Improve navigation & structure of documents

Presently, the new RTD contents list in the sidebar is more or less unusable:

https://www.dropbox.com/s/bl36v087cza6r7v/Screenshot%202014-07-14%2014.48.21.png (image)

The new version looks like:

https://www.dropbox.com/s/soiv9iq4vss1v9k/Screenshot%202014-07-14%2014.49.50.png

The expanded table of contents still appears in the main index page.

conf.py has also been updated to use the new RTD theme locally, if the user has it installed; if not
it will use the built-in theme as usual.

Also includes miscellaneous minor corrections.
Backports documentation restructure from develop

Commits:

52a480beec529955cf2ebbd618666520c238ad39
ea6e46ef874a76b9eebd8d7de8db6782f1d01806
Merge pull request #3307 from evildmp/documentation-backport

Restructure documentation and improve contents tables (backport)