Update log files for example inputs, part 1

Make compute stress/mop and stress/mop/profile compatible with per-atom masses

bug-fix for miscounting atoms for read_dump add keep

First chunk of collected small fixes for the stable release

fix memory issue in POEMS library, where auxiliary data was cast to a data structure of different (smaller) size when deleting.

this commit adds support to a callback function that allows to delete aux data in the Tree with its native size.

remove USER-OMP version of fix nphug, which had intermittant and difficult to track down memory corruption issues with multiple threads.

fix plumed memory leak

Fix bug in lib/plumed/Install.py, some small cleanup and support parallel compile of plumed sources