Add --shallow option

It would speed up `git-fleximod` in CESM significantly if we had the option to do shallow checkouts of the submodules, rather than getting the entire git history of every submodule. I'm thinking `-s|--shallow` by itself would go to depth 1, and an optional argument would allow the user to set a custom depth.

Start at the git-fleximod command-line entry point and trace how submodules are checked out. Add -s/--shallow with depth 1 by default and support an optional custom depth; done means CESM submodule checkouts avoid the full history while existing behavior remains unchanged.

Written by the indexing model from the issue text.