├── .claude └── agents │ ├── ai-engineer.md │ ├── architect-review.md │ ├── backend-architect.md │ ├── cloud-architect.md │ ├── code-reviewer.md │ ├── database-admin.md │ ├── debugger.md │ ├── devops-troubleshooter.md │ ├── frontend-developer.md │ ├── mcp-expert.md │ ├── performance-engineer.md │ ├── python-expert.md │ ├── review-agent.md │ ├── security-auditor.md │ └── test-automator.md ├── .dockerignore ├── .env.example ├── .github └── workflows │ └── docker-build.yml ├── .gitignore ├── CLAUDE.md ├── FAQ.md ├── HomeSystem ├── __init__.py ├── __pycache__ │ └── __init__.cpython-310.pyc ├── graph │ ├── __init__.py │ ├── base_graph.py │ ├── chat_agent.py │ ├── config │ │ ├── llm_providers.yaml │ │ ├── mcp_config.yaml │ │ └── paper_analysis_config.json │ ├── deep_paper_analysis_agent.py │ ├── formatter │ │ ├── __init__.py │ │ └── markdown_formatter.py │ ├── formula_correction_agent.py │ ├── llm_factory.py │ ├── mcp_manager.py │ ├── models │ │ └── analysis_models.py │ ├── paper_analysis_agent.py │ ├── parser │ │ ├── __init__.py │ │ └── paper_folder_parser.py │ ├── simple_formula_corrector.py │ ├── tool │ │ ├── __init__.py │ │ ├── gif_detector.py │ │ ├── gif_downloader.py │ │ ├── image_analysis_tool.py │ │ ├── math_formula_extractor.py │ │ ├── obtain_web_content.py │ │ ├── ocr_document_loader.py │ │ ├── paper_analysis_tools.py │ │ ├── search.py │ │ ├── text_chunk_indexer.py │ │ ├── text_editor.py │ │ ├── video_analysis_tool.py │ │ ├── video_link_detector.py │ │ ├── video_resource_processor.py │ │ └── youtube_downloader.py │ ├── video_utils.py │ ├── vision_agent.py │ └── vision_utils.py ├── integrations │ ├── __init__.py │ ├── database │ │ ├── __init__.py │ │ ├── connection.py │ │ ├── migrations │ │ │ ├── README.md │ │ │ └── add_full_paper_relevance_fields.py │ │ ├── models.py │ │ └── operations.py │ ├── dify │ │ ├── __init__.py │ │ ├── dify.py │ │ ├── dify_knowledge.py │ │ └── service.py │ ├── paper_analysis │ │ ├── __init__.py │ │ └── analysis_service.py │ ├── paperless │ │ ├── __init__.py │ │ └── paperless.py │ └── siyuan │ │ ├── __init__.py │ │ └── siyuan.py ├── utility │ ├── __init__.py │ ├── __pycache__ │ │ └── __init__.cpython-310.pyc │ ├── arxiv │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ └── arxiv.cpython-310.pyc │ │ ├── arxiv.py │ │ ├── database_integration.py │ │ └── paper_metadata_extractor.py │ └── ollama │ │ ├── __init__.py │ │ ├── cli.py │ │ ├── config_updater.py │ │ └── model_manager.py └── workflow │ ├── __init__.py │ ├── engine.py │ ├── paper_gather_task │ ├── __init__.py │ ├── chinese_search_assistant.py │ ├── data_manager.py │ ├── llm_config.py │ └── paper_gather_task.py │ ├── scheduler.py │ └── task.py ├── LICENSE ├── README.md ├── Web └── PaperAnalysis │ ├── .dockerignore │ ├── .env.example │ ├── .gitignore │ ├── Docker-README.md │ ├── Dockerfile │ ├── README.md │ ├── app.log │ ├── app.py │ ├── backup-data.sh │ ├── build.sh │ ├── cleanup_test_data.py │ ├── config.py │ ├── deploy.sh │ ├── docker-compose.yml │ ├── docker-entrypoint.sh │ ├── requirements.txt │ ├── routes │ ├── __init__.py │ ├── analysis.py │ ├── api.py │ ├── collect.py │ ├── explore.py │ ├── main.py │ └── task.py │ ├── services │ ├── __init__.py │ ├── analysis_service.py.bak │ ├── dify_service.py │ ├── paper_explore_service.py │ ├── paper_gather_service.py │ └── task_service.py │ ├── setup-permissions.sh │ ├── start.sh │ ├── static │ ├── css │ │ └── style.css │ ├── favicon.ico │ └── js │ │ ├── batch-operations.js │ │ ├── config.js │ │ ├── main.js │ │ ├── paper-analysis.js │ │ └── papers.js │ ├── stop.sh │ ├── templates │ ├── about.html │ ├── analysis │ │ ├── config.html │ │ └── index.html │ ├── base.html │ ├── collect │ │ ├── base.html │ │ ├── config.html │ │ ├── error.html │ │ ├── results.html │ │ ├── scheduled_tasks.html │ │ ├── task_history.html │ │ ├── task_status.html │ │ └── tasks.html │ ├── error.html │ ├── explore │ │ ├── _batch_modals.html │ │ ├── _batch_toolbar.html │ │ ├── _paper_card.html │ │ ├── _search_filters.html │ │ ├── base.html │ │ ├── batch_operations.html │ │ ├── error.html │ │ ├── index.html │ │ ├── insights.html │ │ ├── paper_analysis.html │ │ ├── paper_detail.html │ │ ├── papers.html │ │ ├── stats.html │ │ ├── tasks.html │ │ └── unassigned.html │ ├── index.html │ └── settings.html │ ├── test-build.sh │ └── utils │ ├── __init__.py │ └── markdown_utils.py ├── assets └── figs │ └── paper_analysis │ ├── LLM_config.png │ └── first_page.png ├── check-ports.sh ├── data └── paper_gather │ ├── .gitignore │ ├── README.md │ ├── config_schema_version.json │ └── task_history │ └── 2025_07_tasks.json.backup ├── database ├── Dockerfile ├── README.md ├── backup.sh ├── check-tables.sh ├── docker-compose.yml ├── init │ ├── 01-init-extensions.sql │ └── 02-create-tables.sql ├── restore.sh ├── start.sh └── stop.sh ├── debug_clear_arxiv_data.py ├── debug_show_arxiv_data.py ├── deploy ├── README.md ├── docker-compose.database.yml ├── docker-compose.ocr-gpu.yml ├── docker-compose.ocr.yml ├── docker-compose.web.yml └── docker-compose.yml ├── docs ├── README.md └── architecture │ └── paperanalysis-web-structure-v2025-09-20.md ├── leader.md ├── package.json ├── pyproject.toml ├── remote_app ├── .gitignore ├── README.md ├── README_DOCKER.md ├── cleanup.sh ├── deploy.sh ├── docker-compose.yml ├── health-check.sh ├── monitoring │ └── prometheus.yml ├── nginx │ ├── conf.d │ │ └── default.conf │ └── nginx.conf ├── ocr_service │ ├── Dockerfile │ ├── app.py │ ├── docker-entrypoint.sh │ ├── processor.py │ ├── requirements.txt │ ├── shared │ │ ├── __init__.py │ │ ├── auth.py │ │ ├── config.py │ │ └── logging.py │ ├── start.sh │ └── utils │ │ ├── __init__.py │ │ ├── file_handler.py │ │ └── image_processor.py ├── scale.sh └── shared │ ├── __init__.py │ ├── auth.py │ ├── config.py │ └── logging.py ├── requirements.txt ├── scripts └── auto_generate_example.py └── sql └── init └── 01-init-extensions.sql 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