Introduce a new prompt "protocol" separate from extras: add LoopData.protocol_temporary and protocol_persistent, include protocol contents before message history during prompt construction, and clear temporary protocol data each turn. Add helper _build_context_message to render protocol/extras, update response input conversion to include protocol, and move project instructions & active/loaded skills injection into protocol. Update docs, prompts, plugin metadata, the SkillsTool message, and add tests to verify protocol placement and behavior.
