Cleanup dependency management

[jku]

We are badly behind in Python dependency updates, need to do something about this.

• Add dependabot config to handle Python: I think this works mostly like we want:
  • requirements/*.txt will get updates at least seemingly generated by the right tools
  • versions in requirements/*.in will also get updated
  • major versions get their own PRs, everything else is bundled
• Remove the requirements-building in Makefile: it was not working and dependabot should now handle it
• Fix the references to the virtual env in the Makefile: .venv is the environment uv venv uses.

This does nothing to fix #216 (but it does remove one use of uv from Makefile so fixing should be a little easier)

Fixes #175. The resulting dependency updates should fix #213