Temporarily stash tracked plugin edits while updating. Restore the original checkout and edits if the update cannot reapply them, and surface the conflict beside the Update button. Add isolated Git regression coverage for merge, no-op, and conflict cases.
Introduce a /stop API handler (api/stop.py) and its DOX to cancel an AgentContext run without deleting the context; it clears pause state, progress and logs an info step. Add tests for stopping behavior, chat working animation, and sidebar timestamp/spacing (tests/*). Update helpers/git._format_git_timestamp to emit UTC timestamps without a timezone suffix and add a test for it. Implement stop-related UI/UX: input-store.js gains a stop state, activateSendButton(), and stopAgent() to call /stop; chat-bar-input.html updates the send button markup, aria-label and stop styles. Update sidebar/chat list CSS to add the working-bubble animation, adjust chat row layout and action-button visibility, and left-sidebar/bottom styling (nowrap timestamp). Modify messages.js to hide kvps.finished from display and complete the active process group when finished. Minor welcome-composer and documentation updates to reflect these behaviors.
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.
