FrogComposband has extensive help files, accessible in-game with the ? command; although they do not explain the differences between the individual chaos patrons, aside from one brief note regarding Chardros and Hionhurn. The help explains mutations as a concept; individual mutations are not covered in detail, but they're usually pretty self-explanatory. Almost everything about items is covered, especially in the dev version, but even the salmiak help has a ton of item content. (Inspecting items is also a good way to figure out what they do.)
