Does the wiki that installs with a GitHub repo support directories? Our wiki is cluttered with pages, and we are looking for a way to organize them better.
We tried pulling the repo, creating local directories, and moving things around, but when committed back, the wiki didn't pick up the changes.
I was having the exact same issue and tried variants of what you tried. Nothing stuck. Asked GitHub support about it and received a reply that essentially said "No, but we'll let the developers know that people are interested in this feature."
So the short answer is "No", and the long answer is "No, but maybe in the future."