feat!: clean up repository [BB-6393]

There were multiple reasons for creating this MR:

1. **Linters.**
   They would have allowed us to catch some bugs faster if we started using them from the beginning. This MR includes a fix for such a bug.
2. **Boilerplate code.**
   We have generated the base of this project with Cookiecutter. While it greatly helped with creating the structure of the project, some of this code is redundant. This is one of the attempts to remove more boilerplate parts.
3. **Dependencies.**
   Dependencies are another redundant part. Since we moved this repo from GitHub, we've lost their rather convenient bot which scans dependencies and proposes updates as PRs. The first part of this change was setting up the security pipelines in !4 (merged). While vulnerabilities do not affect our use cases, we still had a pretty big backlog of updates - that's because boilerplate code can also have requirements that are not fully compatible with newer dependencies. Therefore, this removes redundant requirements and upgrades what we can upgrade without significantly affecting the current functionality. This way, it does not need extensive testing at this point. We will still need to follow up with upgrading all JWT-related dependencies and the Jira library, as these can introduce breaking changes to the current implementation.

Testing instructions

1. I tried preserving the logical context in every commit, so it would be good to skim through these messages. Then, you can just choose commits you are interested in (I can recommend bab7d3da and cb7bfb4f).