Fix restart command for GitOps deployments

- Remove init_operation() from restart - don't regenerate spec from
  commands.py defaults, use existing git-tracked spec.yml instead
- Add docs/deployment_patterns.md documenting GitOps workflow
- Add pre-commit rule to CLAUDE.md
- Fix line length issues in helpers.py

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

stack_orchestrator/deploy/spec.py

@@ -180,7 +180,7 @@ class Spec:
         return self.obj.get(constants.deploy_to_key)
 
     def get_acme_email(self):
-        return self.obj.get(constants.acme_email_key, "")
+        return self.obj.get(constants.network_key, {}).get(constants.acme_email_key, "")
 
     def is_kubernetes_deployment(self):
         return self.get_deployment_type() in [