fix issue with overwritting local mods

[jedwards4b]

Fixes issue #88
I also tested against issue #75

[billsacks]

Thanks a lot for this quick fix, @jedwards4b ! I just want to confirm the intended behavior in these three cases:

(1) If I introduce some local mods in a repository, and that repository is otherwise in sync with the intended tag, then "git-fleximod update" happily proceeds, leaving that repository alone.

(2) If I introduce some local mods in a repository, and that repository is out-of-sync with its intended tag, but git is able to bring it in sync without conflicting with the local mods, it is brought up to date with the intended tag, and the local mods are retained (with a message during update like, "cime has modified files: ['README.md']").

(3) If I introduce some local mods in a repository, and that repository is out-of-sync with its intended tag, and git is not able to bring it in sync due to conflicts with the local mods, I get an exception with an error message like, "ERROR: Failed to checkout cime at tag or hash cime6.1.135 from /Users/sacks/temporary/CESM/cime".

I'm especially wanting to check about cases (1) and (2): I think these differ from the more conservative manage_externals behavior where it would abort without doing any updates if there were local mods. Maybe it's okay for git-fleximod to be less conservative in this respect, but I at least wanted to check in to confirm that it's now operating as designed.

[jedwards4b]

I am currently working on tests, I will try to test all three cases you have listed.

[billsacks]

I am currently working on tests, I will try to test all three cases you have listed.

Awesome - thanks a lot!

[jedwards4b]

@billsacks I believe that I am now testing each scenario. This is ready for your review.

[billsacks]

Thanks a lot for fixing this and for introducing these tests of the different scenarios!