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.

In T126666#2021312, @Ladsgroup wrote:

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.

The "fix" you have found looks like a workaround for T106170: Attribute cache issue with NFS on Trusty