[ty] Track open files in the server (#19264)

## Summary

This PR updates the server to keep track of open files both system and
virtual files.

This is done by updating the project by adding the file in the open file
set in `didOpen` notification and removing it in `didClose`
notification.

This does mean that for workspace diagnostics, ty will only check open
files because the behavior of different diagnostic builder is to first
check `is_file_open` and only add diagnostics for open files. So, this
required updating the `is_file_open` model to be `should_check_file`
model which validates whether the file needs to be checked based on the
`CheckMode`. If the check mode is open files only then it will check
whether the file is open. If it's all files then it'll return `true` by
default.

Closes: astral-sh/ty#619

## Test Plan

### Before

There are two files in the project: `__init__.py` and `diagnostics.py`.

In the video, I'm demonstrating the old behavior where making changes to
the (open) `diagnostics.py` file results in re-parsing the file:


https://github.com/user-attachments/assets/c2ac0ecd-9c77-42af-a924-c3744b146045

### After

Same setup as above.

In the video, I'm demonstrating the new behavior where making changes to
the (open) `diagnostics.py` file doesn't result in re-parting the file:


https://github.com/user-attachments/assets/7b82fe92-f330-44c7-b527-c841c4545f8f

crates/ruff_db/src/files.rs

@@ -486,7 +486,7 @@ impl fmt::Debug for File {
 ///
 /// This is a wrapper around a [`File`] that provides additional methods to interact with a virtual
 /// file.
-#[derive(Copy, Clone)]
+#[derive(Copy, Clone, Debug)]
 pub struct VirtualFile(File);
 
 impl VirtualFile {