[clang][deps] Don't prune search paths used by dependencies

When pruning header search paths (to reduce the number of modules we need to build explicitly), we can't prune the search paths used in (transitive) dependencies of a module. Otherwise, we could end up with either of the following dependency graphs:

```
X:<hash1> -> Y:<hash2>
X:<hash1> -> Y:<hash3>
```

depending on the search paths of the translation unit we discovered `X` and `Y` from.

This patch fixes that.

Depends on D121295.

Reviewed By: dexonsmith

Differential Revision: https://reviews.llvm.org/D121303