diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1e0044c3..0fff21de 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -71,10 +71,13 @@ PyPI version — not the changelog header.
   `ALLOWED_JSON_SUBDIRS` allowlist and a `check_branch_post()` that validates
   `{branch}_json/` subdirs — `custom_config/` and hidden dirs (`.archive`) pass,
   any other split is flagged. `json_structure_content.py` documents the directory
-  structure and operator-config location. 5 new tests. (The new check surfaced
-  `devpulse_json/compass/` as an unsanctioned split — handled via a documented
-  devpulse bypass, compass being a legitimate SQLite/FTS5 decision store that
-  needs its own directory.)
+  structure and operator-config location. The subdir check honors
+  `.seedgo/bypass.json` (bypass rules are threaded through
+  `check_branch_post` → `_check_json_dir_structure`), so a branch can sanction a
+  legitimate data subdir while unsanctioned + unbypassed splits still fail. 7 new
+  tests. (The new check surfaced `devpulse_json/compass/` — the devpulse Compass
+  SQLite/FTS5 decision store, which needs its own directory — now sanctioned via a
+  documented devpulse bypass; audit confirms Json_Structure back to 100%.)
 
 - **`git_gate` block messages now guide external users instead of dead-ending
   (issue #620).** A blocked raw `git`/`gh` command previously just errored. The
diff --git a/src/aipass/devpulse/.seedgo/bypass.json b/src/aipass/devpulse/.seedgo/bypass.json
index 63a3dd4c..bcd62676 100644
--- a/src/aipass/devpulse/.seedgo/bypass.json
+++ b/src/aipass/devpulse/.seedgo/bypass.json
@@ -5,6 +5,11 @@
     "description": "Standards bypass configuration for this branch"
   },
   "bypass": [
+    {
+      "standard": "json_structure",
+      "file": "devpulse_json/compass",
+      "reason": "compass/ is the devpulse-owned Compass decision store (SQLite/FTS5 — db + wal + shm) which needs its own directory. Legitimate data subdir, not operator-config (custom_config/) nor auto-gen root data. Sanctioned exception per #643."
+    },
     {
       "standard": "architecture",
       "reason": "No 'manager' citizen_class template in spawn. Devpulse is the only manager branch."
diff --git a/src/aipass/seedgo/apps/handlers/aipass_standards/json_structure_check.py b/src/aipass/seedgo/apps/handlers/aipass_standards/json_structure_check.py
index 5f79eb9f..ae053c31 100644
--- a/src/aipass/seedgo/apps/handlers/aipass_standards/json_structure_check.py
+++ b/src/aipass/seedgo/apps/handlers/aipass_standards/json_structure_check.py
@@ -270,7 +270,7 @@ def _check_json_handler_config(_handler_path: Path, content: str, _bypass_rules:
             "passed": not has_template_dir,
             "message": "No json_templates/ references (correct — code is the template)"
             if not has_template_dir
-            else "References json_templates/ directory — standard requires auto-create from code defaults, not file templates",
+            else "References json_templates/ directory — use auto-create from code defaults, not file templates",
         }
     )
 
@@ -304,16 +304,18 @@ def _find_json_dir(branch_path: str) -> Path | None:
     return json_dir if json_dir.is_dir() else None
 
 
-def _check_json_dir_structure(branch_path: str) -> list[dict]:
+def _check_json_dir_structure(branch_path: str, bypass_rules: list | None = None) -> list[dict]:
     """Validate {branch}_json/ has no unsanctioned subdirectories.
 
