improvements to AMR description suggested by @mjberger
added page on converting README and code to html pages
fixed section head
merged changes from master
copied netcdf.rst from clawpack-4.x. May need updating?
added info on how to avoid overwriting gauge output when doing a restart
added documentation on algorithms and user-provided routines -- started describing Riemann solvers in 1d.  Still need to describe 2d and 3d solvers and transverse.
added warning about dtopo problems
Merge pull request #45 from rjleveque/updates3

Updates to docs