Support the new repository layout for submodules

Support the new repository layout for submodules

When updating a submodule (e.g. during recursive clone) the repository
for the submodule should be located at <gitdir>/modules/<submodule-path>
whereas the working tree of the submodule should be located at
<working-tree>/<submodule-path> (<gitdir> and <working-tree> are
associated to the containing repository). Since CloneCommand has learned
about specifying a separate gitdir this is easy to implement in
SubmoduleUpdateCommand.

Change-Id: I9b56a3dfa50f97f6975c2bb7c97b36296f331b64