I don't think there is a documentation for the tools themselves, as they are pretty straightforward most of the time. It's mostly open/edit/save/close.
However the files they open usually have a complex structure and aren't really documented. The good thing is that you can also use them on Cyan files to learn.
Here are the files each tool opens:
PlasmaShop: - .age files (encrypted text file)
lists which PRPs are in the Age, along with a few information like sequence prefix and max number of player.
- .fni files (encrypted text file)
list of console commands to execute when linking to the Age. This is used most notably to set fog color and density.
- .sum files
simple list of "checksums". Checksums are used by the engine to determine if someone modified/hacked a PRP file. In other words: each checksum is a single number which sums up the content of the PRP. If you modify a single bit in a PRP, the checksum is completely different and the game refuses to load the Age.
It's an encryption thingy. All you need to know is that if you intend to do PRP hacking you should update the corresponding checksum after each modif, OR remove the checksum entry entirely.
- .sdl files (encrypted text file)
I think you are already a bit familiar with those some of the basics have already been explained in another topic.
- .pak files (python packages)
Stores compiled Python scripts. You can extract and decompile Python scripts, then repack them.
- .cfg, .dat, and a few others
PlasmaShop can open a few of those. Not all, but it's good to keep it in mind.
PrpShop: - .age files
This simply loads all the PRPs associated with the .age file. To view the actual content of the .age file, use PlasmaShop.
- .prp files
This is where PRP hackers like me have all their fun PRPs are binary files containing the Age's models, textures, logic, etc, and are generated by Korman or 3dsMax. PlasmaShop allows you to edit each object in a PRP using either an interface (when available), or an XML representation of the object. Remember: you can right-click each object in the left-hand view to bring more options.
I recommend trying Chacal's city modifications (on Uru CC only) to get the hang of the tool.
Remember that PRPs are extremely complex files, containing thousand of objects of hundred of different types, which were never documented (usually people just figure out on their own how they work, or ask on this forum for informations about those). It will probably be daunting at first depending on what you intend to do, but this is what allow you for instance to add new clothing items like you've been asking for recently (not for the faint of heart, once more...).
You'll probably notice some objects, like Python File Mods correspond to Korman NodeTree objects (but more complex).
(I also recommend to check Tools → show typeids to sort objects by order of importance)
VaultShop: this allows you to alter savegames. I don't know much about it, though, as I never used it.
So yeah, once more you'll probably have to find your own way by learning with the tools themselves and the files we got from Cyan.