mosspa, I do not think you're a dunce at all.
Actually I wrote an issue report based on your post about the Rapture pdf manual so for future versions of Rapture and all our instruments we find a way to make all information for a plugin available easily. Whether the decision will be placing the pdf in the root or not I can't say, but your suggestion has been noticed.
Regarding z3ta+, the MIDI2CMP program which is used to translate MIDI into arpeggio files, removing all unused tags and stuff, was added in version 1.1, after the original release. z3ta+ comes from the old rgc:audio days, which I used to run. Back then, the User Manual remained unchanged for all the dot versions, and it was complemented with Release Notes for each new release. That was what we thought the most organized and simple way, as it provides all the information without forcing users to re-read the manual to find out what's new.
When you install z3ta+, the installer offers you the option to read the Release Notes for the version you installed. As with Rapture, z3ta+ will create a folder called 'Documentation', where the Release Notes document lives. Within that Release Notes document, there's a pointer to where you can find more information about how to create your own arpeggio files (which is inside the \Arpeggio folder). Needless to say, this is more a feature oriented to Sound Designers than End Users, and therefore it lives in some 'non mainstream' place.
It is all about a learning experience. When I released the first version of Triangle I, I created an installer which created many Start menu accesses. It turned out that most VST users did hate it, as VST plugins were thought as a 'simple dll' file which users would manually put in the right folder(s). Then, the shortcuts were considered 'invasive and abusive'. You can still find all those comments if you do a history search in the rgc:audio forum at K-v-R. Then, I changed the installer to be as minimalistic as possible. As weird as it might sound for nowaday's standard, a couple of years ago it was very common for users to have to install VST plugins by copying manually some files, and knowing the folder structure a plugin required wasn't really a strange demand.
Anyways, we do wish to give everyone the best information available in the fastest possible way at any time. I hope we find it is possible. But in case it's not, you can come here anytime for an answer
-René