add number of bonds as an additional per atom compute
need to check against local indices not tags in fix bond/create to be consistent with the code in neigh_bond.cpp otherwise the same bond gets created indefinitely.
added prototype code for reading default settings from .lammpsrc
incorporate bugfix from rolf isele-holder for stalled communications on empty domains
added code to read and parse .lammpsrc files, but cannot apply them yet.
some clarifications to QM/MM interface code
remove redundant code in read_data for extra properties

the same change was applied a few lines above this location
in the upstream version and thus this is no longer needed.