Don't overwrite git dependencies

Closes #33 (closed)

The new behaviour is to bail if any changes have been made to checked out git files in the build directory (both dependencies and compiler) and add a new command swim restore that restores all checked out repositories.

I have added two tests that test this for libraries. Our test suite only has a path compiler and I don't feel like compiling spade again just to test this. Most of the code is shared anyway.