Documentation cleanups.

Documentation cleanups.

Specifically:
  * Escape *nix -> \*nix, because the bare * looks like an emphasis
    start mark.
  * Use :file:`...` to denote files.
  * Fix FHS reference '_ ..' -> '.. _'
  * Add a link to Sphinx's markup extensions.
  * Remove superfluous "Hooke" from section titles.
  * Use correct section linking:
      X.txt -> X
      :doc:`X`
    see
      http://sphinx.pocoo.org/concepts.html#document-names
      http://sphinx.pocoo.org/markup/inline.html#role-doc
  * Use two spaces (not one) at start of sentences.
  * `code` -> ``code`` (the way I had things originally :p).  See
      http://sphinx.pocoo.org/markup/inline.html#role-samp