Force-stop shouldn't be what drops the www. The repo reset should only happen during the git push process. Otherwise I don't think it touches what's in the repo dir.
In any case, I think all of the stuff in the www folder should probably be moved to the data directory, so it doesn't get wiped regularly. I just haven't done it yet; partly because I didn't know exactly where I would put it.
Feel free to make a change to put it where you want it, and then send a pull request.