Add a core startup migration that refreshes /exe/self_update_manager.py from the repository copy when the installed runtime updater is missing the socket-safe backup and Desktop cleanup markers.
Validate the source updater before replacing anything, preserve the previous runtime script as a backup, and leave current or non-regular targets untouched. Add regression coverage for stale runtime replacement, safe no-op/refusal paths, and the real repository updater source.
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.
