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.
Add user-configurable timezone and 12/24-hour preferences, then wire them through settings, runtime snapshots, scheduler payloads, wait handling, notifications, backups, memory, plugin metadata, and frontend formatters.
Keep UTC as the boundary for absolute instants while serializing user-facing dates in the configured or browser-resolved timezone. Preserve scheduler wall-clock inputs in the selected timezone, propagate TZ into desktop/runtime process environments, and restart active desktop sessions when the runtime timezone changes.
Cover the risky paths with timezone regression tests for settings normalization, auto and fixed timezone resolution, scheduler round-trips, memory timestamp conversion, and desktop timezone sync.
Restyle Settings and standard modals around a streamlined left-rail layout, clearer section hierarchy, advanced settings disclosures, and stronger update states.
Add persistent update visibility with quieter once-daily update notifications, plus Remote Link and Space Agent actions in the canvas rail. Refresh the tunnel experience as a normal Remote Link modal with clearer copy, QR/mobile affordances, and safer state handling.
