Shallow clones part 1.
Updating tests.
Line and position should be the same
Refactored repomanagers out of main.
TESTS
Insure assignment happens before access.
REFACTOR PARTY
Merge branch 'master' into shallow-clones

Conflicts:
	imhotep/main.py
	imhotep/main_test.py
ShallowRepoManager should return repo cloned.
don't pass filename to arg parsing.
Merge remote-tracking branch 'github/master'