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### Please describe the problem.
Modifying an annexed file with unlock then commit leaves the link with permissions 777 and git status reports a typechange, which makes checkout impossible. Resolves by running git unlock on the file.
### What steps will reproduce the problem?
echo foo > test.txt
git annex add test.txt
git commit -a -m "first"
git annex unlock test.txt
echo foobar > test.txt
git commit -a -m "second"
git status (notice typechange message)
git unlock test.txt (corrects and retains both versions)
### What version of git-annex are you using? On what operating system?
git-annex version: 3.20120406
local repository version: 3
default repository version: 3
supported repository versions: 3
upgrade supported from repository versions: 0 1 2
git version 1.7.9.5
### Please provide any additional information below.
[[!format sh """
# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
# End of transcript or log.
"""]]
[[!tag confirmed]]
[[!meta title="git commit of unlocked file leaves typechange staged in index"]]
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