Add test cases to show bugs are fixed

* octahedron adds a fully trilinic test case
* dd121 adds a test case that will default to more
  ranks in a direction other than X (here, Y)

The reference data is generated with a "last known good" patch from
release-5-0 from before the fix for #1631 was introduced, not that it
really matters. The reference build is unaffected by any of the bugs,
because it runs single-core.

Refs #1631, #1656

Change-Id: I46c63a91aaae19a37bbe39e0c973cb9888019591
Add test cases for FE+Verlet

One modifies a test case to test the VV integrator, another modifies
a test case to use LINCS instead of SHAKE.

Refs #1647

Change-Id: I090172d475b1c7224e18a52e72767999ce99bf7f
Merge branch 'release-5-0'

The transformAtoB test has already been converted to LINCS in master, so
the transformAtoB-lincs test (which would now be duplicate) has been
removed.

If we need a shake test case that should be added back in a new commit.

Also updates the complex/position-restraints reference warnings.

Change-Id: I38fb725e2a15f4cf5f7952d8a6a2222b71b0b21e