Document the required notebook data layout

[eneskemalergin]

Summary

The HeLa notebooks expect a local data/raw or data/processed structure that is not included in the repository.

Tasks

• document the expected notebook folder structure
• list the required input files at a high level
• explain which paths are expected by each notebook

Acceptance criteria

• notebook data expectations are documented in the repo
• a new user can understand why the notebooks do not run from a fresh clone

Why this matters

This closes the gap between archived notebook outputs and actual reproducibility.