[clang][deps] Add module files for input dependencies earlier

[clang][deps] Add module files for input dependencies earlier

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.

Differential Revision: https://reviews.llvm.org/D142392