refactor: rewire the Snakefile

[AngryMaciek]

Description

Rewire the Snakefile to get rid of dynamic workflow dag reevaluation and cleaner output dirs.

Fixes #10

Type of change

• [x] Codebase refactoring

Checklist:

• [x] My code follows the style guidelines of this project
• [x] I have performed a self-review of my own code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] My changes generate no new warnings
• [x] I have added tests that prove my fix is effective or that my feature works