TWS update

[MattWellie]

I've been using this to check the performance of populationgenomics/cpg-flow#150

During that testing there were a few hiccups - the base image now contains the wrong version of python, the linting setup was well out of date, and various other syntax oddities.

Update to modernise the test workflow:

• don't use default images (US region), instead - set an image for each job
• remove >100 pre-commit ignored rules, and adjust code to pass new inspections
• update to 3.11 and Hail 0.2.137
• various little updates following lint-ignore changes (e.g. limiting number of method arguments, rearranging imports to reflect isort rules)
• changed the job method and the job class for each stage to have different names (my local linter was really unhappy about the previous state - stages.py was importing jobs.name, and due to init.py this was actually importing jobs.name.name, so the linter saw it as a name clash)
• removed the init.py implicit import for Stage jobs, and move to explicitly referencing the stage job method

Successful test run here https://batch.hail.populationgenomics.org.au/batches/1124257

[MattWellie]

Closed in favor of the stacked PR chain #19, #20, #21