Cleaning projects with submodules

Hi,

I'm trying to set up a continuous integration build for Boost, which uses massive amounts of submodules, and keep running into problems when running "git clean" in the toplevel project.

When I switch to a version where a submodule has been removed (e.g. an earlier version), "git clean -dx" will not remove the submodule's directory, because it has its own .git directory. Using a single -f flag, the process fails (because directories containing .git directories are no longer skipped), and using -ff removes all submodules (which is overkill).

Is there a good way to clean a project, leaving valid submodules in place (these are then switched to the new tip and cleaned in separate commands) while removing submodules that are no longer referenced?

   Simon