This is really for Bob, but if anyone else wants to take a crack at it, there's a branch under CmdStan called: feature/issue-4-standalone-doc.
Inside, I've put up a placeholder for the CmdStan guide under src/docs/cmdstan-guide/.
I've already pieced together the makefile under this branch so typing:
make manual
will automatically build both the Stan manual and the CmdStan guide and place it under doc/ with the appropriate version number.
Daniel