Fixed merge conflict
Minor changes to graphics routines
Removed cubes from plot;  Draw contour lines is now in afterframe
Fixed Matlab routines
Added surflight; removed extra setpatchborder commands
Fixed graphics routines
Modified setplot3.m, afterframe.m.

  * Added a flag2refine.f file to try to get refinement to show up. based refinement in pressure gradient.
  * Modified Makefile to add flag2refine.f
  * Removed fort.* files that probably shouldn't be tracked.
  * Modified setrun.py to change tolsp.
Removed debugging flags
Added OutputDir='_output' so that fort files are found.
Added Matlab files
Added setplot2.m and afterframe.m for Matlab graphics
Fixed afterframe so that only non-empty levels are passed to the legend command
Added shg; don't draw noisy contour levels
Changed final time and number of output files to original settings
Show under/over shoots in swirl example
Added Matlab files for annulus example
Added Matlab files to 2d quadrants example
Merge pull request #78 from donnaaboise/3dSrcAndExamples

I'm merging this in since the examples run so we can move forward and sync up, but we need to sort out the refinement issue mentioned on PR #75.
fixed merge conflict in examples/advection_2d_swirl/setrun.py
Merge pull request #79 from rjleveque/donnaaboise-2dExamples

Fixed a merge conflict in @donnaaboise 2dExamples PR#76