From b5f3128f9f06ccf45e384c9f45ef1f2fbf1fdaf4 Mon Sep 17 00:00:00 2001
From: manumishra12 <connectmanumishra@gmail.com>
Date: Sat, 11 Jul 2026 14:44:35 -0700
Subject: [PATCH] okf: don't end a section at a fenced '#' comment line
 (bundle_tools)

_section_content_lines treated any line starting with '# ' as a heading,
including '#' comment lines inside fenced code blocks. A code fence in a
'# Schema' or '# Citations' section therefore ended the section early, so
_schema_field_names and _citation_entry_count under-read it and the web-pass
augmentation guard in write_concept_doc could compare truncated field or
citation sets.

Track fenced code blocks (backtick and tilde fences) and only treat '# '
lines outside a fence as headings. Adds regression tests.
---
 okf/src/reference_agent/tools/bundle_tools.py | 12 +++++-
 okf/tests/test_bundle_tools.py                | 38 ++++++++++++++++++-
 2 files changed, 47 insertions(+), 3 deletions(-)

diff --git a/okf/src/reference_agent/tools/bundle_tools.py b/okf/src/reference_agent/tools/bundle_tools.py
index 18d42cc5..2d898f73 100644
--- a/okf/src/reference_agent/tools/bundle_tools.py
+++ b/okf/src/reference_agent/tools/bundle_tools.py
@@ -18,12 +18,20 @@
 
 
 def _section_content_lines(body: str, heading: str) -> list[str]:
-    """Return non-blank lines under a top-level `# heading` section."""
+    """Return non-blank lines under a top-level `# heading` section.
+
+    Fenced code blocks are treated as content: a `#`-prefixed line inside a
+    fence is not mistaken for a heading, so it does not prematurely end the
+    section.
+    """
     in_section = False
+    in_fence = False
     out: list[str] = []
     for line in body.splitlines():
         stripped = line.strip()
-        if stripped.startswith("# "):
+        if stripped.startswith("```") or stripped.startswith("~~~"):
+            in_fence = not in_fence
+        elif not in_fence and stripped.startswith("# "):
             in_section = stripped == heading
             continue
         if in_section and stripped:
diff --git a/okf/tests/test_bundle_tools.py b/okf/tests/test_bundle_tools.py
index bf60f262..95f82639 100644
--- a/okf/tests/test_bundle_tools.py
+++ b/okf/tests/test_bundle_tools.py
@@ -5,7 +5,11 @@
 
 import pytest
 
-from reference_agent.tools.bundle_tools import write_concept_doc
+from reference_agent.tools.bundle_tools import (
+    _schema_field_names,
+    _section_content_lines,
+    write_concept_doc,
+)
 from reference_agent.tools.context import (
     clear_web_state,
     set_context,
@@ -148,3 +152,35 @@ def test_web_pass_skips_guard_for_non_bigquery_table_types(tmp_path):
         "# Citations\n[1] [Src](https://src)\n",
     )
     assert "error" not in result
+
+
+def test_section_survives_fenced_hash_comment():
+    body = (
+        "# Schema\n"
+        "- `id` STRING\n"
+        "```\n"
+        "# looks like a heading but is code\n"
+        "```\n"
+        "- `name` STRING\n"
+        "# Other\n"
+        "- ignored\n"
+    )
+    text = "\n".join(_section_content_lines(body, "# Schema"))
+    assert "`id`" in text
+    assert "`name`" in text
+    assert "ignored" not in text
+
+
+def test_schema_fields_survive_fenced_hash_comment():
+    body = (
+        "# Schema\n"
+        "- `id` STRING\n"
+        "```sql\n"
+        "# partition by ingestion day\n"
+        "SELECT 1\n"
+        "```\n"
+        "- `name` STRING\n"
+        "# Citations\n"
+        "[1] [BQ](https://bq)\n"
+    )
+    assert _schema_field_names(body) == {"id", "name"}