Was tearing my hair out trying to get git-annex to pair and sync between my laptop and desktop — lots of Permission denied (publickey) lines in the logs. Finally found and deleted the existing keys in the ~/.ssh/git-annex directory. Starting fresh repositories worked perfectly after that.
Also worked out that the configuration used by git-annex-webapp lives in ~/.config/git-annex and each repository's config lives in .git/annex. That helps a lot for clearing up my experiments so I can start afresh.