Clarify how HLS is supposed to access information about files

At the moment it's a little unclear how HLS (rules, plugin handlers, everything really) is supposed to access information about files.

We have two possible sources of information:
- The VFS
- The filesystem

Where do we look? What do we do if something is not in the VFS?

After some discussion on IRC, @fendor and I came to the following conclusion:
- The point of the VFS is to handle _files that are managed by the client_, and whose content may differ from the filesystem.
- For files that are _not_ in the VFS, and hence not managed by the client, it is totally fine to get them from the filesystem.

See also the prose in the spec: https://microsoft.github.io/language-server-protocol/specifications/lsp/3.17/specification/#textDocument_didOpen

However, at the moment, we are most often using e.g. `getFileContents`, which _only_ reads from the VFS. That might be fine (it avoids doing filesystem IO, which might be desirable), but it should be very obvious. There is a function that falls back to the filesystem, the confusingly named `getSourceFileSource`, but it's not as widely used.

We should clarify the situation and try to make things more consistent.