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Merge pull request #107 from jedwards4b/ignore_empty_git_dir

if you encounter an empty directory clone into it

If when cloning a git repository the root directory already exists but is empty go ahead and clone into it anyway.

User interface changes?: No

Fixes: #104 
Testing:
  test removed:
  unit tests: all pass
  system tests: all pass
  manual testing: mom6_interface

366 of 424 branches covered (86.32%)

Branch coverage included in aggregate %.

1090 of 1178 relevant lines covered (92.53%)

3.68 hits per line