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Refactor path naming and handling
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Refactor path naming to be more explicit and consistent during the status and
checkout routines. Try to move any changes in directory down to the lowest
level where they are needed.

Testing: unit tests pass (python2). Manual testing of standalone clm is correct.
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@bjandre
bjandre committed Oct 26, 2017
1 parent 1a7344f commit 27d9567
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