It seems to be working again, after some extensive fixes (see below). Can anyone confirm, or tell me what's missing?
[tech details]
I've done some extensive merging, and an aggressive git history rewrite removing a particular problematic (empty) page.
It seems like the auto-merging functionality of Waliki tries to commit changes to pages in history on top of the pages' last change, resulting in a weird branching/merging model. A merge conflict then leaves the wiki in a detached state in ancient times. I don't really understand the history functionality, but it seems to get confused by these automatic plus my manual merges.
[/tech details]
Either way, the problematic file is removed, and a issue has been posted on the waliki repository. Let's hope it keeps working smoothly now.