Use secrets for Docker

[multiflexi]

Replaces plaintext passwords used for Docker with Docker secrets. It is still possible to use old variables in .env, as before, but it is not advised

also:

• removes .env and replaces it with .env.example file - this is useful because it is always necessary to change the .env file and those changes should not be tracked by Git
• adds example files for secrets
• updates documentation
• updates .gitignore
• updates pre-commit-hooks configuration to exclude .sample file from end-of-file-fixer
• fixes some imperfections
• adds docstrings

[multiflexi]

Test and merge please.