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.
