Modify hcana.param and hmsflags.param to use the
  latest matrix fit.

Modify pcana.param and shmsflags.param to use the
  latest matrix fit.

Modified standard.kinmatics to set ptheta_lab and ppcentral
Modified pcal.param to eliminate stuff left over from when used in standalone
Modified shmsflags.param to eliminate ppcentral and ptheta_lab which should be set in standard.kinematics
Modified phodo.param to have better time offsets and set cosmicflag.