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