Small doc cleanups:

- Fix order of ')' and '.' in a bunch of places

- Remove last reference to "smart packages"

- Fix an Atmosphere link

- Linkify a bunch of other things (CoffeeScript, npm, GitHub bug tracker, etc)

- Added a newline after the dot in "`meteor`. `meteor`".  It looked way more
  like `meteor.meteor` when rendered.

- Name `api.add_files` explicitly.

- Fix capitalization of GitHub

- Explain how weak deps check if the dep is there

- A few other typos