1: On every branch i'm checked out it shows that I have un-commited changes, yet it shows no files with any changes... running `git status` will show that I have sub-modules which haven't been committed. This was always the case with version 1.x but it never said those were un-committed which should be as expected.
2: Sourcetree 2.x will randomly decide to hide actual files with changes in both staging areas... they will just randomly simply disappear without warning and not come back. I believe this is the issue OP is having and the files will come back if I press F5 (refresh)
Currently an issue in 2.1.2.4
This is one of many many issues introduced in 2.x, Please do better testing before releasing new versions, it seems with each update that 1 bug is fixed and 5 more are added. For the last few years I have been using source tree it has been going consistently downhill
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