     Allowed: custom_config/ (operator-editable config).
     Hidden dirs (starting with '.') are ignored (e.g. .archive).
+    Bypassed subdirs (via .seedgo/bypass.json) are also allowed.
     """
     json_dir = _find_json_dir(branch_path)
     if json_dir is None:
         return []
 
+    bp = Path(branch_path)
     violations = []
     for child in sorted(json_dir.iterdir()):
         if not child.is_dir():
@@ -322,6 +324,9 @@ def _check_json_dir_structure(branch_path: str) -> list[dict]:
             continue
         if child.name in ALLOWED_JSON_SUBDIRS:
             continue
+        relative = f"{bp.name}_json/{child.name}"
+        if is_bypassed(relative, "json_structure", bypass_rules=bypass_rules):
+            continue
         violations.append(
             {
                 "file": child.name,
@@ -336,8 +341,8 @@ def _check_json_dir_structure(branch_path: str) -> list[dict]:
     return violations
 
 
-def check_branch_post(branch_path: str) -> tuple[list, list]:
+def check_branch_post(branch_path: str, bypass_rules: list | None = None) -> tuple[list, list]:
     """Post-audit check: validate {branch}_json/ directory structure."""
-    violations = _check_json_dir_structure(branch_path)
+    violations = _check_json_dir_structure(branch_path, bypass_rules=bypass_rules)
     scores = [0] if violations else [100]
     return violations, scores
diff --git a/src/aipass/seedgo/apps/handlers/audit/branch_audit.py b/src/aipass/seedgo/apps/handlers/audit/branch_audit.py
index bd84ecc0..b8668f3f 100644
--- a/src/aipass/seedgo/apps/handlers/audit/branch_audit.py
+++ b/src/aipass/seedgo/apps/handlers/audit/branch_audit.py
@@ -182,7 +182,7 @@ def audit_branch(branch: Dict[str, str], bypass_rules: list, pack_path: Path | N
     for name, checker in checkers.items():
         if hasattr(checker, "check_branch_post") and name in scores:
             try:
-                pv, ps = checker.check_branch_post(str(branch_path))
+                pv, ps = checker.check_branch_post(str(branch_path), bypass_rules=bypass_rules)
                 all_violations.setdefault(name, []).extend(pv)
                 if ps:
                     scores[name] = int(sum(ps + [scores[name]]) / (len(ps) + 1))
diff --git a/src/aipass/seedgo/tests/test_aipass_standards.py b/src/aipass/seedgo/tests/test_aipass_standards.py
index 58758bb0..fbf09fc3 100644
--- a/src/aipass/seedgo/tests/test_aipass_standards.py
+++ b/src/aipass/seedgo/tests/test_aipass_standards.py
@@ -213,6 +213,38 @@ def test_json_structure_check_branch_post(tmp_path):
     assert scores2 == [100]
 
 
+def test_json_structure_bypassed_subdir_passes(tmp_path):
+    """A subdir bypassed via bypass_rules is not flagged."""
+    from aipass.seedgo.apps.handlers.aipass_standards.json_structure_check import _check_json_dir_structure
+
+    branch = tmp_path / "mybranch"
+    branch.mkdir()
+    json_dir = branch / "mybranch_json"
+    json_dir.mkdir()
+    (json_dir / "compass").mkdir()
+
+    bypass_rules = [{"standard": "json_structure", "file": "mybranch_json/compass", "reason": "test"}]
+    violations = _check_json_dir_structure(str(branch), bypass_rules=bypass_rules)
+    assert violations == []
+
+
+def test_json_structure_unbypassed_subdir_still_fails(tmp_path):
+    """An unsanctioned subdir without a bypass entry is still flagged."""
+    from aipass.seedgo.apps.handlers.aipass_standards.json_structure_check import _check_json_dir_structure
+
+    branch = tmp_path / "mybranch"
+    branch.mkdir()
+    json_dir = branch / "mybranch_json"
+    json_dir.mkdir()
+    (json_dir / "compass").mkdir()
+    (json_dir / "random_dir").mkdir()
+
+    bypass_rules = [{"standard": "json_structure", "file": "mybranch_json/compass", "reason": "test"}]
+    violations = _check_json_dir_structure(str(branch), bypass_rules=bypass_rules)
+    assert len(violations) == 1
+    assert "random_dir" in violations[0]["message"]
+
+
 # ---------------------------------------------------------------------------
 # Tests -- naming_check.is_bypassed
 # ---------------------------------------------------------------------------