[[!comment format=mdwn
 username="thowz"
 subject="reinject files"
 date="2016-05-04T00:52:38Z"
 content="""
Here's a way to put files into their proper case-sensitive folders using `git-annex reinject --known`:

    # Enable write permissions on directories containing misfiled items
    chmod u+w `find -xtype l -printf \"%l\n\" | sed -r \"s/.*(\.git\/annex\/objects\/)[^\/]*\/[^\/]*\/([^\/]*).*/\1*\/*\/\2/\" | sort | uniq`
    
    # Reinject those files into the annex
    git-annex reinject --known `find -xtype l -printf \"%l\n\" | sed -r \"s/.*(\.git\/annex\/objects\/)[^\/]*\/[^\/]*\/([^\/]*.*)/\1*\/*\/\2/\" | sort | uniq`

    # Remove empty directories (rmdir will fail on the non-empty directories)
    find .git/annex/objects -mindepth 3 -maxdepth 3 -type d -exec rmdir {} \;
    find .git/annex/objects -mindepth 2 -maxdepth 2 -type d -exec rmdir {} \;
"""]]