[[!comment format=mdwn
 username="joey"
 subject="""comment 1"""
 date="2017-04-07T20:16:45Z"
 content="""
There's nothing special about using the absolute path; "git commit ." 
or "git commit thefile" will behave the same.

This is the git false index problem. Since git commit in these situations
runs the pre-commit hook with a false index file, changes made to that
index file won't be visible after the commit.

So, if `git annex pre-commit` fixes symlinks in this situation,
the right thing will be committed, but then the old index will have the old
symlinks staged, which will result in `git status` after the commit showing
modification to the files you just staged and committed!

Short of having a post-commit hook come along and fix up the index to match
what was committed, I don't see anything git-annex can do better. Well, it
could prevent such commits even being made, I suppose, or warn.

It's a pity git uses this false index file in this situation.
"""]]