[[!comment format=mdwn
 username="http://joeyh.name/"
 nickname="joey"
 subject="comment 1"
 date="2013-03-08T19:44:29Z"
 content="""
I cannot reproduce this using the steps given. Transcript:

<pre>
joey@gnu:~/tmp>mkdir test
joey@gnu:~/tmp>cd test
joey@gnu:~/tmp/test>git init
Initialized empty Git repository in /home/joey/tmp/test/.git/
joey@gnu:~/tmp/test>git annex init
init  ok
(Recording state in git...)
joey@gnu:~/tmp/test>echo file > file
joey@gnu:~/tmp/test>echo file2 > file2
joey@gnu:~/tmp/test>git add file
joey@gnu:~/tmp/test>git annex add file2
add file2 (checksum...) ok
(Recording state in git...)
joey@gnu:~/tmp/test>git annex direct
commit  
[master (root-commit) 8d49cac] commit before switching to direct mode
 2 files changed, 2 insertions(+)
 create mode 100644 file
 create mode 120000 file2
ok
direct file2 ok
direct  ok
joey@gnu:~/tmp/test>git annex indirect
commit  (Recording state in git...)

ok
# On branch master
# Changes not staged for commit:
#   (use \"git add <file>...\" to update what will be committed)
#   (use \"git checkout -- <file>...\" to discard changes in working directory)
#
#	typechange: file2
#
no changes added to commit (use \"git add\" and/or \"git commit -a\")
ok
indirect file2 ok
indirect  ok
ok
joey@gnu:~/tmp/test>ls
file  file2@
joey@gnu:~/tmp/test>file file
file: ASCII text
joey@gnu:~/tmp/test>file file2
file2: symbolic link to `.git/annex/objects/ZV/w4/SHA256E-s6--67ee5478eaadb034ba59944eb977797b49ca6aa8d3574587f36ebcbeeb65f70e/SHA256E-s6--67ee5478eaadb034ba59944eb977797b49ca6aa8d3574587f36ebcbeeb65f70e'
joey@gnu:~/tmp/test>git log --oneline file 
8d49cac commit before switching to direct mode
</pre>

I even tried to reproduce the bug on a mac in case it was somehow only happening on that OS, but still, no go. `file` remains checked into git as a normal file, it is not annexed.

`git annex indirect` does not touch files unless they have a symlink committed to git. The code is pretty clear about that.

Please post a complete transcript that goes all the way from repository creation to the bug happening.
"""]]