Speed-up symlinking of submodules

Fixes #108.

Your version worked, but it was very slow since there was lots of repeated work (adding every file in every submodule for every file in the home).
I didn't use `git submodule`, since git doesn't track folders if a folder appears in `git ls-files` it must be a submodule (I think). The tests all pass.

Let me know what you think.