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.
Redesign extension handling to support explicit async/sync execution. helpers/extension.py rewrites the extensible decorator, adds call_extensions_async / call_extensions_sync, and a helper to gather extension classes; caching flag adjusted. Updated call sites across the codebase (agent, APIs, plugins, tools, settings, extensions) to use extension.extensible and the new call_extensions_async/sync API, and converted several extension handlers from async to sync. Also small frontend tweaks (use globalThis.runtimeInfo) and minor import updates (csrf_protect in run_ui). This centralizes extension discovery/execution and avoids previously scattered asyncio.run usage.
