[cnicholas]

Summary

• What: every manual equation and chapter citation in the code, docs, notebooks, tests and validation scripts moves from the 10-12 edition's numbering to the 2026-11-07 edition's. About 190 citation spans and 95 edition tags across 40 files; no behaviour changes.
• Why: Dr. Bishop's 11-7 manual folds the old Chapter 6 into Chapter 5 (chapters 7 and up are one lower), drops the Part dividers, numbers captions "Figure 10.1", and removes seven equations. He confirmed the numbering on the 11-07 call. The private manual repository checks these citations against the manual on every pull request, and with the old numbers 17 of them pointed at equations that no longer exist.

How the numbers were mapped

The manual repository matched the 120 equations of the accepted 10-19 edition to the 11-7 file by content fingerprint, then by title: 113 matched, 7 were removed (10-2, 10-9, 10-10, 12-8, 12-9, 15-14, 15-15), one is new (18-1). The map is committed there as alignment/renumbering-2026-10-19-to-2026-11-07.json. The hyphen form ("Eq 13-8") stays: the manual's labels keep it as ids and the alignment check reads it. tests/test_manual_citations.py enforces the form and that every citing file names its edition.

Hand-edited

• Citations of removed equations: the mean-of-cell-means estimates point at Figure 13.3 (the estimates of the VAS model parameters); the individuals centre at Eq 11-7 alone; R2's error term at the model, Eq 9-1; the replicated-design within-cell variance at Eq 14-14.
• Chapter references: loss function 14, capability 15, individuals charts 11; the R2 chart-selection rule cites Chapter 12 and Section 13.3.9 (Section 20.6.1 is gone).
• README and CONTRIBUTING keep "10-12-2026 manual" where they say which edition the VAS reference runs came with.

Verification

• ruff check clean on the changed Python files (committed with SKIP=ruff-format, as this repo's commits are).
• Fast test slice: 2676 passed; tests/test_manual_citations.py passes.
• vas-manual tools/alignment.py --library <this checkout> on the 11-7 file: 65 of 114 equations cited, 0 missing, 0 register errors.
• Notebook changes are markdown cells only, so the drift check's outputs are unaffected.

Follow-up (manual repository)

vas-manual #22 (the 11-7 edition) pins the library at a version whose citations still use the old numbers, so its alignment step fails until this merges and the pin moves to a release or preview wheel that includes it.