I would like to use git-annex to synchronize 2 directories in the same manner as unison.
I'm starting with 2 directories. There is an overlap of the same set of files in each directory, but each directory also has additional files as well.
I create a git annex in each directory but when I do a git pull it merges and produces conflicts on those files that are the same.
What is the correct workflow for this type of scenario?
Are the files identical or different? I today did something like that with similar, but not identical directories containing media files, and git happily merged them. but there, same files had same content.
Also, make sure you use the same backend. In my case, one of the machines runs Debian stable, so I use the WORM backend, not the SHA backend.
I'd recommend using the SHA backend for this, the WORM backend would produce conflicts if the files' modification times changed.
syncing non-git trees with git-annex describes one way to do it.