What is writing all these files and folders to my Documents?
A few things for you to try: 

Per this SO link, do lsof path-to-filename to list all processes accessing that file. There's also a frontend to lsof called Sloth. The problem with this is if the programme doing the writes only edits the file momentarily (like if it did touch foldername) then you probably wouldn't see it, since lsof only lists current processes' access to the file.

Alternatively, get FSeventer (direct download link from archive.org - in my (klanomath's) opinion the only reliable source), which graphically monitors filesystem IO events. You could probably set it to run on your documents folder and then wait for one of those writes to happen, although based on your description that may take a while. The website for FSeventer seems to be down right now :(, but if/when it goes back up it may be able to solve your problem. FSeventer isn't really ElCap ready and often fails to work after the first launch - usually it works after launching it a second time.