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>

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)