[[!comment format=mdwn
 username="joey"
 subject="""comment 1"""
 date="2015-07-02T16:57:56Z"
 content="""
git-annex contains no code whatsoever that writes to .git/config. It relies
entirely on `git config` to write that file. I'm pretty sure that `git
config` doesn't contain code to write garbage (in this case a symlink
target belonging to another file) to the .git/config file either.

The fact that you're having IO errors also points strongly at this being
a level above userspace, so either encfs or the SD card. I think your tech
stack contains at least one POS (namely encfs), and probably more problems
(SD card, whatever nonsense filesystem Android is using for it, etc).
"""]]