diff --git a/src/aipass/aipass/apps/handlers/structure_scan/structure_scanner.py b/src/aipass/aipass/apps/handlers/structure_scan/structure_scanner.py
index be1b2092..7685e165 100644
--- a/src/aipass/aipass/apps/handlers/structure_scan/structure_scanner.py
+++ b/src/aipass/aipass/apps/handlers/structure_scan/structure_scanner.py
@@ -93,7 +93,7 @@ def find_project_root(start: Path) -> Optional[Path]:
 # =============================================================================
 
 
-_SCAN_SKIP_DIRS = {".archive", ".venv", ".git", "__pycache__", "node_modules", ".chroma"}
+_SCAN_SKIP_DIRS = {".archive", ".backup", ".venv", ".git", "__pycache__", "node_modules", ".chroma", "templates"}
 
 
 def scan_agents(project_root: Path) -> List[AgentInfo]:
@@ -286,12 +286,15 @@ def detect_pollution(agents: List[AgentInfo]) -> List[PollutionHit]:
 def check_registry_consistency(
     registry_path: Path,
     agents: List[AgentInfo],
+    project_root: Optional[Path] = None,
 ) -> List[RegistryIssue]:
     """Validate that registry branches[].path entries match actual filesystem.
 
     Returns:
         List of RegistryIssue for each problem found.
     """
+    anchor = (project_root or registry_path.parent).resolve()
+
     try:
         data = json.loads(registry_path.read_text(encoding="utf-8"))
     except (json.JSONDecodeError, OSError) as exc:
@@ -309,7 +312,8 @@ def check_registry_consistency(
             issues.append(RegistryIssue(name, "", "missing"))
             continue
 
-        reg_path = Path(path_str).resolve()
+        p = Path(path_str)
+        reg_path = p.resolve() if p.is_absolute() else (anchor / p).resolve()
         if not reg_path.exists():
             issues.append(RegistryIssue(name, path_str, "missing"))
         elif str(reg_path) not in agent_paths:
diff --git a/src/aipass/aipass/apps/modules/doctor.py b/src/aipass/aipass/apps/modules/doctor.py
index b74ff049..260669a0 100644
--- a/src/aipass/aipass/apps/modules/doctor.py
+++ b/src/aipass/aipass/apps/modules/doctor.py
@@ -670,7 +670,7 @@ def _check_structure() -> List[CheckResult]:
     # Registry consistency
     reg_path = _discover_registry(start_path=project_root)
     if reg_path and reg_path.exists():
-        reg_issues = check_registry_consistency(reg_path, agents)
+        reg_issues = check_registry_consistency(reg_path, agents, project_root=project_root)
         if reg_issues:
             for issue in reg_issues:
                 glyph = GLYPH_FAIL if issue.problem == "missing" else GLYPH_WARN
@@ -686,7 +686,7 @@ def _check_structure() -> List[CheckResult]:
     root_hits = check_root_artifacts(project_root)
     if root_hits:
         for hit in root_hits:
-            glyph = GLYPH_WARN if hit.severity == "warn" else GLYPH_PASS
+            glyph = GLYPH_PASS if hit.severity == "pass" else GLYPH_WARN
             results.append(CheckResult(f"root: {hit.name}", glyph, hit.description, ""))
     else:
         results.append(CheckResult("root artifacts", GLYPH_PASS, "none misplaced", ""))