[MSFT] [Module] Use `modifyPorts` instead of previous `removePorts` and `addPorts`

[teqdruid]

HWModule has a modifyPorts method which we just added to MSFTModule. (It actually uses hw::modifyPorts since the ops are compatible in that regard.) Make all the old code use that method (or one of the two convenience ones in HWMutableModuleLike) instead of the old ones.