keep checkpoints file aside (c.FileCheckpoints)

Follow up of https://github.com/jupyterlab/jupyterlab/issues/5809.

We are kind of getting polluted by all these checkpoints files, and setting them aside with
```python
c.FileCheckpoints.checkpoints_dir =...
```
helps but the filename is only based of the opened file basename, not the path. So if two files are opened, with the same basename, they will overwrite the same checkpoint files.
Why not simply add the path in the checkpoint filename (or base64 encode it)

Start by tracing the implementation behind c.FileCheckpoints.checkpoints_dir and how checkpoint filenames are derived. Confirm the collision case with two opened files sharing a basename, then define done as keeping their checkpoint files separate while preserving the configured checkpoint directory.

Written by the indexing model from the issue text.