codex/wiki.py

@@ -402,6 +402,13 @@ def _detect_conflicts(
 
 _INLINE_CODE_RE = re.compile(r"`[^`]+`")
 
+# LaTeX math spans — protected from cross-ref injection so a concept name inside
+# a formula is not rewritten to a [[slug]] link, corrupting the LaTeX (audit R-9).
+_MATH_SPAN_RE = re.compile(
+    r"\$\$.*?\$\$|\$[^$\n]*?\$|\\\(.*?\\\)|\\\[.*?\\\]",
+    re.DOTALL,
+)
+
 
 def _inject_cross_refs(
     markdown: str,
@@ -411,11 +418,12 @@ def _inject_cross_refs(
     """Replace occurrences of other concept titles/aliases with ``[[slug]]`` links.
 
     Only exact case-insensitive whole-word matches outside of existing
-    ``[[…]]`` blocks or inline code spans are replaced.
-    Inline-code spans (`` `…` ``) are temporarily protected by null-byte
-    placeholders and restored after injection.
+    ``[[…]]`` blocks, inline code spans, or LaTeX math spans are replaced.
+    Inline-code (`` `…` ``) and math (``$…$``, ``$$…$$``, ``\\(…\\)``,
+    ``\\[…\\]``) spans are temporarily protected by null-byte placeholders and
+    restored after injection.
     """
-    # Step 1: protect inline-code spans from replacement
+    # Step 1: protect inline-code and math spans from replacement
     placeholders: dict[str, str] = {}
 
     def _protect(m: re.Match[str]) -> str:
@@ -424,6 +432,7 @@ def _inject_cross_refs(
         return key
 
     markdown = _INLINE_CODE_RE.sub(_protect, markdown)
+    markdown = _MATH_SPAN_RE.sub(_protect, markdown)  # don't rewrite names inside LaTeX (R-9)
 
     # Step 2: inject cross-refs on unprotected text
     for concept in all_concepts:
@@ -602,14 +611,14 @@ def compile_concept(
     claims = _parse_claims(raw_output)
     claims = _run_grounding_guard(claims, chunks)
 
-    _all_concepts = all_concepts or []
-    raw_output = _inject_cross_refs(raw_output, _all_concepts, concept.slug)
-
-    # Graceful: try to embed formula chunks (F-09) — skip if table missing
+    # Graceful: formula-embedding hook (F-09) — currently a no-op (audit C-12).
     _try_embed_formulas(concept, chunks)
 
     compiled_at = datetime.now(UTC)
+    # Mark ungrounded claims on the raw body FIRST, then inject cross-refs: a
+    # concept name inside a claim must not stop the ⚠ regex from matching (C-13).
     markdown = _render_page_markdown(concept, raw_output, claims, compiled_at)
+    markdown = _inject_cross_refs(markdown, all_concepts or [], concept.slug)
 
     return ConceptPage(
         concept=concept,
@@ -621,20 +630,13 @@ def compile_concept(
 
 
 def _try_embed_formulas(concept: Concept, chunks: list[dict[str, Any]]) -> None:
-    """Attempt to look up formula chunks for the concept — graceful no-op if F-09 absent."""
-    try:
-        from codex.db import get_conn
+    """Reserved hook for embedding F-09 formula chunks into a page.
 
-        with get_conn() as conn:
-            # Check if formulas table exists
-            row = conn.execute(
-                "SELECT 1 FROM information_schema.tables WHERE table_name = 'formulas'"
-            ).fetchone()
-            if row is None:
-                return  # F-09 not present
-            # (Future: embed relevant raw_latex into the page)
-    except Exception:  # noqa: BLE001
-        return  # DB not reachable or other error — degrade gracefully
+    Currently a no-op — formula embedding is not implemented yet. Kept as a stable
+    seam for compile_concept's call site. The previous body issued a per-concept
+    DB round-trip (information_schema lookup) that did nothing (audit C-12).
+    """
+    return
 
 
 # ---------------------------------------------------------------------------

tests/wiki/test_compile.py

@@ -274,6 +274,19 @@ def test_inject_cross_refs_skips_inline_code() -> None:
     assert "[[circle-packing]]" in result  # bare occurrence replaced
 
 
+def test_inject_cross_refs_skips_math_spans() -> None:
+    """Concept names inside LaTeX math are NOT rewritten to [[slug]] links (audit R-9)."""
+    concepts = [
+        Concept(slug="energy", title="Energy", aliases=[]),
+        FIXTURE_CONCEPT,
+    ]
+    text = "Prose Energy here. Math $x = Energy^2$ and inline \\(Energy\\) stay literal."
+    result = _inject_cross_refs(text, concepts, current_slug="lobachevsky-function")
+    assert "$x = Energy^2$" in result  # display/inline $...$ math untouched
+    assert "\\(Energy\\)" in result  # \(...\) math untouched
+    assert "Prose [[energy]] here." in result  # prose occurrence still linked
+
+
 def test_inject_cross_refs_full_list_even_when_single_concept() -> None:
     """Cross-ref injection uses the full concept list, not just the compiled concept."""
     concepts = [