[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

crates/ruff_db/src/system.rs

@@ -63,9 +63,6 @@ pub trait System: Debug {
     /// representation fall-back to deserializing the notebook from a string.
     fn read_to_notebook(&self, path: &SystemPath) -> std::result::Result<Notebook, NotebookError>;
 
-    /// Reads the metadata of the virtual file at `path`.
-    fn virtual_path_metadata(&self, path: &SystemVirtualPath) -> Result<Metadata>;
-
     /// Reads the content of the virtual file at `path` into a [`String`].
     fn read_virtual_path_to_string(&self, path: &SystemVirtualPath) -> Result<String>;