This doesn't affect snapshots, alphas, or betas (where the collection of SHA1 ids is sufficient); but release builds of libcl should tag all git repos with their directory name.
These tags will ensure that the proper git tree is always available (fetch/push --tags), especially in the case of branch switches.

Alternatively, it probably makes more sense to have a parent project which used submodules to track the libcl sources and upstream libraries...