`ruff server`: Defer notebook cell deletion to avoid an error message (#11864)
## Summary
Fixes https://github.com/astral-sh/ruff-vscode/issues/496.
Cells are no longer removed from the notebook index when a notebook gets
updated, but rather when `textDocument/didClose` is called for them.
This solves an issue where their premature removal from the notebook
cell index would cause their URL to be un-queryable in the
`textDocument/didClose` handler.
## Test Plan
Create and then delete a notebook cell in VS Code. No error should
appear.