Honor Galaxy test timeouts across uploads and workflows

[jmchilton]

Summary

• apply one monotonic deadline across uploads, job execution, and workflow polling
• allow one final state poll at the deadline before timing out
• report whether uploads, a job, or a workflow invocation timed out
• propagate test_timeout through file-based engine execution and workflow_test_on_invocation
• keep the timeout argument typed and accepted by the Galaxy, cwltool, and Toil engine interfaces

Tests

• 29 focused polling, activity, engine, and workflow-invocation tests
• Black, isort, Ruff, and diff checks

[mvdbeek]

The implementation looks fine, but the tests are very mock / patch heavy, are you happy with those ? (also local imports)

[jmchilton]

Of course I am not 😅😢.