This is an unnecessary layer
Everywhere in code we need to look at custom, when there's no such thing in Jupyter (specification) metdata.
This is a carry over from the old VS Code notebook Notebook format.
All metadata had to be stored under custom and this was never migrated when custom in core was removed.

This shows up in SCM view as well
I.e. when using the diff view, the custom node is displayed, and this is wrong, as there's no such thing in the spec.

Removing this will:

• Improve SCM
• Make it easier for extensions to access the metadata
• Ensure the API lines up with the Jupyter specification

### Tasks
- [ ] https://github.com/microsoft/vscode-jupyter/issues/15378
- [ ] https://github.com/microsoft/vscode/issues/207968#issuecomment-2002992138
- [ ] https://github.com/microsoft/vscode-jupyter/issues/15380
- [ ] https://github.com/julia-vscode/julia-vscode/issues/3568
- [ ] https://github.com/microsoft/vscode-jupyter/issues/15402