Applying preference changes does not re-run diagnostics

[jandubois]

I turned PATH configuration from Automatic to Manual and applied the change, but the diagnostics didn't update; I had to manually press the Re-run button.

This is supposed to happen automatically, but it is also somewhat complicated, as the run has to be delayed until the backend has updated to the desired new state. E.g. if we enable k8s, we can't immediately run k8s checks, we need to wait until the apiserver is actually running and responsive.