Added BasisReconciliationTests to DPGTests, and added tests against 3D topologies to BasisReconciliationTests.
Added signatures to doubleBasisConstruction.
Added permutationMatchingOrder method.
Switched to using unsigned ints in RefinementPattern for some index values.  This meant changing a bunch of other methods, though I tried to limit the impact (i.e. I didn't always propagate the change to outward-facing API, and often still rely on implicit conversion from unsigned to int and back).