CHANGELOG.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
docs/CONFIGURATION_GUIDE.md
docs/DOCTOR.md
docs/KNOWN_ISSUES.md
docs/LLM_WIKI_PRINCIPLES.md
docs/MCPORTER_DEPLOYMENT.md
docs/MCP_SETUP.md
docs/MIGRATION_v0.36.md
docs/MIGRATION_v0.38.md
docs/ONBOARDING.md
docs/QMD_SETUP.md
docs/README.md
docs/REFACTORING.md
docs/REFERENCE_TRACKING_GUIDE.md
docs/TODO.md
docs/USAGE_MODES.md
docs/dynamic-workflow-dsl.md
docs/dynamic-workflow-impl.md
docs/dynamic-workflows-guide.md
docs/dynamic-workflows-research.md
docs/llm-inventory.md
docs/quantnodes.md
docs/api/agent.md
docs/archive/done/cli-help-and-aliases.md
docs/archive/done/wiki-backend-interface.md
docs/archive/plans/MANUAL_TEST_PLAN_v2_2026-07-08.md
docs/archive/plans/MANUAL_TEST_RESULTS_2026-07-08.md
docs/archive/plans/MIGRATION_DEPENDENCY_MAP.md
docs/archive/plans/MIGRATION_DISPATCH_GUIDE.md
docs/archive/plans/MIGRATION_REPORT_2026-07-04.md
docs/archive/plans/PROJECT_STATUS_0.30.0.md
docs/archive/plans/PR_2026-07-08_fix-raw-file-and-wikilink.md
docs/archive/plans/README.md
docs/archive/plans/SESSION_SUMMARY_2026-07-08.md
docs/archive/plans/auto-research-v0.24.0.md
docs/archive/plans/multi_factor_paper.md
docs/archive/plans/v0.15.0.md
docs/archive/plans/v0.40-refocus.md
docs/archive/plans/v0.40-release-notes-draft.md
docs/archive/plans/v0.40-ui-merge-app-shell.md
docs/archive/plans/v021-v023-roadmap.md
docs/archive/poc/apply-plan.md
docs/archive/poc/compare.md
docs/archive/poc/m1-decision.md
docs/archive/poc/m1-research.md
docs/archive/poc/nanobot-framework.md
docs/archive/poc/phase-a-steps.md
docs/archive/poc/plan-b-results.md
docs/archive/poc/python-design-patterns.md
docs/archive/status/autoresearch-phase1-status.md
docs/designs/AGENT_INTEGRATION_PLAN.md
docs/designs/AI_TEST_FRAMEWORK.md
docs/designs/MULTI_WIKI_PLAN.md
docs/designs/P3_INGEST_LINT_DESIGN.md
docs/designs/SINK_DESIGN_DECISIONS.md
docs/designs/WEBUI_UNIFIED_SERVER.md
docs/designs/WIKI_LLM_PROMPT_ARCHITECTURE.md
docs/designs/agent-backend-implementation-plan.md
docs/designs/agent-framework-design.md
docs/designs/agent-ui-optimization-plan.md
docs/designs/auth-and-sharing-roadmap.md
docs/designs/auto-patch-library-bugs.md
docs/designs/autoresearch-compounding-wiki-upgrade.md
docs/designs/autoresearch-structured-reasoning.md
docs/designs/chat-redesign-v0.1.md
docs/designs/code-reuse-modernization.md
docs/designs/deep-research-analysis.md
docs/designs/deep-research-display-language.md
docs/designs/deep-research-implementation-plan.md
docs/designs/in8-entity-resolution.md
docs/designs/llm-access-layer-migration.md
docs/designs/llm-access-layer.md
docs/designs/llm_compile_loop_v4.md
docs/designs/logging-unification.md
docs/designs/managed-connection-design.md
docs/designs/phase3_merge_input_design.md
docs/designs/ppt-generator.md
docs/designs/ppt-v0.6.2-patch1.md
docs/designs/pptchat-harness-v0.7.md
docs/designs/react-quality-gates.md
docs/designs/react-research-engine.md
docs/designs/refactor-4layer-architecture.md
docs/designs/self_feedback_planning.md
docs/designs/skill-system-research-and-autoresearch-plan.md
docs/designs/unified-agent-loop.md
docs/designs/v0.32-execution-plan.md
docs/designs/v0.32-skill-restructure.md
docs/designs/v0.33-service-refactor.md
docs/designs/v0.36-agentchat-hardening.md
docs/designs/v0.37-react-loop.md
docs/designs/v0.38-chat-stabilization.md
docs/designs/v0.39-web-search-skill.md
docs/designs/v0.40-chat-bug-retro.md
docs/designs/v0.41-chat-service-split.md
docs/designs/vibe-coding-self-heal.md
docs/designs/workflow-optimization-plan.md
docs/designs/principles/skill-taxonomy.md
docs/designs/principles/unix-philosophy.md
docs/diagnostics/chat-architecture-2026-06.md
docs/issues/issues.md
docs/issues/snapshots/2026-05-31.md
docs/llm_code_generation/LESSONS_LEARNED.md
docs/llm_code_generation/PARSING_FAILURE_MODES.md
docs/llm_code_generation/PROMPT_ENGINEERING.md
docs/llm_code_generation/REACT_FLOW_OPTIMIZATION.md
docs/llm_code_generation/README.md
docs/migration/from-v0.39.md
docs/releases/phase-6-11-cumulative.md
docs/releases/v0.32.0.md
docs/releases/v0.32.5.md
docs/releases/v0.33.0.md
docs/releases/v0.36.0.md
docs/releases/v0.37.0.md
docs/releases/v0.38.0.md
docs/releases/v0.40.1-search-cjk.md
docs/releases/v0.40.2.md
docs/research/html-ppt-landscape.md
docs/research/llmwikify-competitive-analysis.md
docs/summaries/101_alphas_v4.md
docs/summaries/hybrid_ab_results.md
docs/summaries/hybrid_ab_results_v2.md
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