Diagnostics are not cleaned up after a file is deleted or moved

[award999]

Describe the bug
Diagnostics linger when they should be cleaned up when files

To Reproduce
Steps to reproduce the behavior:

1. Write an error to a file
2. Delete or rename the file
3. Notice the diagnostic still exists in the collection
4. Clicking the link brings up an error editor

Expected behavior
Diagostics are cleaned up. SourceKit-LSP may send a new diagnostic for the new file if it was moved.

Environment
All

Additional context
N/A

[rbenegal]

Verified with 3a615aa. The issues no longer show up in the "Problems" panel if the file is deleted, but updated issues do show up if the file is renamed.