I tried installing git-annex yesterday to backup my files. I ran git annex add . in the root of my repository tree and then a git commit. So far everything is fine.
What I didn't know git-annex was doing was turning my entire file tree into a whole bunch of symlinks. Every single file in my whole tree is now symlinked into .git/annex/objects! This is messing up my application which depends on files not being symlinks.
My question is, how do I get rid of git-annex and restore my file system to its original state? For a normal git repo I could do rm -r .git, but I'm afraid that won't do the job in git-annex. Thanks in advance.
Okay, so I stumbled upon some docs for git-annex, and they give two commands that achieve what I wanted to do:
unannex [path ...]
Use this to undo an accidental git annex add command. You can use git annex unannex to move content out of the annex at any point, even if you've already committed it. This is not the command you should use if you intentionally annexed a file and don't want its contents any more. In that case you should use git annex drop instead, and you can also git rm the file.
uninit
Use this to stop using git annex. It will unannex every file in the repository, and remove all of git-annex's other data, leaving you with a git repository plus the previously annexed files.
I started running git annex uninit, but my god was it slow. It took about 5 minutes to "unannex" just a single file. My filesystem tree is about 200,000 files, so that was just unacceptable.
What I ended up doing was actually surprisingly simple and worked well. I used the cp -rL flags to automatically duplicate the contents of my file tree and reverse all symlinks in the duplicate copy. And it was blazing fast: around 30 seconds for my entire file tree. Only problem was that the file permissions were not retained from my original state, so I needed to run some chmod and chcon commands to fix up the permissions.
This second method worked for me because there were no other symlinks in my schema. If you do have symlinks in your schema beyond those created by git-annex, then my little shortcut probably isn't the right choice for you, and you should consider sticking with just git annex uninit.