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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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Document Query Plugin DOX
Purpose
- Own document loading, parsing, indexing, and Q&A over local and remote documents.
Ownership
tools/document_query.pyowns the agent-facing query tool.helpers/owns fetching, parser routing, indexing, and query orchestration.prompts/owns document-query tool and optimization prompts.hooks.py,default_config.yaml,plugin.yaml,skills/,extensions/, andwebui/own dependency bootstrap, settings, metadata, skill guidance, hooks, and UI.
Local Contracts
- Respect configured size, timeout, retry, parser concurrency, and OCR limits.
- Fetch local and remote resources safely and avoid leaking document contents beyond intended prompt/tool use.
- Keep optional dependency installation targeted to the framework runtime.
Work Guidance
- Coordinate parser changes with timeout handling and fallback behavior.
Verification
- Smoke-test representative PDF, text/HTML, image/OCR, and remote-document queries after parser changes.
Child DOX Index
No child DOX files.