Further upgrade key dependencies

[bdewilde]

changes

• bumps python version, 3.7 => 3.8
• bumps most python package dependencies' versions, most importantly
  • flask: 1.1 => 2.2
  • flask-migrate: 2.7 => 4.0
  • flask-sqlalchemy: 2.5 => 3.0
  • flask-restx: 0.4 => 1.1
  • jinja2: 2.0 => 3.0
  • itsdangerous: 1.1 => 2.0
• removes some unnecessary dependencies: bcrypt, importlib-metadata, pyyaml
• fixes bugs in app configuration
• removes dummy api endpoint at /

@samanz please give this a quick scan and holler if you see any issues. i've confirmed that builds and tests all work locally with the docker setup. (still haven't gotten that all working in CI, but soon.)

[bdewilde]

alright, merging without review so i can continue hacking. there are a few bits that really need updating, but they're bigger lifts, so wanted to handle separately.