Fix detection of git submodules

[djhoese]

Closes #48

This uses the "--show-superproject-working-tree" flag in the get_toplevel_path call to git to add an additional line of output if the current directory is a git submodule of another project (a super project). When provided along with the --show-toplevel flag and when in a git submodule you will get two lines of output. One for the git submodule root and one for the super project root (note: order of the flags in the command determine the order of the lines in the output). If it isn't a git submodule then there will only ever be one line of output.

[djhoese]

So I'm trying to make this work for my own project and it turns out this won't work when we get to the ref filtering as the file_exists function uses git cat-file which doesn't seem to work properly with git submodules.

[djhoese]

Ok even if I hack that to work (modifying file_exists) it still fails because the copy_tree function uses git_archive which doesn't support git submodules. Wow, I didn't think this was going to be this hard.