Okay so say you are on a clean porteus system freshly installed. I install Gparted which has a few dependencies.
This is what is required to be installed:
gparted-0.12.1-x86_64-1sl --> porteus repo
atkmm-2.22.4-x86_64-1sl --> porteus repo
cairomm-1.9.8-x86_64-1sl --> porteus repo
gtkmm-2.24.0-x86_64-1sl --> porteus repo
glibmm-2.27.99.2-x86_64-1sl --> porteus repo
pangomm-2.28.1-x86_64-1sl --> porteus repo
libsigc++-2.2.9-x86_64-1sl --> porteus repo
All of these modules are placed into the root of the modules folder, This eventually leads to a very messy modules folder. I have thought up a few ideas that could tidy this up, two in particular I like best for different usage applications so I will discuss them.
The first one would be for a desktop system where porteus would be stored upon a usb drive or a hard drive.
This also has two branching ways of doing things, one being more static and standard the latter being more dynamic and flexible. The boot up would need to ignore symlinks in order for this to work correctly.
A) Have all packages be within their own folders and organized via preflagged categories, I purpose that dependencies are symbolically linked to where they are located within the required programs folder. Thus dependencies are simple to track on the system.
1) CLI - More Splits in Categories and then folders with program names, dependencies are symlinked for simple CLI or file browser tracking.
2)GUI - More Splits in Categories and then folders with program names, dependencies are symlinked for simple CLI or file browser tracking.

in the case of gparted the structure would look like this:
$MODULES/gparted/gparted*.xzm
$MODULES/gparted/atkmm/atkmm*.xzm
$MODULES/gparted/atkmm/depends/symlinks
$MODULES/gparted/atkmm/required/symlinks
$MODULES/gparted/cairomm/cairomm*.xzm
$MODULES/gparted/cairomm/depends/symlinks
$MODULES/gparted/cairomm/required/symlinks
$MODULES/gparted/gtkmm/gtkmm*.xzm
$MODULES/gparted/gtkmm/depends/symlinks
$MODULES/gparted/gtkmm/required/symlinks
$MODULES/gparted/glibmm/glibmm*.xzm
$MODULES/gparted/glibmm/depends/symlinks
$MODULES/gparted/glibmm/required/symlinks
$MODULES/gparted/pangomm/pangomm*.xzm
$MODULES/gparted/pangomm/depends/symlinks
$MODULES/gparted/pangomm/required/symlinks
$MODULES/gparted/libsigc++/libsigc++*.xzm
$MODULES/gparted/libsigc++/depends/symlinks
$MODULES/gparted/libsigc++/required/symlinks
Next you install a program that depends upon both gtkmm and glibmm.
$MODULES/proggy/proggy*.xzm
$MODULES/proggy/depends/symlinks >> $MODULES/gparted/gtkmm && $MODULES/gparted/glibmm
$MODULES/gparted/gtkmm/required/symlink && $MODULES/gparted/glibmm/required/symlink >> $MODULES/proggy
The second suggestion would be more for a server setup using NFS and this is modules within modules. Doing so you can have a centralized module location in one place and have many different machines connect to those modules and load them via network to the decentralized location. I could see this being useful for a business or school network. modify packages in one location, reload the machines and the changes are reflected upon all of them.