fix(wiki): pass chunks explicitly to compile_concept (single retrieve)

compile_concept now accepts chunks as a positional parameter; compile_all
retrieves chunks once and passes them directly, avoiding double-retrieve.
Also separates all_concepts (full list) from compile_concepts (filtered),
so cross-ref injection always uses the complete concept list regardless of
--concept filter (Fix 6 + Fix 8).

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

codex/wiki.py

@@ -426,6 +426,7 @@ def _render_page_markdown(
 
 def compile_concept(
     concept: Concept,
+    chunks: list[dict[str, Any]],
     *,
     top_k: int,
     llm: LLMClient,
@@ -434,19 +435,24 @@ def compile_concept(
 ) -> ConceptPage:
     """Compile a single concept page.
 
-    1. Retrieve Top-K chunks (hybrid dense+FTS) for concept title + aliases.
+    Parameters
-    2. Synthesise via LLM (Ollama) with per-claim citation format.
+    ----------
-    3. Run Grounding-Guard: mark ungrounded claims as ⚠.
+    concept:
-    4. Inject cross-references to other concepts as [[slug]] links.
+        The concept to compile.
-    5. Embed formula chunks if ``formulas`` table is present (graceful).
+    chunks:
+        Pre-retrieved source chunks for this concept (from :func:`_retrieve_chunks`).
+        Passing chunks explicitly avoids a second retrieve and ensures the stored
+        hash matches the chunks actually used for synthesis.
+
+    1. Synthesise via LLM (Ollama) with per-claim citation format.
+    2. Run Grounding-Guard: mark ungrounded claims as ⚠.
+    3. Inject cross-references to other concepts as [[slug]] links.
+    4. Embed formula chunks if ``formulas`` table is present (graceful).
 
     Returns a :class:`ConceptPage` with full markdown and claim list.
     """
     settings = get_settings()
-    _wiki_dir = wiki_dir or Path(settings.wiki_dir)
+    _wiki_dir = wiki_dir or Path(settings.wiki_dir)  # noqa: F841 — kept for future use
-
-    queries = [concept.title] + concept.aliases
-    chunks = _retrieve_chunks(queries, top_k=top_k)
 
     h = _chunk_hash(chunks)
     prompt = _build_synthesis_prompt(concept, chunks)
@@ -532,10 +538,13 @@ def compile_all(
     if not concepts_path.exists():
         # Fall back to sibling concepts.yaml next to wiki/ dir
         concepts_path = wiki_dir.parent / "wiki" / "concepts.yaml"
-    concepts = load_concepts(str(concepts_path))
+    # Load the FULL concept list — used for cross-reference injection regardless of filter
+    all_concepts = load_concepts(str(concepts_path))
 
-    if concept_filter:
+    # Apply filter only to the set of concepts that will be (re-)compiled
-        concepts = [c for c in concepts if c.slug == concept_filter]
+    compile_concepts = (
+        [c for c in all_concepts if c.slug == concept_filter] if concept_filter else all_concepts
+    )
 
     state_path = wiki_dir / ".compile-state.json"
     state = _load_compile_state(state_path)
@@ -549,8 +558,8 @@ def compile_all(
 
     report = CompileReport()
 
-    for concept in concepts:
+    for concept in compile_concepts:
-        # Fast check: retrieve chunks and compare hash
+        # Retrieve chunks once — reuse for hash check and synthesis
         queries = [concept.title] + concept.aliases
         chunks = _retrieve_chunks(queries, top_k=k)
         h = _chunk_hash(chunks)
@@ -561,9 +570,10 @@ def compile_all(
 
         page = compile_concept(
             concept,
+            chunks,
             top_k=k,
             llm=_llm,
-            all_concepts=concepts,
+            all_concepts=all_concepts,  # always the full list for cross-refs
             wiki_dir=wiki_dir,
         )
 

