fix(wiki): basic conflict detection in CompileReport

Add _detect_conflicts() using adversative keyword heuristic (but,
however, in contrast, …) between chunks of different bibkeys; results
populate CompileReport.conflicts and appear in wiki/log.md.
Also add CompileReport.quarantined field (used by Fix 2).

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

tests/wiki/test_check.py

@@ -161,3 +161,67 @@ def test_wiki_check_index_and_log_ignored(
     assert result.exit_code == 0, (
         f"index.md / log.md should be excluded. exit={result.exit_code}, out={result.output}"
     )
+
+
+def test_wiki_check_exit_2_when_draft_not_empty(
+    tmp_path: Path,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """codex wiki check exits 2 when wiki/draft/ is non-empty (quarantined pages)."""
+    wiki = tmp_path / "wiki"
+    wiki.mkdir()
+    draft = wiki / "draft"
+    draft.mkdir()
+
+    (draft / "bad-concept.md").write_text(
+        "# Bad Concept\n\n⚠ Ungrounded hallucination. [FakeBib2025 #chunk 0]\n",
+        encoding="utf-8",
+    )
+
+    from unittest.mock import MagicMock
+
+    from codex.config import Settings
+
+    mock_settings = MagicMock(spec=Settings)
+    mock_settings.wiki_dir = str(wiki)
+    monkeypatch.setattr("codex.cli.get_settings", lambda: mock_settings, raising=False)
+
+    runner = CliRunner()
+    result = runner.invoke(app, ["wiki", "check", "--output-dir", str(wiki)])
+    assert result.exit_code == 2, (
+        f"Expected exit 2 (quarantined pages), got {result.exit_code}. Output: {result.output}"
+    )
+
+
+def test_wiki_check_exit_2_takes_priority_over_exit_1(
+    tmp_path: Path,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    """Exit 2 (quarantined) takes priority over exit 1 (ungrounded in wiki/)."""
+    wiki = tmp_path / "wiki"
+    wiki.mkdir()
+    draft = wiki / "draft"
+    draft.mkdir()
+
+    # Main wiki with ungrounded claim
+    (wiki / "concept-a.md").write_text(
+        "# Concept A\n\n⚠ Ungrounded claim. [SomeBib #chunk 0]\n",
+        encoding="utf-8",
+    )
+    # Draft with quarantined page
+    (draft / "concept-b.md").write_text(
+        "# Concept B\n\nQuarantined content.\n",
+        encoding="utf-8",
+    )
+
+    from unittest.mock import MagicMock
+
+    from codex.config import Settings
+
+    mock_settings = MagicMock(spec=Settings)
+    mock_settings.wiki_dir = str(wiki)
+    monkeypatch.setattr("codex.cli.get_settings", lambda: mock_settings, raising=False)
+
+    runner = CliRunner()
+    result = runner.invoke(app, ["wiki", "check", "--output-dir", str(wiki)])
+    assert result.exit_code == 2

tests/wiki/test_compile.py

@@ -18,6 +18,7 @@ from codex.wiki import (
     Concept,
     ConceptPage,
     _chunk_hash,
+    _detect_conflicts,
     _inject_cross_refs,
     _parse_claims,
     _run_grounding_guard,
@@ -278,6 +279,7 @@ def mock_settings(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> Path:
     mock.wiki_llm_url = None
     mock.ollama_base_url = "http://localhost:11434"
     mock.wiki_top_k = 6
+    mock.wiki_min_grounding_rate = 0.5
 
