refactor(config)!: re-design and clean-up configuration

[Alex6323]

Description and Motivation

This PR changes the way how Chronicle can be configured. This was motivated by the fact that we defined defaults in multiple locations and naturally ... conflicts appeared and bit us ... some place. Although those defaults were in theory (if they had been consistent) documented in the config.template.toml file, we think those are better documented in the CLI itself (if you invoke --help). Another problem with such a file is that users were supposed to make a copy of that file and change it to their liking. This resulted in the config.toml being invalidated earlier than it needed to be since often times no parameter that the user actually adapted was conflicting with the newer version. This PR changes the preferred mode of configuration for Chronicle as it makes everything configurable through the CLI itself and also limits supported environment variables to credentials basically (which are more unlikely to be deprecated). Together with the focus of Chronicle as a Docker deployment, this also allows for making our docker-compose.yml the main location of configuration as it's no longer needed to copy over the template file.

Linked Issues

• Closes Refactor Chronicle Configuration #966
• Closes GenerateJWT CLI command does not seem to be generating valid tokens #947
• Closes Load .env file in docker-compose.yml #1000

Notes to Reviewer

As a reviewer, please pay particular attention to the following areas when reviewing this PR and tick the above boxes after you have completed the steps.

Config Changes

• Ensure proper order in which CLI and config arguments are applied.
• Ensure that config changes work with individual build features by running cargo ci-check-features.

[grtlr]

Please make sure cargo ci-check-features command passes.

[grtlr]

Could you please also do #1000 as part of this PR? 🙏