fixes extractIntegratedMass to involve V_ff and advective velocity explicitly.
got rid of stub files which were confusing.
removing deprecated, generalizing and renaming others.
adds lp inputs for other formulations.
moving the inputs around so they have a more uniform naming convention.
unifying the input files.
more uniform test specs
Merge branch 'develop' into input_org
turns on solubility limitation in mcII
turns off containment in mcII
turns off containment in mc cases
turned on sorption limitation in mcIII
turned on sorption limitation in mcIII and both kd and sol in mcIV
turned on sorption limitation in mcIII and both kd and sol in mcIV
adds optional reference diffusitivity sol_lim, and k_d params
not finished, started implemented reference and relative data params. going to leave it as is for now.
moving ref and rel out of materialdb
making a table id that incorporates the ref ids
make defaults in header not cpp
make defaults in header not cpp