moved reading of init file from crop to init.for in 2DSOIL
Moved reading of init file to 2dsoil (init.for); added variable to flag output to soil files. if no output, soil files won't be created; cleaned up some other variables
had a half completed line of code I had to remove
added some variables for tracing carbon flow
reduced the amount of additional carbon that can come from the shoot carbon to augment root growth under water stress after  grainfill. Only 75% of total shoot carbon is available.
changed minimum RH back to 10%
reduced staygreen parameter to speed up senescence
added variables to track carbon flow when debugging
fixed allocation from C_pool to C_reserve at midnight. Previously (if time==0) did not trigger if block because float time was rarely equal only zero

Also reduced the calculation of reservePart to the difference between shootPart and all the other partitioned organs (sheat, leaf, ear, shoot). Previously we were over estimating reservePart such that total carbon allocation was more than shootPart. The parition component inf Grant, 1999 needs to be revisited.
Merge remote-tracking branch 'origin/master' into WorkingCopy

Conflicts:
	Crop source/gas_exchange.cpp
Merge pull request #15 from ARS-CSGCL-DT/WorkingCopy

Working copy