Ensure completely offline changes are applied post startup

- Add a test case to pick up regressions
- Handle the current scope a bit more reliably in the test suite
- Keep the enabled-plugins file in a (scope specific) sub-directory
- Set up a shorter timeout for the suite*

* The suite runs in around 20sec on my laptop, but just in CI is
running thin when we're executing, I've given the suite up to 1 min
to complete before it's cut short.