Default for saving per-job files

[mattwthompson]

• Not feasible to keep ALL intermediate files
• Do want to keep production trajectories (or at least some compressed/stride-reduced subset)
• Need to enable developers to see what jobs are potentially problematic
  • Often this is equilibration issues
  • Could track which jobs are slowest and keep some of those trajectories by default?
• Probably don't keep equilibration trajectories, but DO keep equilibration statistics (pymbar, OpenMM reporters)
• In general want to keep some provenance about MD settings (i.e. barostat or integrator)
• Save per-component analyses
  • i.e. enthalpy of mixing has multiple components, useful to save this