[LSP] Diagnostics are not cleared out when a file is deleted.

[linkpy]

Godot version:
3.2.3

OS/device including version:
Linux 5.4.0 (Linux Mint)

Issue description:
The LSP implementation doesn't seem to detect file deletion and thus doesn't clear out the diagnostics of that file.

Linked to godotengine/godot-vscode-plugin#243.
The LSP specification specifies that the creator of the diagnostics is responsible for their deletion (see microsoft/language-server-protocol#463).

Steps to reproduce:
Create a new file, write anything invalid in it then save (not saving the file then closing clears out the diagnostics).
Delete the file, notice the diagnostics are still here.

Minimal reproduction project:

[akien-mga]

Fixed in 3.3 by #47553, but not fixed in master yet.