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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.
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Default Agent Profile DOX
Purpose
- Own base profile metadata and default prompt specifics inherited by specialized profiles.
- Provide the shared behavior layer for bundled and custom profiles.
Ownership
agent.yamlowns default profile metadata.agent.system.main.specifics.mdowns default profile-specific system prompt content.- Additional prompt overrides under this directory become shared defaults unless a child profile overrides them.
Local Contracts
- Keep default behavior broad, framework-compatible, and safe for inheritance.
- Avoid role-specific instructions that belong in specialist profiles.
- Prompt filenames must match the framework prompt override names they target.
Work Guidance
- Prefer small, explicit prompt changes with clear inheritance impact.
- Check bundled specialist profiles after changing default behavior.
Verification
- Manually inspect YAML and prompt rendering assumptions after edits.
- Run prompt/profile tests when changing inherited prompt behavior.
Child DOX Index
No child DOX files.