split regions checking out of flag2refine2.f90 and into new routine flagregions.f90.
Still need to call this routine from appropriate place.
setrun to test regions
bug fix in new regions code
added call to new flagregions routine
valout.f with binary output copied from rjl-omp-tests branch, but with bugs when outaux==True
in middle of reorg, recovering richardson
part of reorg
Improved flagregions as flagregions2 - loop over regions
fixed binary output of aux arrays
test swirl with new regions
richardson working with spatial gradients. still needs more cleanup
richardson working with spatial gradients. still needs more cleanup
increased max1d for tsunami problem
Temporary fix to colate2 due to integer overflow with 7 levels
cleaned up richardson
Merge remote-tracking branch 'upstream/master' into regions

* upstream/master:
  simple bug fix for counting larger than kind 1
cleaner Richardson error estimation using stack based arrays
larger formats to avoid output conversion error
changed length of rstfile variable for full path cases
larger format statements for WA run