Fix using the outputfolder as a classpath jar

The ProjectBuilder currently uses the output folder of a project as an
additional classpath jar, this then can even confuse BND as it thinks we
have a split package and try to copy that class into the jar itself.

This extends the default ProjectBuilder, check if the jar is sourced at
the output location and then skip adding the jar.

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);