[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/memory_fs.rs

@@ -136,22 +136,6 @@ impl MemoryFileSystem {
         ruff_notebook::Notebook::from_source_code(&content)
     }
 
-    pub(crate) fn virtual_path_metadata(
-        &self,
-        path: impl AsRef<SystemVirtualPath>,
-    ) -> Result<Metadata> {
-        let virtual_files = self.inner.virtual_files.read().unwrap();
-        let file = virtual_files
-            .get(&path.as_ref().to_path_buf())
-            .ok_or_else(not_found)?;
-
-        Ok(Metadata {
-            revision: file.last_modified.into(),
-            permissions: Some(MemoryFileSystem::PERMISSION),
-            file_type: FileType::File,
-        })
-    }
-
     pub(crate) fn read_virtual_path_to_string(
         &self,
         path: impl AsRef<SystemVirtualPath>,