Allow customization in themes without overwritting

Currently we do, on pod initialization, a copy from our repository to the persistent storage of plugins and themes that we provide.

This not only overwrites any changes made by users (which can be valid for extending the usability of themes), but also undoes any automatic updates done to the plugins (that can be outdated on the image). This could be problematic if plugins are upgraded to versions that will break if downgraded again.

Due to all these reasons, I believe not force-copying of plugins and themes to be a better approach to the script copy.