Work with git submodules in nested folder structure.

Projectile currently assumes git submodules folders match the submodule name and are contained in the root of the git repository. This change allows projectile to see submodules in a deeper folder structure. Example `.gitmodules` below.

```
[submodule "library-fork"]
	path = /frontend-src/modules/library
	url = git://github.com/fork/fork.git
```

Addresses #532 too, latest master doesn't fail for `C-c p f` but doesn't include submodule files with the example `.gitmodule` because of the silent failure.