Usability improvements

[renatav]

Description (e.g. "Related to ...", etc.)

Contains a number of fixes and usability improvements, mostly related to some recent work (like updates made to logging, creation of a configuration directory, automatically finding an authentication repository), as well as some create repo fixes and a couple of new features.
Adds a function for exporting keys-description.json based on the repository's current state. This is initial work towards storing this file in the repo's configuration directory and potentially using it to make operations like adding new roles or updating current ones easier.
Also contains work on handling more edge cases, catching more errors and cleaning up a repository after an error occurs.
Simplified two CLI commands by allowing specification of a custom file containing additional data. Determined that implementing < or | would require substantial rework, since we'd no longer be able to use prompts (which we rely on at the moment to ask the users to insert their yubikey, enter their pins securely etc.). I believe that this is a good compromise and that we shouldn't spend too much time on such a feature.
Added support for cloning a new dependency when adding it to dependencies.json if it is not on disk
Closes #536
Closes #531
Closes #526
Closes #347
See #497

Code review checklist (for code reviewer to complete)

• Pull request represents a single change (i.e. not fixing disparate/unrelated things in a single PR)
• Title summarizes what is changing
• Commit messages are meaningful (see this for details)
• Tests have been included and/or updated, as appropriate
• Docstrings have been included and/or updated, as appropriate
• Changelog has been updated, as needed (see CHANGELOG.md)