Filtering of git repository

Hm, looking back at your original pull output, I see that some refs were not updated by fetch. Probably that's why fetch failed, and the pull bailed out. For example, it says

error: Ref refs/remotes/origin/branches/hubbe is at 06983fde1434ab5470b2fb656c40db32b2e6a971 but expected 108b128dfb32fbdf2a5bc6335266a1676d64e9f9 ! 108b128...5c8e890 branches/hubbe -> origin/branches/hubbe (unable to update local ref)

But this is really weird. Why was your branch origin/branches/hubbe pointing to 06983fde1434ab5470b2fb656c40db32b2e6a971? That commit does not even exist in the old repository. It does exist in the new one though, and branches/Hubbe points to it.

Eh, you don't happen to run on a case-insensitive filesystem, do you?