[[!comment format=mdwn
 username="https://launchpad.net/~arand"
 nickname="arand"
 subject="comment 2"
 date="2013-03-13T12:05:49Z"
 content="""
Based on the hints given here I've worked on a filter to both annex and add urls via filter-branch:

[https://gitorious.org/arand-scripts/arand-scripts/blobs/master/annex-filter](https://gitorious.org/arand-scripts/arand-scripts/blobs/master/annex-filter)

The script above is very specific but I think there are a few ideas that can be used in general, the general structure is

    #!/bin/bash
    
    # links that already exist
    links=$(mktemp)
    find . -type l >\"$links\"
    
    # remove from staging area first to not block and then annex
    git rm --cached --ignore-unmatch -r bin*
    git annex add -c annex.alwayscommit=false bin*

    # compare links before and after annexing, remove links that existed before
    newlinks=$(mktemp -u)
    mkfifo \"$newlinks\"
    comm -13 <(sort \"$links\") <(find . -type l | sort) > \"$newlinks\" &
    
    # rewrite links
    while IFS= read -r file
    do
        # link is created below .git-rewrite/t/ during filter-branch, strip two parents for correct target
        ln -sf \"$(readlink \"$file\" | sed -e 's%^\.\./\.\./%%')\" \"$file\"
    done < \"$newlinks\"

    git annex merge

which would be run using

    git filter-branch --tree-filter path/annex-filter --tag-filter cat -- --all

or similar.

* I'm using `find` to make sure the only rewritten symlinks are for the newly annexed files, this way it is possible to annex an unknown set of filenames
* If doing several git annex commands using `-c annex.alwayscommit=false` and doing a `git annex merge` at the end instead might be faster.
"""]]