I am restarting my whole Factions based server. It's running 1.8.8 PaperSpigot and I need to reset Factions, Economy, player homes, while NOT resetting McMMO or ranks / permissions.
Well you probably need to figure out where that information is stored. I'm guessing its in the plugin folders for those specific plugins. You can probably just delete them. If you want to be safe, save your configurations for those plugins, delete the jar and folder for them, and redownload them. That should wipe them. Don't forget to save the configuration files if you don't want to reconfigure them again.