Add check (and fix for) N ruff rules

[DominicOram]

We want to use more ruff rules, as discussed in #1112. However, adding all of them at once caused a big PR that went stale very quickly so we should instead do them piecemeal. A good first pass is the naming rules https://docs.astral.sh/ruff/rules/?query=naming#pep8-naming-n

Acceptance Criteria

• Linting for naming rules is turned on
• Linting passes on the existing codebase

[DominicOram]

This has been enabled in the copier template (DiamondLightSource/python-copier-template#283) we should update to the latest template but maybe we do this first then do the update so it's separate

[DominicOram]

See also https://diamondlightsource.slack.com/archives/C04TCA0AF2P/p1758027126338759 where we decided to change RE to run_engine