rsync to homer is deprecated
New docs for setrun_amrclaw and bc
Moved some docs from visclaw, added flags, regions description
moved geoclaw rst files into doc/doc
removed visclaw_doc from index. Note that plotting examples in 1d and 2d have not been merged in.  Need to decide what to do with these.
renamed plotting to plotting_python.rst
improved some plotting docs
added docs on regression testing
new plotting.rst file summarizing options