relatively tiny documentation changes

Spec/vere/stage.txt refers to files and processes that do not exist anymore. If you'd like to step back a stage in vere you're doing it for wild archeological reasons anyway, and you'll be working in a version of the repository that has these instructions already.

doc/atoms.txt updated to clarify how Ints work in Hoon, as people have been confused by (issue #39).

Sorry that I'm making tons of tiny PRs but I think the repo is almost clean!