Here is a proposed patch to add include/exclude functionality. As this is my first venture into JXR I would appreciate if someone could review this patch. If it is considered good I can apply it myself.
Please note the @todo on line 108 in JXR.java. I see that there is some extra handling in the JXR-version of DirectoryScanner, but I don't think subclassing is the most elegant solution. As it is now the includes/excludes must be added twice. Once for PackageManager and once for DirectoryScanner.