d
housekeeping
Merge branch 'develop'

Conflicts:
	conf/midway.cf
	conf/midway.xml
Parallel merge as part of Swift workflow
Refactor command line arguments, and instead pass param file directly to apps
Merge branch 'develop'

Conflicts:
	bin/combine_ascii.sh
	conf/midway.cf
	conf/midway.xml
Formatting
Set wrapperlog always transfer = false
Documentation for running on Midway and debugging
Added description of output files
update readmo

a few changes to the readme regarding the params file
Update README.md
Add tar_inputs to params descriptions
Formatting
Add site definition for midway-long, with longer walltimes, and limiting it to 1 task per worker
Set heapmax limits and foreach.max.threads
Adjust max threads
Small fixes to camp2json.py and jsons2dssat.py to handle three-digit nyers and numbers in variable names
Removed setting co2 to M in jsons2dssat.py
simple cleanup
Reverting to Swift 0.94 to workaround caching issues
Doc updates
Add a new activity plot script that measures active, stageins, and stageouts