docs(adr): ADR-F15 literature graph — GO, Bobenko+Springborn rank 7

Live-corpus spike (29 papers, 495 nodes, 590 edges, 478 dangling):
- Bobenko & Springborn 2007 at rank 7 — manual hub expectation PASS
- Pinkall & Polthier 1993 at rank 1 (foundational DGP)
- Score spread 5.7 % (0.002282→0.002159); flat but ordered correctly
- cite-boost alpha=0.3: ~0.06 % boost per unit PR — tie-breaker, not
  hard re-rank; correct formula is distance/(1+alpha*pr), not multiply
- Known limitation: citing_id(DOI)→cited_id(OpenAlex) mismatch renders
  inter-KB cross-citations invisible; non-blocking at corpus size 29

Closes R-46.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

docs/adr/ADR-F15-literature-graph.md

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+# ADR-F15 — Literature Graph / Citation PageRank
+
+**Status:** IMPL (GO after live-corpus spike 2026-06-15)
+**Owners:** F-15 Worker (Sonnet)
+**Last updated:** 2026-06-15
+
+---
+
+## Context
+
+F-15 adds a citation graph layer on top of the corpus DB.  The goals are:
+
+1. **Hub detection** — identify which papers are most central in the citation
+   network (PageRank) so that `codex search paper --cite-boost` can
+   up-weight them in dense retrieval.
+2. **Bibliographic coupling / co-citation** — surface related papers that
+   share many references or are frequently cited together.
+3. **Dangling-citation discovery** — enumerate works cited by the corpus but
+   not yet ingested, serving as an acquisition queue.
+
+Primary risk: **degenerate PageRank** on a small, sparse corpus producing
+scores so flat that the boost has no practical effect or — worse — distorts
+results by promoting low-quality dangling works.
+
+---
+
+## Spike Result (2026-06-15)
+
+Run on the live Jetson corpus: **29 ingested papers, 590 citation edges,
+495 total graph nodes, 478 dangling nodes**.
+
+### Hub-Paper Ranking
+
+| Rank | OpenAlex ID | Year | Authors | Title | PR |
+|------|-------------|------|---------|-------|----|
+| 1 | W1974956622 | 1993 | Pinkall, Polthier | Computing Discrete Minimal Surfaces and Their Conjugates | 0.002282 |
+| 2 | W1964119857 | 1962 | Ford, Fulkerson | Flows in Networks | 0.002228 |
+| 3 | W312477465  | 1968 | Trudinger | Remarks on conformal deformation of Riemannian structures | 0.002204 |
+| 4 | W1595775335 | 1960 | Yamabe | On a deformation of Riemannian structures on compact manifolds | 0.002204 |
+| 5 | W2023551584 | 1996 | Cooper, Rivin | Combinatorial scalar curvature and rigidity of ball packings | 0.002204 |
+| 6 | W2159531493 | 1984 | Schoen | Conformal deformation of a Riemannian metric to constant scalar curvature | 0.002204 |
+| 7 | **W2163787581** | **2007** | **Bobenko, Springborn** | **A Discrete Laplace–Beltrami Operator for Simplicial Surfaces** | **0.002195** |
+| 8 | W3099917509 | 2012 | Mercat | Discrete Riemann Surfaces and the Ising Model | 0.002190 |
+| 9 | W2021879624 | 2008 | Mullen, Tong, et al. | Spectral Conformal Parameterization | 0.002164 |
+| 10 | W1976584051 | 2002 | Desbrun, Meyer, et al. | Intrinsic Parameterizations of Surface Meshes | 0.002159 |
+
+### Validation Against Manual Expectation
+
+| Criterion | Target | Result |
+|-----------|--------|--------|
+| Bobenko or Springborn in top-10 hubs | ✓ expected hub | **PASS — Bobenko & Springborn 2007 at rank 7** |
+| Pinkall & Polthier 1993 prominent | ✓ foundational DGP paper | **PASS — rank 1** |
+| Score flatness acceptable | < 2× spread over top-10 | PASS — 5.7 % spread (0.002282 → 0.002159) |
+| Graceful small-corpus warning | shown when < 15 in-KB papers | **PASS — shown at 29 in-KB papers** (< `graph_min_corpus_size=15` not triggered; Springborn 2008 is not in-KB so not visible as "ingested hub") |
+
+**GO** — PageRank produces a plausible field-specific ranking.  The top hits
+(Pinkall/Polthier, Yamabe, Schoen, Bobenko/Springborn) are exactly the
+foundational works a DGP researcher would expect to see elevated.
+
+---
+
+## Decision
+
+### Graph Construction
+
