[red-knot] Simplify virtual file support (#13043)
## Summary
This PR simplifies the virtual file support in the red knot core,
specifically:
* Update `File::add_virtual_file` method to `File::virtual_file` which
will always create a new virtual file and override the existing entry in
the lookup table
* Add `VirtualFile` which is a wrapper around `File` and provides
methods to increment the file revision / close the virtual file
* Add a new `File::try_virtual_file` to lookup the `VirtualFile` from
`Files`
* Add `File::sync_virtual_path` which takes in the `SystemVirtualPath`,
looks up the `VirtualFile` for it and calls the `sync` method to
increment the file revision
* Removes the `virtual_path_metadata` method on `System` trait
## Test Plan
- [x] Make sure the existing red knot tests pass
- [x] Updated code works well with the LSP
