I can confirm this bug with Xcode Version 7.2.1 (7C1002). The following steps reproduce it too (i.e. it doesn't depend on a git operation):
1) Fix all misplaced views.
2) Close Xcode.
3) Delete derived data folder.
4) Open Xcode.
It looks like Xcode stores some settings of the storyboard in the derived data folder?!
It seems like there are at least 2 factors at play here:
- IB incorrectly marks a document as modified ("dirty") when no user action has happened. This usually has to do with undo events being created when they should not be, and there are many things which can cause this, tracked in a number of related bugs. We are very aware that this is a persistent annoyance, and have plans to dedicate time to improve this.
- Editing a storyboard or xib is known to cause 0.5 pixel changes and misplacement when moving between retina and non-retina displays. This is tracked in radar://20175879, and exacerbated by point #1, since just opening a document often causes spurious edits.