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Merge pull request 'fix: audit remediation Wave 3 — M-1, MED/LOW sweep, ingest robustness + D-1 close-out' (#14) from fix/audit-wave-3 into main

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2026-06-16 04:53:59 +00:00
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@@ -177,13 +177,28 @@ was measured on a graph the current code no longer produces:
diverge (audit C-1). Ingest stores the caller's canonical id as `papers.id`
instead of OpenAlex's URL-form doi (audit C-7). Inter-KB citations are
therefore represented as edges — the "Known Limitation" above is obsolete.
- **Spike numbers are stale.** The 478 dangling nodes, the rank-7
Bobenko/Springborn result, and the 5.7 % score spread were measured *before*
the resolution + canonicalisation. They must be **re-measured after the corpus
is re-ingested** onto canonical ids (the chosen C-7 migration); until then the
GO rests on a superseded topology.
- **Spike re-measured after migration (2026-06-15).** The corpus was re-ingested
onto canonical bare ids (29 papers, all bare — verified `url_form_ids = 0`), and
the graph re-run on the post-migration corpus:
**Action (pending):** after re-ingesting via `ingest_all.sh`, re-run
`codex graph report`, refresh the Spike Result table, and confirm the
foundational hubs (Pinkall/Polthier, Yamabe, Schoen, Bobenko/Springborn) still
surface.
| Metric | Original spike (pre-fix) | Post-migration (re-measured) |
|--------|--------------------------|------------------------------|
| Ingested papers | 29 | 29 |
| Graph nodes | 495 | 489 |
| Graph edges | 590 | 590 |
| Dangling nodes | 478 | 472 |
| Top-10 PR spread | 5.7 % | 5.4 % |
| Rank-1 hub | W1974956622 (dangling) | **Pinkall/Polthier 1993 — in-KB (resolved)** |
| Bobenko/Springborn 2007 | rank 7 | rank 7 |
The resolution fix's signature is visible: Pinkall/Polthier 1993 now resolves to
its canonical DOI and rises to **rank 1 as an in-KB hub** (previously a dangling
OpenAlex node). Bobenko/Springborn 2007 holds rank 7, and the foundational works
(Pinkall/Polthier, Yamabe, Schoen, Bobenko/Springborn) still surface. **GO
re-affirmed** on the shipping topology.
Migration footnotes: two papers initially survived in URL form because the
id-keyed upsert did not catch a `papers.openalex_id` collision, and `2305.10988`
failed on a `papers.bibkey` collision with `2310.17529` (both →
`BobenkoLutz2023`). Same upsert gap — resolved by the bibkey-retry (audit C-15)
plus a delete + re-ingest of the two stragglers; corpus is now 29/29 canonical.