I originally thought we needed to add module file inputs for modular deps at the same time as outputs because they depend on the lookupModuleOutput callback, but this is not the case: they only depend on the callback results for other modules, which have already been computed by this point. So move them earlier so that they're set in the CompilerInvocation at the same time as other inputs. This makes the code easier to understand.
This change is effectively NFC, though it technically changes the module exact value of the context hash.