Fixed degree of freedom calculation for 2D rigid bodies
Add support for logging momentum scaling factors from nvt_rigid
Fix bug: nlist.reset_exclusions() with empty arguments not working
Added missing synchronization statements for MPI_CUDA
Only update ghosts when necessary (when overlapping comm is off)
Extended unit test which should have caught the exclusions bug
Linked replicate documentation to command index

added replicate example
Merge add_nvt_logs

# By Matthew Spellings
# Via Matthew Spellings
* codeblue/add_nvt_logs:
  Add support for logging momentum scaling factors from nvt_rigid