Remove deleted notes from the workspace index

[jevakallio]

Right now we have an issue where, when you delete a note, it will get re-added to reference lists until you restart VS Code.

The "short-term" fix for this is to implement the missing removeNote method in foam-workspace-manager and call that when a note is deleted in the VS Code workspace.

In the long term, I want to rewrite the workspace manager to be a language server / external process, so we can run it outside of VS Code, and update references in the background, not just in the active editor.

Workaround

Cmd+Shift+P, "Reload" after deleting a file