You could definitely include them in the same repo. In your local, put the renamed repos in your nodebb/node_modules folder. (make sure you change the name in their package.json and plugin.json too) Then put an exclusion in your .gitignore for that directory, example !node_modules/nodebb-theme-my-persona then git add node_modules/nodebb-theme-my-persona and when you push your changes, it should include the plugin.
What you set in the ACP is saved in the database, so it should persist. For user uploads, you should be using an external service like imgur, or the uploads may not persist between pushes.
