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.
Replace JSON-based agent and plugin metadata/config files with YAML equivalents and update code paths to read/write YAML. Added python/helpers/yaml for YAML load/dump and files.read_file_yaml helper; subagents, plugins, and files helpers now prefer agent.yaml/plugin.yaml and default_config.yaml. Migration now includes convert_agents_json_yaml and startup_migration is invoked from initialize to perform conversions. Plugin toggle/config handling was refactored (META_FILE_NAME/CONFIG_DEFAULT_FILE_NAME changes, new determined_toggle_from_paths helper) and memory plugin defaults and extensions were updated to use per-agent plugin config lookups with guards for missing configs.
