Support setting the bundleroot for manifest generated projects

Currently we have only the option to set the bundleroot to a different
folder (what the will become the outputfolder). In some cases one might
want to set the bundle root also to the project root.

This now adds special handling for the case where bundle root != output
folder.

Fix #803

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

@@ -14,6 +14,7 @@
 package org.eclipse.pde.internal.core.bnd;
 
 import java.util.Map;
+import java.util.Objects;
 import java.util.Optional;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicBoolean;
@@ -131,7 +132,25 @@ private static void buildProjectJar(IProject project, IProgressMonitor monitor)
 			if (monitor.isCanceled()) {
 				return;
 			}
-			try (Project bnd = bndProject.get(); ProjectBuilder builder = new ProjectBuilder(bnd)) {
+			try (Project bnd = bndProject.get(); ProjectBuilder builder = new ProjectBuilder(bnd) {
+				@Override
+				public void addClasspath(aQute.bnd.osgi.Jar jar) {
+					try {
+						// If the output exits, the ProjectBuilder adds the
+						// output as a classpath jar, this on the other hand
+						// later confuses BND because it thinks there is a
+						// splitpackage and tries to copy the class into the jar
+						// again...
+						if (Objects.equals(jar.getSource(), bnd.getOutput())) {
+							jar.close();
+							return;
+						}
+					} catch (Exception e) {
+						// can't do anything useful...
+					}
+					super.addClasspath(jar);
+				}
+			}) {
 				builder.setBase(bnd.getBase());
 				ProjectJar jar = new ProjectJar(project, CLASS_FILTER);
 				builder.setJar(jar);

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

@@ -26,6 +26,7 @@
 import org.eclipse.core.resources.IWorkspaceRoot;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
+import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.jdt.core.IClasspathEntry;
 import org.eclipse.jdt.core.IJavaProject;
 import org.eclipse.jdt.core.JavaCore;
@@ -38,10 +39,11 @@
 public class ProjectJar extends Jar {
 
 	private final IContainer outputFolder;
+	private IFile manifestFile;
 
 	public ProjectJar(IProject project, Predicate<IResource> filter) throws CoreException {
 		super(project.getName());
-		outputFolder = PDEProject.getBundleRoot(project);
+		outputFolder = PDEProject.getJavaOutputFolder(project);
 		FileResource.addResources(this, outputFolder, filter);
 		if (project.hasNature(JavaCore.NATURE_ID)) {
 			IJavaProject javaProject = JavaCore.create(project);
@@ -57,12 +59,53 @@ public ProjectJar(IProject project, Predicate<IResource> filter) throws CoreExce
 				}
 			}
 		}
+		manifestFile = PDEProject.getManifest(project);
 	}
 
 	@Override
 	public void setManifest(Manifest manifest) {
 		super.setManifest(manifest);
-		putResource(JarFile.MANIFEST_NAME, new ManifestResource(manifest));
+		ManifestResource resource = new ManifestResource(manifest);
+		// We must handle this with a little care here, first we put it as a
+		// resource, what will make other parts of BND find it and copy it to
+		// the output location(so it can be found when using the output as a
+		// classpath)
+		putResource(JarFile.MANIFEST_NAME, resource);
+		// but we also need to make sure if BUNDLE_ROOT != output location
+		// another copy for PDE and other things that expect it at the bundle
+		// root...
+		IFile file = outputFolder.getFile(IPath.fromOSString(JarFile.MANIFEST_NAME));
+		if (!file.getFullPath().equals(manifestFile.getFullPath())) {
+			// bundle root is currently not where we store it...
+			if (manifestFile.exists()) {
+				try (InputStream stream = resource.openInputStream()) {
+					manifestFile.setContents(stream, true, false, null);
+				} catch (RuntimeException e) {
+					throw e;
+				} catch (Exception e) {
+					throw new RuntimeException(e);
+				}
+			} else {
+				try {
+					mkdirs(manifestFile);
+				} catch (CoreException e) {
+					throw new RuntimeException(e);
+				}
+				try (InputStream stream = resource.openInputStream()) {
+					manifestFile.create(stream, true, null);
+				} catch (RuntimeException e) {
+					throw e;
+				} catch (Exception e) {
+					throw new RuntimeException(e);
+				}
+			}
+			try {
+				manifestFile.setDerived(true, new NullProgressMonitor());
+			} catch (CoreException e) {
+				// if only that don't work just go on...
+			}
+		}
+
 	}
 
 	@Override
@@ -104,4 +147,9 @@ private void mkdirs(IResource resource) throws CoreException {
 		}
 	}
 
+	@Override
+	public String toString() {
+		return "Project" + super.toString(); //$NON-NLS-1$
+	}
+
 }

ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/project/PDEProject.java

@@ -60,18 +60,18 @@ public static IContainer getBundleRoot(IProject project) {
 		if (node != null) {
 			String string = node.get(BUNDLE_ROOT_PATH, null);
 			if (string != null) {
+				if (string.isBlank()) {
+					return project;
+				}
 				IPath path = IPath.fromPortableString(string);
 				return project.getFolder(path);
 			}
 		}
 		if (BndProject.isBndProject(project)) {
-
 			try {
-				if (project.hasNature(JavaCore.NATURE_ID)) {
-					IJavaProject javaProject = JavaCore.create(project);
-					IPath outputLocation = javaProject.getOutputLocation();
-					IWorkspaceRoot workspaceRoot = project.getWorkspace().getRoot();
-					return workspaceRoot.getFolder(outputLocation);
+				IFolder outputFolder = getJavaOutputFolder(project);
+				if (outputFolder != null) {
+					return outputFolder;
 				}
 			} catch (CoreException e) {
 				// can't determine the bundle root then from java settings!
@@ -81,6 +81,16 @@ public static IContainer getBundleRoot(IProject project) {
 		return project;
 	}
 
+	public static IFolder getJavaOutputFolder(IProject project) throws CoreException {
+		if (project.hasNature(JavaCore.NATURE_ID)) {
+			IJavaProject javaProject = JavaCore.create(project);
+			IPath outputLocation = javaProject.getOutputLocation();
+			IWorkspaceRoot workspaceRoot = project.getWorkspace().getRoot();
+			return workspaceRoot.getFolder(outputLocation);
+		}
+		return null;
+	}
+
 	/**
 	 * Returns the launch shortcuts configured for this project
 	 * or <code>null</code> if default launchers should be used.
@@ -117,10 +127,10 @@ public static String getExportWizard(IProject project) {
 	}
 
 	/**
-	 * Sets the root of the bundle related artifacts in the specified project
-	 * to the specified container. When <code>null</code> is specified, the
-	 * bundle root will be the project itself. The container must be within
-	 * the specified project.
+	 * Sets the root of the bundle related artifacts in the specified project to
+	 * the specified container. When <code>null</code> is specified, the bundle
+	 * root will be the project itself. The container must be within the
+	 * specified project.
 	 *
 	 * @param project project
 	 * @param root project relative bundle root path, or <code>null</code> (or an empty path)