As discussed on the Felix Users mailing list regarding a problem with a third-party component (non relevant but QDox in that specific case), there was a clear indication that having the ability to control which directories are processed by the Maven SCR Plugin would be helpful.
This feature would allow things like:
The JavaClassDescriptorManager constructor gets all source directories from MavenProject.getCompileSourceRoots(). The exclusion should be coded here consulting the plugin configuration block.
Since the plugin is currently "include all exclude explicit" there may be no purpose in actually having an include directive, unless it would support sub-tree checking, which would complicate things quite a bit (as in exclude target/foo but include target/foo/bar).