docs: Better describe the tool's logic, also visually with graphs

[berntpopp]

Description:
Enhance the documentation by providing a detailed description of the tool's logic. Include visual representations and graphs to make the logic more comprehensible.

Tasks:

• Write detailed descriptions of each step in the tool's pipeline.
• Create visual diagrams and graphs to illustrate the tool's logic.
• Integrate these descriptions and visuals into the documentation.