Bug 82839 [misc] Breakpoint icons disappear
I am using 3.1M4 1 - Open a file and set a breakpoint. The breakpoint icon appears in the left and right margins. 2 - Close the file. 3 - Open the same file. Note the breakpoint icons no longer appear. The breakpoint is still there but the icons don't appear and you can't select them. This is a major problem because I can't see the breakpoints I've previously set so I have to clear those breakpoints and set new ones each time I run a debug session.
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/javaeditor/ClassFileMarkerAnnotationModel.java
public void setClassFile(IClassFile classFile) {
		fClassFile= classFile;
	}
	/**
	 * @see AbstractMarkerAnnotationModel#isAcceptable
	 */
	protected boolean isAcceptable(IMarker marker) {
		try {
			return JavaCore.isReferencedBy(fClassFile, marker);
		} catch (CoreException x) {
			handleCoreException(x, JavaEditorMessages.ClassFileMarkerAnnotationModel_error_isAcceptable);
			return false;
		}
	}
	protected boolean isAffected(IMarkerDelta markerDelta) {
		try {
			return JavaCore.isReferencedBy(fClassFile, markerDelta);
		} catch (CoreException x) {
			handleCoreException(x, JavaEditorMessages.ClassFileMarkerAnnotationModel_error_isAffected);
			return false;
		}
	}
	/**
	 * @see AbstractMarkerAnnotationModel#createMarkerAnnotation(IMarker)
	 */
	protected MarkerAnnotation createMarkerAnnotation(IMarker marker) {
		return new JavaMarkerAnnotation(marker);
	}
	/**
	 * @see AbstractMarkerAnnotationModel#listenToMarkerChanges(boolean)