Load active-project AGENTS.md path-chain guidance into the protocol area without duplicating the project root instructions.
Move the AGENTS.md protocol wording into a prompt template, reuse existing file/path helpers, and cover direct-path discovery plus prompt assembly with focused tests.
Introduce generic project edit-data extension hooks so plugins can contribute named project settings sections without coupling helpers.projects to plugin-specific storage.
Move _model_config project LLM payload handling behind those hooks and preserve inherited global model settings unless a project override already exists or is explicitly selected.
Cover the inheritance regression, existing scoped overrides, multiple plugin sections, core-field collision protection, and extension payload filtering in focused project/model-config tests.
Create the .a0proj/skills directory during project metadata setup so Project Settings can open the skills folder for new projects. Repair the folder when loading existing project settings, and cover both creation and repair with regression tests.
Add project-scoped MCP server configuration with global/project merge semantics, a richer settings UI, and chat composer access. Introduce MCP config scanning plus project-aware status/detail/log/apply APIs while preserving the raw JSON editor. Strengthen MCP runtime handling for dotted tool names, timeouts, status accuracy, and project-aware tool execution, with focused regression coverage.
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.
