Add missing ResolveKinds/ResolveFlows invalidates

Update the dependencies of transforms which empirically invalidate
ResolveKinds or ResolveFlows.

This was discovered with some to-be-committed work that automates
looking for incorrect transform dependencies. Specifically, the
deficient transforms were found to not invalidate ResolveKinds or
ResolveFlows, yet running ReslveKinds or ResolveFlows after these
transforms would result in modifications to the circuit.

The LoweringCompilersSpec was updated with patches to indicate the
location of these new transforms.

Signed-off-by: Schuyler Eldridge <schuyler.eldridge@ibm.com>