Packaging themes and plugins for Habari based applications

[TexasMynsted]

What is the typical way that folks bundle or package together plugins and themes when creating a Habari based application?

I am still not clear about the Habari bundle idea, so until I better understand that perhaps something like the following?

A git repository with submodules for each plugin and theme needed for the habari based application.  It would be simplified if this could be created in a new tree like:

habari
   ├──user
   │    ├──plugins
   │    └──themes      
   ├──system
   │    ├──plugins
   │    └──themes
   └──myapp
        ├──plugins
        └──themes
         
Is there a way to alter the tree like this (and have Habari correctly load the new plugins and themes)?