.getWorkspace().getRoot();
@@ -54,7 +74,7 @@ public ProjectJar(IProject project, Predicate<IResource> filter) throws CoreExce
 					IPath location = cp.getOutputLocation();
 					if (location != null) {
 						IFolder otherOutputFolder = workspaceRoot.getFolder(location);
-						FileResource.addResources(this, otherOutputFolder, filter);
+						FileResource.addResources(this, otherOutputFolder, resourceScanner);
 					}
 				}
 			}
@@ -127,11 +147,13 @@ public boolean putResource(String path, Resource resource, boolean overwrite) {
 					file.create(stream, true, null);
 				}
 			}
+			file.setPersistentProperty(GENERATED_PROPERTY, path);
 		} catch (RuntimeException e) {
 			throw e;
 		} catch (Exception e) {
 			throw new RuntimeException(e);
 		}
+		orphanFilesMap.remove(path);
 		return super.putResource(path, new FileResource(file), overwrite);
 	}
 
@@ -152,4 +174,20 @@ public String toString() {
 		return "Project" + super.toString(); //$NON-NLS-1$
 	}
 
+	@Override
+	public void close() {
+		cleanup();
+		super.close();
+	}
+
+	private void cleanup() {
+		for (IFile file : orphanFilesMap.values()) {
+			try {
+				file.delete(true, null);
+			} catch (Exception e) {
+				// must wait for next clean then...
+			}
+		}
+	}
+
 }