Revise structure snakemake

[davide-f]

Closes # (if applicable).

Changes proposed in this Pull Request

Finalize the structuring of the repo; bus_maps and line_maps were left in the resources folders and not in subfolders

Checklist

• I tested my contribution locally and it seems to work fine.
• Code and workflow changes are sufficiently documented.
• Newly introduced dependencies are added to envs/environment.yaml and envs/environment.docs.yaml.
• Changes in configuration options are added in all of config.default.yaml, config.tutorial.yaml, and test/config.test1.yaml.
• Changes in configuration options are also documented in doc/configtables/*.csv and line references are adjusted in doc/configuration.rst and doc/tutorial.rst.
• A note for the release notes doc/release_notes.rst is amended in the format of previous release notes, including reference to the requested PR.