Proper git submodules handling in the Makefile based build system.

I will need to maintain several fcserver installations and that patch will
help me to do so.

I've not tested yet a from scratch cloning and building but as far as
the directories for each submodule is not is the main repository, the
code is doing the right thing for that case ;-)

Signed-off-by: Jérôme Benoit <jerome.benoit@grenouille.com>