It sounds like you have some permissions issues in your .git subdirectories. Most likely that is the result of running a git command as root. You should never do that. To fix that run
sudo chown -R wwadmin:wwadmin .git
in both the /opt/webwork/webwork2 and /opt/webwork/pg directories.
What is the output when you run:
git log -1 --pretty=format:%at
in /opt/webwork/libraries/webwork-open-problem-library
Also, what is the output when you run:
ls -l /opt/webwork/webwork2/htdocs/DATA
Are you still getting the messages about not being able to find the branch main in the remote origin in the webwork2/admin course? I suspect that you are. In fact, that is all anyone is ever going to get from the webwork2 update notification from now on it seems. Looking closer at this, it seems that the approach that has been used of having the server execute git commands to determine if upgrades are available is dead in the water. The server user (usually www-data on Ubuntu) can not run git commands on a repository it does not own. This is something that has changed recently with git. There may be workarounds to make it work, but none of them are secure.
I recommend that you disable webwork2 upgrade notifications. Set "$enableGitUpgradeNotifier = 1;" in localOverrides.conf.
Yes, I was still getting the messages, but I did turn off the upgrade notifications (I think you meant to write setting it equal to 0, not 1) and now they are gone.
Thank you again, Glenn, for all your help and suggestions.