Clean up toctrees

[ketch]

This is an attempt to make the hierarchy of the docs a little bit clearer and at the same time deal with all warnings currently being thrown by sphinx.

Embed TOC for AMRClaw, GeoClaw, etc. in pages dedicated to them
and reduce the length of the main TOC in contents.rst.

Add :orphan: tag to pages not listed in any toctree, so that
sphinx doesn't complain about them.

Various other improvements to the documentation.

I deleted flag.rst since it is included completely in refinement.rst.

[ketch]

After these changes, the only remaining warnings from Sphinx are #153 and #154.

[ketch]

Since nobody has objected, I'm going to go ahead and merge this because my next step is to start including Jupyter notebooks in the docs via nbsphinx, and both of these involve substantial changes and I'd like to avoid dealing with conflicts.