Currently the shared pywikibot seems nonexistent on labs, version file indicates an update at 12:06 utc today, but the rest of the framework seems to be erased.
I manually ran the crontab, and this seems to have fixed it (at least for now). The underlying issues seems to be something like this:
The code to update runs:
# Current version of core cd /data/project/pywikibot/public_html/ rm -rf core/ git clone --depth 1 https://gerrit.wikimedia.org/r/pywikibot/core.git
but the log file reports
rm: cannot remove `core/pywikibot': Directory not empty fatal: destination path 'core' already exists and is not an empty directory.
so somehow it can't delete all files (specifically, that version file?), and git clone refuses to clone into the non-empty directory.
OK, I think PR will fix the issue for now. Feel free to merge it. I know it's not best option possible. That's why I made some more changes but they are too radical to be deployed directly. So, I put it in here. Please check it and if you liked it, put it in the repo. New bash file. I think it has some issues with zipping files.