     monkeypatch.setattr("codex.wiki.get_settings", lambda: mock)
     monkeypatch.setattr("codex.cli.get_settings", lambda: mock, raising=False)
@@ -568,3 +570,147 @@ def test_chunk_hash_differs_on_content_change() -> None:
     h1 = _chunk_hash(FIXTURE_CHUNKS)
     h2 = _chunk_hash(modified)
     assert h1 != h2
+
+
+# ---------------------------------------------------------------------------
+# LLM error handling (Fix 4)
+# ---------------------------------------------------------------------------
+
+
+def test_compile_concept_llm_unavailable_returns_empty_page(
+    mock_retrieve: None,
+    mock_formulas: None,
+    mock_settings: Path,
+) -> None:
+    """When LLM raises an exception, compile_concept returns an empty ConceptPage (no crash)."""
+
+    class FailingLLM:
+        def generate(self, prompt: str, model: str) -> str:
+            raise ConnectionError("Ollama unavailable")
+
+    page = compile_concept(
+        FIXTURE_CONCEPT, FIXTURE_CHUNKS, top_k=6, llm=FailingLLM(), wiki_dir=mock_settings
+    )
+    assert isinstance(page, ConceptPage)
+    assert page.markdown == ""
+    assert page.claims == []
+    assert page.chunk_hash != ""  # hash still computed from chunks
+
+
+# ---------------------------------------------------------------------------
+# Quarantine (Fix 2)
+# ---------------------------------------------------------------------------
+
+
+def test_compile_all_quarantines_low_grounding_page(
+    mock_retrieve: None,
+    mock_formulas: None,
+    mock_settings: Path,
+) -> None:
+    """A page with grounding rate < 0.5 goes to wiki/draft/ not wiki/."""
+    from codex.wiki import compile_all
+
+    (mock_settings / "concepts.yaml").write_text(
+        textwrap.dedent(
+            """\
+            concepts:
+              - slug: lobachevsky-function
+                title: Lobachevsky Function
+                aliases: [Milnor Lobachevsky]
+            """
+        ),
+        encoding="utf-8",
+    )
+
+    # Ungrounded LLM output → all claims ungrounded → grounding rate 0.0 < 0.5
+    llm = MockLLM(UNGROUNDED_LLM_OUTPUT)
+    report = compile_all(changed_only=False, llm=llm, output_dir=str(mock_settings))
+
+    draft_dir = mock_settings / "draft"
+    assert draft_dir.exists(), "draft/ directory should have been created"
+    draft_pages = list(draft_dir.glob("*.md"))
+    assert len(draft_pages) >= 1, "Quarantined page should exist in wiki/draft/"
+    assert "lobachevsky-function" in report.quarantined
+    # Normal wiki/ path must NOT exist for this page
+    assert not (mock_settings / "lobachevsky-function.md").exists()
+
+
+def test_compile_all_does_not_quarantine_grounded_page(
+    mock_retrieve: None,
+    mock_formulas: None,
+    mock_settings: Path,
+) -> None:
+    """A page with grounding rate >= 0.5 is written to wiki/, not quarantined."""
+    from codex.wiki import compile_all
+
+    (mock_settings / "concepts.yaml").write_text(
+        textwrap.dedent(
+            """\
+            concepts:
+              - slug: lobachevsky-function
+                title: Lobachevsky Function
+                aliases: [Milnor Lobachevsky]
+            """
+        ),
+        encoding="utf-8",
+    )
+
+    llm = MockLLM(GROUNDED_LLM_OUTPUT)
+    report = compile_all(changed_only=False, llm=llm, output_dir=str(mock_settings))
+
+    assert "lobachevsky-function" not in report.quarantined
+    assert (mock_settings / "lobachevsky-function.md").exists()
+
+
+# ---------------------------------------------------------------------------
+# Conflict detection (Fix 9)
+# ---------------------------------------------------------------------------
+
+
+def test_detect_conflicts_finds_adversative_keywords() -> None:
+    """Chunks from different bibkeys both containing adversative keywords → conflict."""
+    chunks = [
+        {
+            "id": 10,
+            "paper_id": "p1",
+            "ord": 0,
+            "content": "The discrete map works well, but diverges in degenerate cases.",
+            "bibkey": "Smith2020",
+        },
+        {
+            "id": 11,
+            "paper_id": "p2",
+            "ord": 0,
+            "content": "However, the approach from Jones is more stable.",
+            "bibkey": "Jones2019",
+        },
+    ]
+    conflicts = _detect_conflicts("test-concept", chunks)
+    assert len(conflicts) >= 1
+    slugs, bk1s, bk2s = zip(*conflicts, strict=True)
+    assert "test-concept" in slugs
+
+
+def test_detect_conflicts_no_conflict_when_single_bibkey() -> None:
+    """Only one bibkey → no conflict possible."""
+    conflicts = _detect_conflicts("test-concept", FIXTURE_CHUNKS)
+    assert conflicts == []
+
+
+# ---------------------------------------------------------------------------
+# append_log quarantine rendering
+# ---------------------------------------------------------------------------
+
+
+def test_log_append_records_quarantined(
+    mock_settings: Path,
+) -> None:
+    """Quarantined slugs appear in the log entry."""
+    report = CompileReport(
+        compiled=[],
+        quarantined=["some-concept"],
+    )
+    append_log(report, wiki_dir=mock_settings)
+    content = (mock_settings / "log.md").read_text(encoding="utf-8")
+    assert "some-concept" in content
+    assert "QUARANTINED" in content