tests: add a test to make sure that patched specs can be round-tripped

- previously, if a concrete sub-DAG with patched specs was written out
  and read back in, its patches would not be found because the dependent
  that patched it was no longer in the DAG.

- Add a test to ensure that the PatchCache handles this case.

- Also add tests to ensure that patch objects are properly created from
  Specs -- previously we only checked that the patches were on the Spec.