[clang] Avoid reparsing VFS overlay files for module dep collector (#158372)
This PR uses the new-ish `llvm::vfs::FileSystem::visit()` interface to
collect VFS overlay entries from an existing `FileSystem` instance
rather than parsing the VFS YAML file anew. This prevents duplicate
diagnostics as observed by `clang/test/VFS/broken-vfs-module-dep.c`.