NFC: Clean up construction of IntrusiveRefCntPtr from raw pointers for llvm::vfs::FileSystem. (#151407)

This switches to `makeIntrusiveRefCnt<FileSystem>` where creating a new
object, and to passing/returning by `IntrusiveRefCntPtr<FileSystem>`
instead of `FileSystem*` or `FileSystem&`, when dealing with existing
objects.

Part of cleanup #151026.

NOKEYCHECK=True
GitOrigin-RevId: 9ddbb478ce11e43ae18aa6d04937a51621021482