Variable::sys() is now Variable::system()

This commit throws in a couple fixes for uncommon compiler warnings
SolutionTransfer fix for dof_id_type!=unsigned int
Various int size changes, warning fixes

Fixing -Wconversion is incredibly tedious, but so far it's been the
only thing that caught multiple "this would have broken us as soon as
we topped 2 billion elements" bugs at compile time.  I don't want to
catch those bugs at run time.

Some -Wshadow fixes are mixed in here.
Unit test uses processor_id_type now
Fix for previous getpot commit

I had an off-by-one error...
Fix for dof_id_type==int16_t failure

This actually could have manifested with the default
dof_id_type==int32_t, if anyone had tried to run more than a few tens
of millions of dofs on Laspack