The webapp showed "(metadata only)" behind a repository. Running git annex upgrade in the repositories didn't change that. I had top to "upgrade" the repository under "edit" in the webapp to fix that.
What did upgrading in the webapp do, that running git annex upgrade did not?
This sets
remote.<name>.annex-ignoreto false in the git config.You would normally only see this if the remote server didn't have git-annex-shell installed so was only a git repository with no annex. If it then got installed, so you were able to use git-annex to store files there, this makes git-annex try again to use git-annex-shell in that repository.
The naming is unfortunate since it's not related to upgrading the repository version at all. I'll rename it to "Convert Repository".