[protobuf] Handle cross-package references correctly in some buggy cases. #3561
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Closes #3534
Closes #3556
This PR adds cross-package resolution in some cases where it was missing.
In the case of operation inputs, missing effective model type calculation was causing some input types not to be resolved to external packages.
In the case of map value types, the calculation of the right hand side type did not correctly account for the possibility of the type being in another package, and it now uses the same machinery as other type references to instrument imports and cross-package references.
The existing scenario test has been extended to prevent regressions and also extended to test arrays for good measure, though those were working as expected.