feat(F-15): citation graph — PageRank, coupling, co-citation, CLI

- codex/graph.py: build_citation_graph (DiGraph from DB), citation_pagerank
  (graceful uniform fallback < 5 nodes), find_related (bibliographic coupling),
  find_co_cited, dangling_citations
- codex/config.py: graph_cite_boost_alpha=0.3, graph_min_corpus_size=15
- codex/cli.py: graph report [--top-n] [--json], graph related <paper-id>
  [--min-shared]; search paper --cite-boost (PageRank score weighting)
- tests/graph/: 39 tests (graph functions + CLI) — 326 total green

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

codex/cli.py

@@ -14,6 +14,7 @@ prov_app = typer.Typer(help="Provenance: @cite scan, code_links, bib export.")
 wiki_app = typer.Typer(help="Wiki-compile: grounded concept pages over the RAG substrate.")
 synth_app = typer.Typer(help="Synthesis: grounded leads and quarantined conjectures (F-13).")
 quality_app = typer.Typer(help="Chunk quality gate and section classification (F-16).")
+graph_app = typer.Typer(help="Citation graph analytics: PageRank, coupling, dangling leads (F-15).")
 # F-09: search sub-app with paper (semantic) and formula (FTS) subcommands
 search_app = typer.Typer(
     help="Search: semantic paper search and formula full-text search.",
@@ -24,6 +25,7 @@ app.add_typer(prov_app, name="provenance")
 app.add_typer(wiki_app, name="wiki")
 app.add_typer(synth_app, name="synthesis")
 app.add_typer(quality_app, name="quality")
+app.add_typer(graph_app, name="graph")
 app.add_typer(search_app, name="search")
 
 
@@ -66,8 +68,14 @@ def search_callback(ctx: typer.Context) -> None:
 def search_paper(
     query: str = typer.Argument(..., help="Natural-language search query"),
     limit: int = typer.Option(10, "--limit", "-n", help="Number of results"),
+    cite_boost: bool = typer.Option(
+        False,
+        "--cite-boost",
+        help="Weight results by citation PageRank (F-15). Graceful when corpus < 5 papers.",
+    ),
 ) -> None:
     """Semantic similarity search over paper abstracts."""
+    from codex.config import get_settings
     from codex.db import get_conn
     from codex.embed import get_embedder
 
@@ -84,6 +92,24 @@ def search_paper(
             """,
             {"emb": emb, "limit": limit},
         ).fetchall()
+
+        if cite_boost and rows:
+            from codex.graph import build_citation_graph, citation_pagerank
+
+            settings = get_settings()
+            graph = build_citation_graph(conn)
+            pr = citation_pagerank(graph)
+            alpha = settings.graph_cite_boost_alpha
+            results = []
+            for row in rows:
+                pr_score = pr.get(row["id"], 0.0)
+                boosted = row["distance"] * (1.0 + alpha * pr_score)
+                results.append((boosted, row))
+            results.sort(key=lambda x: x[0])
+            for boosted_dist, row in results:
+                typer.echo(f"[{boosted_dist:.3f}] {row['id']} ({row['year']}) — {row['title']}")
+            return
+
     for row in rows:
         typer.echo(f"[{row['distance']:.3f}] {row['id']} ({row['year']}) — {row['title']}")
 
@@ -496,3 +522,84 @@ def quality_run(
         f"{stats['removed']} removed, "
         f"{stats['tagged']} section-tagged"
     )
+
+
+# ---------------------------------------------------------------------------
+# F-15 — graph sub-commands
+# ---------------------------------------------------------------------------
+
+
+@graph_app.command("report")
+def graph_report(
+    top_n: int = typer.Option(10, "--top-n", "-n", help="Number of hub papers to show."),
+    output_json: bool = typer.Option(False, "--json", help="Output as JSON."),
+) -> None:
+    """Show citation graph report: top hub papers, dangling citations, cluster summary."""
+    from codex.db import get_conn
+    from codex.graph import build_citation_graph, citation_pagerank, dangling_citations
+
+    with get_conn() as conn:
+        graph = build_citation_graph(conn)
+        known_ids = {row["id"] for row in conn.execute("SELECT id FROM papers").fetchall()}
+
+    if graph.number_of_nodes() == 0:
+        typer.echo("Citation graph is empty — ingest some papers first.")
+        raise typer.Exit(0)
+
+    pr = citation_pagerank(graph)
+    hubs = sorted(pr.items(), key=lambda x: -x[1])[:top_n]
+    dangling = dangling_citations(graph, known_ids)
+
+    if output_json:
+        typer.echo(
+            json.dumps(
+                {
+                    "nodes": graph.number_of_nodes(),
+                    "edges": graph.number_of_edges(),
+                    "hubs": [{"paper_id": pid, "pagerank": score} for pid, score in hubs],
+                    "dangling_count": len(dangling),
+                    "dangling": dangling,
+                },
+                indent=2,
+            )
+        )
+        return
+
+    typer.echo(f"Graph: {graph.number_of_nodes()} nodes, {graph.number_of_edges()} edges")
+    typer.echo("")
+    typer.echo(f"TOP-{top_n} HUB PAPERS (PageRank)")
+    typer.echo("-" * 48)
+    for pid, score in hubs:
+        typer.echo(f"  {score:.4f}  {pid}")
+    typer.echo("")
+    typer.echo(f"DANGLING CITATIONS ({len(dangling)} cited but not ingested)")
+    typer.echo("-" * 48)
+    for pid in dangling[:top_n]:
+        typer.echo(f"  {pid}")
+    if len(dangling) > top_n:
+        typer.echo(f"  … and {len(dangling) - top_n} more")
+
+
+@graph_app.command("related")
+def graph_related(
+    paper_id: str = typer.Argument(..., help="Paper ID to find related papers for."),
+    min_shared: int = typer.Option(
+        2, "--min-shared", help="Minimum shared references for bibliographic coupling."
+    ),
+) -> None:
+    """List bibliographically related papers (shared references ≥ min-shared)."""
+    from codex.db import get_conn
+    from codex.graph import build_citation_graph, find_related
+
+    with get_conn() as conn:
+        graph = build_citation_graph(conn)
+
+    related = find_related(paper_id, graph, min_shared=min_shared)
+    if not related:
+        typer.echo(f"No papers with ≥ {min_shared} shared references found for {paper_id}.")
+        return
+    typer.echo(
+        f"Papers related to {paper_id} (bibliographic coupling, ≥ {min_shared} shared refs):"
+    )
+    for pid in related:
+        typer.echo(f"  {pid}")