I'm trying to set up an archive instance of our production Moodle. Production is on 2.8.6. I've successfully installed it on the MOODLE_28_STABLE branch. I ran the admin/cli/upgrade.php script just fine.
The issue is that I have several plugins that I need to add. So I follow the git checkout instructions, and then try running the upgrade script. It fails with an error complaining about wanting to downgrade the plugin. See http://pastebin.com/VqAK0Ra4 for what happens with I try to install mod_certificate. I've also run into this issue with hsuforum and questionnaire.
If I don't run the upgrade script, the plugins page says "Higher version already installed!" in the status column.
Our production instance is on Moodlerooms. Did they use an updated version of the plugins that is newer than the MOODLE_28_STABLE branch?
My server is running Ubuntu 14.04 and php 5.5.9.