Initialize caches for packages and standalone files (#5237)
## Summary
While fixing https://github.com/astral-sh/ruff/pull/5233, I noticed that
in FastAPI, 343 out of 823 files weren't hitting the cache. It turns out
these are standalone files in the documentation that lack a "package
root". Later, when looking up the cache entries, we fallback to the
package directory.
This PR ensures that we initialize the cache for both kinds of files:
those that are in a package, and those that aren't.
The total size of the FastAPI cache for me is now 388K. I also suspect
that this approach is much faster than as initially written, since
before, we were probably initializing one cache per _directory_.
## Test Plan
Ran `cargo run -p ruff_cli -- check ../fastapi --verbose`; verified
that, on second execution, there were no "Checking" entries in the logs.
