deleted duplicated setup.py
added other options for specifying transverse solver choice in 3d, e.g. 'all' or 2 give same as 22
Merge pull request #62 from rjleveque/transverse3d

 Added 3d transverse options to data.py
pass num_dim into RegionData and GaugeData to print error if num_dim==3
Merge pull request #63 from rjleveque/rm_3d_gauges_regions

pass num_dim into RegionData and GaugeData to print error if num_dim==3
Remove extraneous include directives

Remove the duplicate paths from the MODULE_PATH variable that were causing
extraneous include directives on every compile line.  This was accomplished
by using the sort command so there is a chance that something might get mucked
up in the order of the includes but that should not matter for Fortran unless
one is using replacement modules with the same name.  May add a better solution
to this later.
Merge pull request #49 from ahmadia/rm_setup

deleted duplicated setup.py
Merge pull request #64 from mandli/rm-extra-include-directives

Remove extraneous include directives
Fix '==' output format bug
Merge pull request #65 from mandli/fix-setrun-templates

Fix '==' output format bug
added script to convert README.rst files to README.html.  Needs more work...
Need to run 'make .htmls' first to create html files, links to clawpack style, css files, etc. are currently broken in clawcode2html.py
convert_rst2html.py: check for missing .rst file and don't include _output or multiple _plots directories in list
Merge pull request #66 from rjleveque/convert_rst2html

Script to convert README.rst to README.html in application directory
improved scripts to convert README.rst and code files to html
renamed convert_rst2html.py to convert_readme.py and added clawicon
Merge pull request #67 from rjleveque/convert2html

Improved scripts to convert README and code files to html
Add -I flag if INCLUDE variable set
Merge pull request #69 from mandli/include-flag-bug-fix

Add `-I` to the front of the environment or Makefile defined `INCLUDE` variable
added touch to rules for making .mod files
Merge pull request #70 from rjleveque/touch

added touch to rules for making .mod files