Latest changes while preparing ASTMH talk.
Prior to ASTMH.
Changes made in Washington.
Several bugs:
 - wrong treatment of age classes: no infants in the surface code. Fixed
in Batch__TreatmentSep2.R 
 - Allowed L to be not at equilibrium in ...Sep2.R. 
 - Bad handling of state vector in treatmentRun md all previous output
wrong.
Correct some more bugs in the separatrix scripts, such as the incorrect
calculation of mortality rates from the survival curve in Time series
plotting script.
Merge remote-tracking branch 'choose_remote_name/master'
TreatmentSep3.R - does 3 rather than 4 age groups. 
		- also generates a primitive log file. 
Deleted TreatmentSep.R.
Added some code to inference bit.