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[[!comment format=mdwn
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 username="joey"
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 subject="""comment 1"""
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 date="2017-04-07T20:16:45Z"
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 content="""
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There's nothing special about using the absolute path; "git commit ." 
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or "git commit thefile" will behave the same.
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This is the git false index problem. Since git commit in these situations
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runs the pre-commit hook with a false index file, changes made to that
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index file won't be visible after the commit.
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So, if `git annex pre-commit` fixes symlinks in this situation,
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the right thing will be committed, but then the old index will have the old
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symlinks staged, which will result in `git status` after the commit showing
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modification to the files you just staged and committed!
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Short of having a post-commit hook come along and fix up the index to match
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what was committed, I don't see anything git-annex can do better. Well, it
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could prevent such commits even being made, I suppose, or warn.
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It's a pity git uses this false index file in this situation.
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"""]]
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