DISCLAIMER: These notes are from the defunct k8 project which precedes SquirrelJME. The notes for SquirrelJME start on 2016/02/26! The k8 project was effectively a Java SE 8 operating system and as such all of the notes are in the context of that scope. That project is no longer my goal as SquirrelJME is the spiritual successor to it.
Thinking about the package manager stuff, the singular set of paths would make my current plans not possible. My plan is to have user-only packages, then packages for the local system, then remotely managed packages. In a live CD sense, the remote area will just be the CD mounted at that specified point while local will either be on a disk somewhere or existing in memory. Installing the system is as simple as copying files and setting up a boot loader to load the system.
The addition of a special cross zone makes things easier as I can setup a cross system without magical chroot magic.
Another thing I can do is require a date code for the k8 help snippets so that say if they get translated in the future (this is the help documentation) if the source stuff has been changed then the newest information is always shown. So this would be sort of a mini version control thing of sorts.