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.
- Change @extensible decorator to generate extension paths from full module and qualname hierarchies instead of flattened names
- Update extension path format from `{module}_{qualname}_{start|end}` to `_functions/<module>/<qualname>/{start|end}`
- Move all extension files to new deep directory structure under `_functions/` to match new path format
- Replace PathSpec.from_lines(GitWildMatchPattern, ...) with PathSpec.from_lines
