AN-296 Upgrade Werkzeug to 3.0.6

[jgainerdewar]

This upgrade ended up being, uh, nontrivial.

• The Werkzeug 2 -> 3 upgrade also resulted in Flask and Connexion needing the same major version upgrade, and Connexion's update required code changes.
• The Flask update from 2 -> 3 broke flask_testing, which seems to be abandonware, so updated tests to use plain unittest instead.
• Needed to re-order endpoints in the swagger yaml to put narrower definitions at the beginning (ex. /jobs/operationDetails before /jobs/{id}), otherwise parameter parsing failed.
• I removed the special handling for PyYAML because I see no evidence that we still need it.

[aednichols]

Nice work!

High time to replace Job Manager so we don't do this again in two years.

[LizBaldo]

Amazing, thanks for figuring this out 😱 I only have a couple of minor comments, lmk what you think.

[LizBaldo]

Nit, and not necessarily something to tackle in this PR as it seemed to have n=been the prior behavior, but using relative paths to import modules are not very robust, and setting up each init.py file so that we can import like from test import create_app would be a lot nicer

[jgainerdewar]

Agreed... I'm not going to do that in this PR, I think there's enough churn already, but good to keep in mind next time we're in here.