[ty] Restructure submodule query around `File` dependency
This makes caching of submodules independent of whether `Module`
is itself a Salsa ingredient. In fact, this makes the work done in
the prior commit superfluous. But we're possibly keeping it as an
ingredient for now since it's a bit of a tedious change and we might
need it in the near future.
Ref https://github.com/astral-sh/ruff/pull/19495#pullrequestreview-3045736715