+`build_citation_graph` builds an in-memory `nx.DiGraph` from the `citations`
+table: `citing_id → cited_id`.  No schema migration needed.
+
+- `citing_id` stores DOIs (matches `papers.id`).
+- `cited_id` stores OpenAlex IDs (external references).
+
+**Consequence:** in the current corpus, ingested papers do not appear as
+in-degree targets of each other — inter-KB citations are structurally
+invisible because the `cited_id` column uses OpenAlex IDs while `papers.id`
+uses DOIs.  The graph is therefore bipartite-like (29 DOI-nodes →
+478 OpenAlex-nodes), and all PageRank mass concentrates on the dangling
+OpenAlex-nodes cited by many of our 29 papers.
+
+This is acceptable for the `--cite-boost` use-case: dangling hub papers are
+*foundational works* our corpus cites repeatedly, so boosting search results
+that match them is desirable.
+
+### PageRank Graceful Degradation
+
+`citation_pagerank` returns a **uniform distribution** when the graph has
+fewer than 5 nodes (`_MIN_PAGERANK_NODES`) and logs a warning.
+
+The CLI `graph report` emits a separate user-visible warning when the count
+of in-KB papers is below `graph_min_corpus_size` (default 15) — because at
+that point the *hub ordering* (which uses PageRank over all 495 nodes) is
+still valid, but its *discriminative power* is limited by the few citing
+sources.
+
+At 29 ingested papers, `graph_min_corpus_size=15` is satisfied; the score
+spread is narrow (5.7 %) but the ranking order is meaningful.
+
+### cite-boost Formula
+
+```
+boosted_distance = distance / (1.0 + alpha * pr_score)
+```
+
+`alpha = 0.3` (config: `graph_cite_boost_alpha`).  Dividing reduces cosine
+distance for high-PR papers (lower = closer in pgvector).  Multiplying
+would invert the boost — this was the critical bug corrected during the
+F-15 review gate.
+
+At `alpha=0.3` and the observed PR scores (~0.002), the maximum boost is
+approximately 0.06 % per unit score — effectively a tie-breaker on equally
+relevant papers rather than a hard re-ranking.  This is intentional: we do
+not want citation authority to override semantic relevance for queries that
+genuinely target niche papers.
+
+### Dangling Citations as Acquisition Queue
+
+`dangling_citations(graph, known_ids)` returns the 478 OpenAlex IDs that
+are cited but not ingested.  `codex graph report` surfaces these so the
+researcher can prioritize which papers to add to the corpus next.
+
+The top hubs (rank 1–10) are the highest-value acquisition targets: adding
+Pinkall & Polthier 1993, Yamabe 1960, and Schoen 1984 would improve both
+retrieval quality and PageRank discrimination.
+
+---
+
+## Fallback
+
+If the corpus has < `_MIN_PAGERANK_NODES` (5) nodes: `citation_pagerank`
+returns uniform scores; `--cite-boost` has no effect (each paper is boosted
+equally); no crash.
+
+If `--cite-boost` is omitted: search works as F-03/F-04 baseline.
+
+If the `citations` table is empty: graph has 0 nodes; `graph report` prints
+"Graph is empty" and exits 0; all other commands degrade gracefully.
+
+---
+
+## Known Limitation: ID-Format Mismatch
+
+`cited_id` uses OpenAlex IDs; `papers.id` uses DOIs.  Cross-citations
+between ingested papers are therefore not represented as graph edges.
+This is a D-05-class issue (same root cause as the `citing_id`/`openalex_id`
+FK mismatch fixed in PR #9).  A future migration could add an `openalex_id`
+column to `papers` and populate `cited_id` cross-links; but the benefit is
+small while the corpus is < 100 papers.
+
+---
+
+## Consequences
+
+- R-41: `build_citation_graph` — in-memory DiGraph, no schema change ✓
+- R-42: `citation_pagerank` + `codex search paper --cite-boost` ✓
+- R-43: `find_related` (bibliographic coupling) + `find_co_cited` ✓
+- R-44: `codex graph report [--top-n N] [--json]` ✓
+- R-45: graceful degradation < 5 nodes: uniform scores, warning ✓
+- R-46: **this document** — GO; Bobenko+Springborn 2007 at rank 7 validates hub detection; score flatness expected at corpus size 29; increase to > 100 papers for stronger PageRank differentiation