Acuru, you're right. We will update wiki page to clearly describe that CPK/MPK are just a ZIP archive with no compression and they should contain files directly, not in an extra subfolder.
Regarding the mod bundles - we have plans for this in CryoFall. Perhaps, we will port this feature back to VoidExpanse (core engine part of the games are shared, but VoidExpanse will require several non-trivial engine/UI modifications to support this feature).
Basically, the idea is to have our own mods repository at AtomicTorch.com with fast CDN (Azure or Amazon) where anyone will be able to upload their mods with our Mod Uploader tool (the same tool as our Steam Mod Uploader, but modified to work with AtomicTorch.com CDN instead and, perhaps, ported to Linux/Mac to smooth out the process for everyone).
The game will be able to download a mod by its ID and version number and install/activate automatically accordingly to the game server configuration. This is necessary as there will be many modded servers and manual installation/updating of mods on the client is something we want to avoid.
With this architecture, the mods bundle is trivial to implement - it will contain just a single XML manifest file with the bundle information (id, version, title, author, description, date) and the list of mods (with their versions) in the order of activation (plus an icon for the bundle, but nothing more). So the game client and server will be able to automatically download all the required mods from the list and install/activate them.
