I would like to use git annex with github. Here what I did:

1. Create github directory "a". Added all the special remote and git annex files. Pushed them to the "a" using "git annex sync."
2. Fork the repository on gihub to "b". Clone it and enable remote and I could pull annexed files.
3. Added repository "a" as "upstream" tracking remote to "b".
3. Created a second special remote for "b". Added new git annex files to it. Used "git annex sync origin" to push the changed files to the forked repository "b".
4. Now I would like to create a pull request. What are branches I should create pull request for?  a:synced/git-annex vs b:synced/git-annex? Or, a:synced/git-annex vs b:git-annex? Do I need to create separate pull request for the "master"?

Thanks for the help.

 
