The Git for Administrators page describes a rather convenient way to maintain Moodle by checking it out of git. It also has information about installing extensions similarly, which is the way I use.
However, for that to really work well, the extensions in question should have a stable branch for checking out (because you probably don't want to end up with a WIP state of the extension). Simple Clock doesn't, hence this issue.
Please create a `MOODLE_31_STABLE` or similar branch in your repository, and only push changes to that branch upon releasing a new version. Thank you!