prevent reordering for simple ph_test runs

Conflicts:
	test/ph_test.cc
use 1-based indexing for global node numbers
use upward model adjacencies to get attributes
fix typo in boundary connectivity code
fix some bugs in phasta BCs

Apparently "comp 1" should be "comp1",
likewise for comp3. Also, IBC bits were
not initially zeroed, now they are.
There still remain inheritance issues...