tests/wiki/test_compile.py

@@ -259,7 +259,9 @@ def test_compile_concept_returns_concept_page(
 ) -> None:
     """compile_concept returns a ConceptPage with non-empty markdown."""
     llm = MockLLM(GROUNDED_LLM_OUTPUT)
-    page = compile_concept(FIXTURE_CONCEPT, top_k=6, llm=llm, wiki_dir=mock_settings)
+    page = compile_concept(
+        FIXTURE_CONCEPT, FIXTURE_CHUNKS, top_k=6, llm=llm, wiki_dir=mock_settings
+    )
     assert isinstance(page, ConceptPage)
     assert page.concept.slug == "lobachevsky-function"
     assert len(page.markdown) > 0
@@ -272,7 +274,9 @@ def test_compile_concept_has_chunk_hash(
 ) -> None:
     """Compiled page has a non-empty chunk_hash."""
     llm = MockLLM(GROUNDED_LLM_OUTPUT)
-    page = compile_concept(FIXTURE_CONCEPT, top_k=6, llm=llm, wiki_dir=mock_settings)
+    page = compile_concept(
+        FIXTURE_CONCEPT, FIXTURE_CHUNKS, top_k=6, llm=llm, wiki_dir=mock_settings
+    )
     assert len(page.chunk_hash) == 64  # SHA-256 hex
 
 
@@ -283,7 +287,9 @@ def test_compile_concept_grounded_claim_not_flagged(
 ) -> None:
     """A grounded claim does NOT receive the ⚠ marker in the output markdown."""
     llm = MockLLM(GROUNDED_LLM_OUTPUT)
-    page = compile_concept(FIXTURE_CONCEPT, top_k=6, llm=llm, wiki_dir=mock_settings)
+    page = compile_concept(
+        FIXTURE_CONCEPT, FIXTURE_CHUNKS, top_k=6, llm=llm, wiki_dir=mock_settings
+    )
     # When all claims are grounded, no ⚠ in markdown
     # (may still have 0 ⚠ if claims found; just check no false positive for grounded)
     grounded = [c for c in page.claims if c.grounded]
@@ -298,7 +304,9 @@ def test_compile_concept_ungrounded_claim_marked(
 ) -> None:
     """An ungrounded claim is marked ⚠ in the page markdown."""
     llm = MockLLM(UNGROUNDED_LLM_OUTPUT)
-    page = compile_concept(FIXTURE_CONCEPT, top_k=6, llm=llm, wiki_dir=mock_settings)
+    page = compile_concept(
+        FIXTURE_CONCEPT, FIXTURE_CHUNKS, top_k=6, llm=llm, wiki_dir=mock_settings
+    )
     ungrounded = [c for c in page.claims if not c.grounded]
     if ungrounded:
         assert "⚠" in page.markdown
@@ -311,7 +319,9 @@ def test_compile_concept_header_present(
 ) -> None:
     """Page markdown starts with an H1 header for the concept title."""
     llm = MockLLM(GROUNDED_LLM_OUTPUT)
-    page = compile_concept(FIXTURE_CONCEPT, top_k=6, llm=llm, wiki_dir=mock_settings)
+    page = compile_concept(
+        FIXTURE_CONCEPT, FIXTURE_CHUNKS, top_k=6, llm=llm, wiki_dir=mock_settings
+    )
     assert page.markdown.startswith("# Lobachevsky Function")
 
 
@@ -434,10 +444,12 @@ def test_idempotent_no_rewrite_when_unchanged(
     call_count = 0
     original_compile = compile_concept
 
-    def counting_compile(concept: Concept, **kwargs: Any) -> ConceptPage:
+    def counting_compile(
+        concept: Concept, chunks: list[Any], **kwargs: Any
+    ) -> ConceptPage:
         nonlocal call_count
         call_count += 1
-        return original_compile(concept, **kwargs)
+        return original_compile(concept, chunks, **kwargs)
 
     monkeypatch.setattr("codex.wiki.compile_concept", counting_compile)
 
@@ -478,10 +490,12 @@ def test_force_all_recompiles_even_when_unchanged(
     call_count = 0
     original_compile = compile_concept
 
-    def counting_compile(concept: Concept, **kwargs: Any) -> ConceptPage:
+    def counting_compile(
+        concept: Concept, chunks: list[Any], **kwargs: Any
+    ) -> ConceptPage:
         nonlocal call_count
         call_count += 1
-        return original_compile(concept, **kwargs)
+        return original_compile(concept, chunks, **kwargs)
 
     monkeypatch.setattr("codex.wiki.compile_concept", counting_compile)