“I cannot reproduce my own Chapter 3” is the concrete failure this prevents, and it has a specific mechanism: processed data overwrote raw data, or a script’s output became its own input, and now there is no path back to the numbers in the draft. It surfaces at the worst possible moment — during revisions, under a deadline, when the person who could explain the directory is you eight months ago.
Wilson et al., “Good Enough Practices in Scientific Computing”, PLOS Computational Biology 2017 — section 3, project organisation. This is the paper behind the Carpentries lesson. It is genuinely good and the standard’s Part 1 is close to a strict superset of it.
Part 1, and Archetype A.
Restructure your actual thesis repo to the archetype. Not a copy, not a sample — the one your chapter depends on.
Then the second half, which is the part that teaches: read Wilson et al. §3, and find two places where the standard is stricter. State each in one sentence, with one sentence on why the extra strictness exists. You are not being asked to agree with it; you are being asked to notice it, because a rule you have located yourself is one you will follow when nobody is checking.
Repo URL, plus one paragraph on what moved where, plus the two stricter-points.
This replaces your arithmetic entry for the week you do it. Submit it to that week’s WA assignment in Canvas — the same one you would have submitted anyway. It is not an extra piece of work on top of the log.
You do not submit anything to the milestone yet. When all four skills in M2 are done, submit the M2 — Reproducible Code assignment, which is just an index saying which week each one went in.