Errors after moving to multisite set up

[efeefe]

Hi all... I recently migrated my GRAV website to a multisite setting, and I am having trouble making gitsync work. I tried running the wizard and seemed to get it reconfigured correctly. But when I try to run the sync I get the following error:

On branch master Changes not staged for commit: (use "git add ..." to update what will be committed) (use "git restore ..." to discard changes in working directory) (commit or discard the untracked or modified content in submodules) modified: plugins/problems (modified content) modified: themes/quark (modified content) no changes added to commit (use "git add" and/or "git commit -a")

During the migration I removed some unused themes and plugins, and that seems to be showing here. Should I SSH to the server and try to fix it there? If so, in what folder would the git setup be initialized typically?

Thanks for your help.

[efeefe]

Update: I have removed the two submodules that were giving me trouble. Now I don't see errors when running git-sync, but in effect it's not syncing. I noticed that the wizard generates a config file that points only to sync folders in the usual location (user/pages, user/plugins, user/themes). Then I tried editing that file manually, clearing cache and running gitsync. Again, it does not throw any errors but is effectively not syncing with the remote repo.