feat(synthesis): Lead/Provenance model + grounded leads + conjecture generator

- codex/synthesis.py: Lead/Provenance dataclasses, find_connections/gaps/improvements,
  propose_conjectures (status=unverified, quarantined in leads/conjectures/),
  write_leads (grounded→leads/grounded/, conjectures→leads/conjectures/ HARD invariant)
- codex/cli.py: synthesis leads/conjectures/report command group
- codex/config.py: F-13 settings (leads_dir, synthesis_llm_*, synthesis_top_k,
  synthesis_min_grounded_ratio, synthesis_gap_min_coverage)
- tests/synthesis/: 42 tests covering model, grounding, conjecture invariant, quarantine, CLI
- spike/: F-13 spike script + output (live run attempted)

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

tests/synthesis/test_cli.py

@@ -0,0 +1,179 @@
+"""Tests for the ``codex synthesis`` CLI command group."""
+
+from __future__ import annotations
+
+from pathlib import Path
+from unittest.mock import MagicMock
+
+import pytest
+from typer.testing import CliRunner
+
+from codex.cli import app
+from codex.synthesis import Lead, Provenance
+
+runner = CliRunner()
+
+
+def _grounded_lead(lead_id: str = "L-0001") -> Lead:
+    return Lead(
+        id=lead_id,
+        kind="connection",
+        title="Connection — X ⇄ Y",
+        body="Some grounded body. [X2020 #chunk 1]",
+        provenance=[Provenance(bibkey="X2020", locator="chunk 1")],
+        confidence=0.8,
+    )
+
+
+def _conjecture(lead_id: str = "L-0002") -> Lead:
+    return Lead(
+        id=lead_id,
+        kind="conjecture",
+        title="Bold guess",
+        body="Hypothetical.",
+        provenance=[Provenance(bibkey="X2020", locator="chunk 1")],
+        confidence=0.0,
+        suggested_validation="Run a falsification spike.",
+    )
+
+
+@pytest.fixture
+def isolated_leads_dir(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> Path:
+    """Point Settings.leads_dir at tmp_path/leads for CLI tests."""
+    from codex.config import Settings
+
+    leads_path = tmp_path / "leads"
+
+    settings = MagicMock(spec=Settings)
+    settings.leads_dir = str(leads_path)
+    settings.synthesis_llm_model = "test-model"
+    settings.synthesis_llm_url = None
+    settings.ollama_base_url = "http://localhost:11434"
+    settings.synthesis_top_k = 6
+    settings.synthesis_min_grounded_ratio = 0.5
+    settings.synthesis_gap_min_coverage = 2
+
+    monkeypatch.setattr("codex.cli.get_settings", lambda: settings, raising=False)
+    monkeypatch.setattr("codex.synthesis.get_settings", lambda: settings)
+    monkeypatch.setattr(
+        "codex.config.get_settings", lambda: settings, raising=False
+    )
+    return leads_path
+
+
+def test_synthesis_leads_invokes_three_finders(
+    monkeypatch: pytest.MonkeyPatch,
+    isolated_leads_dir: Path,
+) -> None:
+    """`codex synthesis leads --lib-path` calls connection + gap + improvement."""
+    calls: list[str] = []
+
+    def fake_connections(*, top_k: int, llm: object) -> list[Lead]:
+        calls.append("connection")
+        return [_grounded_lead("L-0001")]
+
+    def fake_gaps(
+        *,
+        lib_path: str | None = None,
+        llm: object,
+        topics: list[str] | None = None,
+    ) -> list[Lead]:
+        calls.append("gap")
+        return []
+
+    def fake_improvements(lib_path: str, *, top_k: int, llm: object) -> list[Lead]:
+        calls.append("improvement")
+        return []
+
+    monkeypatch.setattr("codex.synthesis.find_connections", fake_connections)
+    monkeypatch.setattr("codex.synthesis.find_gaps", fake_gaps)
+    monkeypatch.setattr("codex.synthesis.find_improvements", fake_improvements)
+    monkeypatch.setattr("codex.synthesis.default_llm_client", lambda: object())
+
+    result = runner.invoke(app, ["synthesis", "leads", "--lib-path", "/tmp/fake"])
+
+    assert result.exit_code == 0, result.stdout
+    assert calls == ["connection", "gap", "improvement"]
+    assert (isolated_leads_dir / "grounded" / "L-0001.md").exists()
+
+
+def test_synthesis_leads_without_lib_path_skips_improvement(
+    monkeypatch: pytest.MonkeyPatch,
+    isolated_leads_dir: Path,
+) -> None:
+    """Without --lib-path, the improvement finder must be skipped (graceful)."""
+    calls: list[str] = []
+
+    monkeypatch.setattr(
+        "codex.synthesis.find_connections",
+        lambda *, top_k, llm: (calls.append("connection"), [])[1],
+    )
+    monkeypatch.setattr(
+        "codex.synthesis.find_gaps",
+        lambda *, lib_path=None, llm, topics=None: (calls.append("gap"), [])[1],
+    )
+    monkeypatch.setattr(
+        "codex.synthesis.find_improvements",
+        lambda *args, **kwargs: (calls.append("improvement"), [])[1],
+    )
+    monkeypatch.setattr("codex.synthesis.default_llm_client", lambda: object())
+
+    result = runner.invoke(app, ["synthesis", "leads"])
+
+    assert result.exit_code == 0, result.stdout
+    assert "improvement" not in calls
+    assert "connection" in calls
+    assert "gap" in calls
+
+
+def test_synthesis_conjectures_writes_to_conjectures_dir(
+    monkeypatch: pytest.MonkeyPatch,
+    isolated_leads_dir: Path,
+) -> None:
+    """`codex synthesis conjectures` lands files under leads/conjectures/."""
+    monkeypatch.setattr(
+        "codex.synthesis.propose_conjectures",
+        lambda *, top_k, llm: [_conjecture("L-0042")],
+    )
+    monkeypatch.setattr("codex.synthesis.default_llm_client", lambda: object())
+
+    result = runner.invoke(app, ["synthesis", "conjectures"])
+
+    assert result.exit_code == 0, result.stdout
+    assert (isolated_leads_dir / "conjectures" / "L-0042.md").exists()
+    assert not (isolated_leads_dir / "grounded" / "L-0042.md").exists()
+
+
+def test_synthesis_report_separates_sections(
+    monkeypatch: pytest.MonkeyPatch,
+    isolated_leads_dir: Path,
+) -> None:
+    """`codex synthesis report` shows grounded and conjectures in distinct headers."""
+    from codex.synthesis import write_leads
+
+    write_leads(
+        [_grounded_lead("L-0001"), _conjecture("L-0002")],
+        str(isolated_leads_dir),
+    )
+
+    result = runner.invoke(app, ["synthesis", "report"])
+
+    assert result.exit_code == 0, result.stdout
+    assert "GROUNDED LEADS" in result.stdout
+    assert "CONJECTURES" in result.stdout
+    # Visible separation: GROUNDED header strictly precedes CONJECTURES header
+    assert result.stdout.index("GROUNDED LEADS") < result.stdout.index("CONJECTURES")
+    # UNVERIFIED tag in the conjectures header
+    assert "UNVERIFIED" in result.stdout
+
+
+def test_synthesis_report_empty(
+    isolated_leads_dir: Path,
+) -> None:
+    """`codex synthesis report` with no leads still prints both sections."""
+    result = runner.invoke(app, ["synthesis", "report"])
+
+    assert result.exit_code == 0
+    assert "GROUNDED LEADS" in result.stdout
+    assert "CONJECTURES" in result.stdout
+    assert "(none)" in result.stdout