Implementation of --run-system-tests for pytests breaks collection options

[samtygier-stfc]

Summary

To enable running of system tests we have a flag --run-system-tests. However the way that this is implemented breaks using --ignore pytest option. This is probably because it messes with the test collection methods. See conftest.py

Steps To Reproduce

pytest --ignore=mantidimaging/gui should run tests that are not in the gui directory.

Current Behaviour

All tests still run

--collect-only can be useful for debugging.

Context

current main