V2 Make FileId type opaque and use consistently throughout project (#4307)

# Description of Changes
The `FileId` type in V2 currently is just defined to be a string. This
makes it really easy to accidentally pass strings into things accepting
file IDs (such as file names). This PR makes the `FileId` type [an
opaque
type](https://www.geeksforgeeks.org/typescript/opaque-types-in-typescript/),
so it is compatible with things accepting strings (arguably not ideal
for this...) but strings are not compatible with it without explicit
conversion.

The PR also includes changes to use `FileId` consistently throughout the
project (everywhere I could find uses of `fileId: string`), so that we
have the maximum benefit from the type safety.

> [!note]
> I've marked quite a few things as `FIX ME` where we're passing names
in as IDs. If that is intended behaviour, I'm happy to remove the fix me
and insert a cast instead, but they probably need comments explaining
why we're using a file name as an ID.