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.
Add comprehensive file-level DOX documentation across the repo and update directory AGENTS.md indexes. Many new `*.py.dox.md` files were added under api, helpers, tools, plugins, extensions, webui, and other dirs to document endpoint purpose, ownership, runtime contracts, work guidance, and verification. Several AGENTS.md files were created or updated (agents profiles, api, docker, extensions, helpers, plugins, skills, webui components, etc.) to list child DOX files and clarify documentation/work guidance. Also add example and bundled profile DOX files (agent0, default, developer, hacker, researcher) and minor updates to helpers/dirty_json.py and its tests. These changes improve on-disk documentation coverage and establish the convention that each direct runtime file should have a matching `*.dox.md` describing its contracts and verification steps.
Introduce DOX (AGENTS.md) contracts across the repository to formalize ownership and local work contracts: adds .github/AGENTS.md plus AGENTS.md files for agents, api, conf, docker, docs, extensions, helpers, knowledge, lib, plugins, prompts, scripts, skills, tests, tools, usr, webui (and several subfolders). Update root AGENTS.md (content and last-updated date) to include DOX framework guidance and a child DOX index. Update .gitignore to allow usr/ and usr/plugins AGENTS.md files. Remove legacy deep-dive files under docs/agents (banners, components, modals, plugins) and migrate frontend/plugin references to webui/ and plugins/ DOX locations. Also adjust plugins/README.md and several skills/*/SKILL.md files to align with the new DOX layout.
