feat(F-16): chunk quality gate + section classification

- codex/quality.py: 3-signal filter (length / alpha-ratio / bib-score)
  + rule-based section classifier + run_quality_pass retroactive DB pass
- codex/ingest.py: promote quality imports to module level; apply
  filter_chunks before embedding; store section column in chunks INSERT
- codex/config.py: CHUNK_MIN_CHARS / CHUNK_MIN_ALPHA_RATIO / CHUNK_MAX_BIB_SCORE
- infra/schema.sql: ALTER TABLE chunks ADD COLUMN IF NOT EXISTS section TEXT
- .env.example: document F-16 quality thresholds
- codex/cli.py: quality run sub-command (scope by --paper-id or all papers)
- tests/quality/: 35 new tests covering all quality functions
- tests/ingest/: patch filter_chunks in source-path tests to isolate ingest

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

codex/cli.py

@@ -13,6 +13,7 @@ discover_app = typer.Typer(help="Discovery queries over the citation graph.")
 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).")
 # 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.",
@@ -22,6 +23,7 @@ app.add_typer(discover_app, name="discover")
 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(search_app, name="search")
 
 
@@ -419,9 +421,7 @@ def synthesis_conjectures(
     conjectures = propose_conjectures(top_k=settings.synthesis_top_k, llm=llm)
     write_leads(conjectures, leads_dir)
 
-    typer.echo(
-        f"Conjectures (UNVERIFIED) written to {leads_dir}/conjectures/: {len(conjectures)}"
-    )
+    typer.echo(f"Conjectures (UNVERIFIED) written to {leads_dir}/conjectures/: {len(conjectures)}")
 
 
 @synth_app.command("report")
@@ -454,13 +454,45 @@ def synthesis_report(
 
     typer.echo("")
     typer.echo("=" * 72)
-    typer.echo(
-        f"CONJECTURES  ({len(conj_files)})  → {conj_dir}  "
-        "[UNVERIFIED — never in wiki/]"
-    )
+    typer.echo(f"CONJECTURES  ({len(conj_files)})  → {conj_dir}  [UNVERIFIED — never in wiki/]")
     typer.echo("=" * 72)
     if not conj_files:
         typer.echo("(none)")
     for f in conj_files:
         first = f.read_text(encoding="utf-8").splitlines()[0]
         typer.echo(f"  {first}")
+
+
+# ---------------------------------------------------------------------------
+# F-16 — quality sub-commands
+# ---------------------------------------------------------------------------
+
+
+@quality_app.command("run")
+def quality_run(
+    paper_id: Optional[str] = typer.Option(  # noqa: UP045
+        None,
+        "--paper-id",
+        help="Restrict pass to one paper (omit to process all papers).",
+    ),
+) -> None:
+    """Apply quality gate + section classification to existing chunks.
+
+    Iterates over chunks in the database, removes those that fail the
+    quality thresholds, and back-fills the ``section`` column for the rest.
+    """
+    from codex.config import get_settings
+    from codex.db import get_conn
+    from codex.quality import run_quality_pass
+
+    settings = get_settings()
+    with get_conn() as conn:
+        stats = run_quality_pass(paper_id=paper_id, conn=conn, settings=settings)
+
+    scope = f"paper {paper_id}" if paper_id else "all papers"
+    typer.echo(
+        f"Quality pass ({scope}): "
+        f"{stats['kept']} kept, "
+        f"{stats['removed']} removed, "
+        f"{stats['tagged']} section-tagged"
+    )