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Toggling a skill wrote resolved secrets into extensions_config.json. The Gateway skill toggle and DeerFlowClient.update_skill loaded the file with ExtensionsConfig.from_file(), which replaces every "$VAR" string with the environment value (and an unset variable with ""), then serialized that model back through to_file_dict(). A "$GITHUB_TOKEN" reference was persisted as the plaintext token, and an unset reference was erased for good. DeerFlowClient.update_mcp_config had the same flaw for every key other than mcpServers. Every writer now does a raw read-modify-write, the way the MCP router already did: read_raw_extensions_config reads the on-disk JSON, set_raw_skill_enabled changes only the target entry, and validate_raw_extensions_config checks the candidate the way the runtime will load it before the atomic write. When the file does not exist yet, the Gateway seeds it with the cached skill states only, never the resolved cached model. The MCP router's raw loader and candidate validation delegate to the same helpers, so the rule lives in one place, and to_file_dict() is removed so the unsafe serialization has no entry point left. Co-authored-by: Willem Jiang <willem.jiang@gmail.com>