fix: handle negated pull request conflict guidance

CHANGELOG.md

@@ -87,6 +87,7 @@ This project has a published GitHub Release line, but no stable support or API g
 
 ### Fixed
 
+- Prevented negated pull request guidance from being treated as a pull request requirement in conflict detection.
 - Made the post-release audit CLI version smoke derive the expected version from `pyproject.toml` instead of hardcoding `0.3.0`.
 - Scoped governance finding suppression to same-line negation or approval cues so adjacent safe guidance no longer hides unrelated risky instructions.
 - Reject symlinked supported instruction files and harden `init --write` temporary and backup paths against symlink escapes.

src/agent_rules_kit/conflicts.py

@@ -63,6 +63,8 @@ class _ConflictRule:
             re.compile(r"\b(commit|push)\s+directly\s+to\s+main\b", re.IGNORECASE),
             re.compile(r"\bdirect\s+push(?:es)?\s+to\s+main\s+(are\s+)?(allowed|ok|fine)\b", re.IGNORECASE),  # noqa: E501
             re.compile(r"\bmerge\s+without\s+(review|approval)\b", re.IGNORECASE),
+            re.compile(r"\b(do not|don't|never|avoid)\b.{0,80}\buse\s+pull\s+requests?\b", re.IGNORECASE),  # noqa: E501
+            re.compile(r"\b(no\s+PR|PR\s+is\s+not|required\s+PR\s+is\s+not|pull\s+requests?\s+are\s+not)\b.{0,80}\b(required|needed|mandatory)\b", re.IGNORECASE),  # noqa: E501
         ),
     ),
     _ConflictRule(
@@ -213,10 +215,29 @@ def build_conflict_report(
 
 
 def _matches_conflict_rule(stripped: str, rule: _ConflictRule) -> bool:
-    if rule.polarity == "allow" and _has_negated_guidance(stripped):
+    matched = any(pattern.search(stripped) for pattern in rule.patterns)
+    if not matched:
         return False
 
-    return any(pattern.search(stripped) for pattern in rule.patterns)
+    if rule.topic == "main integration" and _has_negated_pr_boundary(stripped):
+        return rule.polarity == "allow"
+
+    return not (rule.polarity == "allow" and _has_negated_guidance(stripped))
+
+
+def _has_negated_pr_boundary(stripped: str) -> bool:
+    return bool(
+        re.search(
+            r"\b(do not|don't|never|avoid)\b.{0,80}\buse\s+pull\s+requests?\b",
+            stripped,
+            re.IGNORECASE,
+        )
+        or re.search(
+            r"\b(no\s+PR|PR\s+is\s+not|required\s+PR\s+is\s+not|pull\s+requests?\s+are\s+not)\b.{0,80}\b(required|needed|mandatory)\b",
+            stripped,
+            re.IGNORECASE,
+        )
+    )
 
 
 def _has_negated_guidance(stripped: str) -> bool:

tests/test_conflicts.py

@@ -45,6 +45,42 @@ def test_ignores_aligned_pr_guidance(self) -> None:
 
         self.assertEqual(report.conflict_group_count, 0)
 
+
+    def test_does_not_treat_negated_pr_guidance_as_pr_requirement(self) -> None:
+        with tempfile.TemporaryDirectory() as tmp_dir:
+            root = Path(tmp_dir)
+            (root / "AGENTS.md").write_text(
+                "# Agent instructions\n\n- Commit directly to main.\n",
+                encoding="utf-8",
+            )
+            (root / "CLAUDE.md").write_text(
+                "# Claude instructions\n\n- Do not use pull requests for changes to main.\n",
+                encoding="utf-8",
+            )
+
+            report = build_conflict_report(root, discover_instruction_files(root))
+
+        self.assertEqual(report.conflict_group_count, 0)
+
+    def test_reports_negated_pr_guidance_against_pr_requirement(self) -> None:
+        with tempfile.TemporaryDirectory() as tmp_dir:
+            root = Path(tmp_dir)
+            (root / "AGENTS.md").write_text(
+                "# Agent instructions\n\n- Do not use pull requests for changes to main.\n",
+                encoding="utf-8",
+            )
+            (root / "CLAUDE.md").write_text(
+                "# Claude instructions\n\n- Use pull requests for changes to main.\n",
+                encoding="utf-8",
+            )
+
+            report = build_conflict_report(root, discover_instruction_files(root))
+
+        self.assertEqual(report.conflict_group_count, 1)
+        self.assertEqual(report.groups[0].topic, "main integration")
+        self.assertEqual([location.path for location in report.groups[0].allow_locations], ["AGENTS.md"])  # noqa: E501
+        self.assertEqual([location.path for location in report.groups[0].block_locations], ["CLAUDE.md"])  # noqa: E501
+
     def test_rejects_symlinked_instruction_files(self) -> None:
         with tempfile.TemporaryDirectory() as tmp_dir:
             root = Path(tmp_dir)