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With the storage layout v3, pulling the git-annex branch into the master branch is... less than ideal.
The fact that the two branches contain totally different data make an accidental merge worse, arguably.
Adding a tiny binary file called .gitnomerge to both branches would solve that without any noticeable overhead.
Yes, there is an argument to be made that this is too much hand-holding, but I still think it's worth it.
-- Richard