[[!comment format=mdwn
 username="http://joeyh.name/"
 ip="209.250.56.43"
 subject="comment 5"
 date="2014-01-14T19:14:35Z"
 content="""
Analysis: pre-commit hook is run with `GIT_INDEX_FILE=.git/index.lock`; this seems to be causing git-annex branch commits to land in that index file instead of where they are supposed to go. Also, commits of the files in the work tree also end up adding the symlinks to the git-annex branch when this happens. Apparantly because again it's using the wrong index file when committing to the git-annex branch.

So, an easy workaround (disable pre-commit hook or make it `unset GIT_INDEX_FILE`, but I need to dig into why this env var is messing with git-annex like this.. I thought git-annex set the env var itself!
"""]]
