[[!comment format=mdwn
 username="https://www.google.com/accounts/o8/id?id=AItOawln3ckqKx0x_xDZMYwa9Q1bn4I06oWjkog"
 nickname="Michael"
 subject="git checkout --orphan"
 date="2013-07-19T17:49:37Z"
 content="""
Instead of rebase, --orphan seems to be the right answer for pruning history: create a new git-annex orphan branch and git add and commit the files. So:
<pre><code>

git status 

# verify there are no uncommitted or untracked files

# master branch
git branch -m old-master
git checkout --orphan master
git add .
git commit -m 'first commit'

# git annex branch
git branch -m git-annex old-git-annex
git checkout git-annex
git checkout --orphan git-annex
git add .
git commit -m 'first commit'
git checkout master

# at this point, you may want to double-check that everything is still OK

# finally, remove branches and clean up the objects:
git branch -D old-master old-git-annex
git reflog expire --expire=now --all
git prune
git gc

</code></pre>

The repo remains functional and .git is smaller.

"""]]