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Trouble Shooting
If, while merging, you encounter the following scary message:
warning: too many files, skipping inexact rename detection
You'll get a whole lot of merge conflicts which one would imagine git could have take care of. The problem, at least in my case, is that because detecting file name changes is currently O(n^2), git has a configurable limit, after which it will stop searching. To resolve this, you can set diff.renamelimit to something higher. 400, in my case, seemed to do the trick.