SideSetsAroundSubdomain runs with ParallelMesh.

The algorithm doesn't use flood().

Refs #2129.
rz cylindrical gap conductance capability comments incorporated per #3142
Fixing warnings.

Refs #1777.
Fixing overloaded virtual warning.

@friedmud, I think the threadJoin() function prototype was wrong,
it took a UserObject reference before... this was also part of the
warning and is addressed by the patch.

Refs #1777.
Made meshChanged a virtual function #3163
Merge pull request #3164 from jwpeterson/warnings

Fixing warnings.
Merge pull request #3146 from novasr/feature_3142

rz cylindrical gap conductance capability per #3142
Merge pull request #3165 from snschune/feature_3163

Made meshChanged a virtual function
CISRO - closes #3170
Merge pull request #3171 from permcody/CISRO_fixes

CISRO - closes #3170
Re-apply removal of AuxBCs (#3021)
Minor tweaks related to internal applications
{#3021)