Documentation Index

Architecture & Foundation

| File | Topic | |——|——-| | 0A-ARCHITECTURE.md | System architecture, core loop, design principles | | 0B-QUICKSTART.md | Installation, first marker, first run |

Core Domain

| File | Topic | |——|——-| | 1A-MARKER.md | .autoresearch/config.yaml schema, marker states, lifecycle | | 1B-ENGINE.md | Experiment loop, escalation, commit/discard logic | | 1C-METRICS.md | Metric extraction, guard gates, dual-gate verification | | 1D-STATE.md | state.json, local overrides, atomic read-modify-write |

CLI & Operations

| File | Topic | |——|——-| | 2A-CLI.md | CLI commands, interactive + headless modes | | 2B-DAEMON.md | Daemon service, scheduling, cron integration | | 2C-WORKTREE.md | Git worktree management, branch naming, parallel runs |

Agent Profiles

| File | Topic | |——|——-| | 3A-AGENTS.md | Default agent, copilot agent, profile scaffolding | | 3B-IDEAS-PROGRAM.md | Idea generation, program synthesis, finalize flow | | 3C-BUDGET-COUNTDOWN.md | PostToolUse hook for time awareness, urgency tiers |

Gates & Auto-Merge

| File | Topic | |——|——-| | 1E-GATES.md | Gate chain, auto-publish PRs, GitHub audit trail |

Configuration & Telemetry

| File | Topic | |——|——-| | 4A-CONFIGURATION.md | Global config, ~/.autoresearch/, env vars | | 4B-TELEMETRY.md | Telemetry, results tracking, results.tsv |

Harnesses (Production-Validated)

| File | Topic | |——|——-| | 6A-HARNESS-RUFF.md | Ruff harness — zero infra, 2s execution, production results | | 6B-PRODUCTION-DEPLOYMENT.md | Step-by-step deployment guide, common issues, scaling |

Development

| File | Topic | |——|——-| | 5A-TESTING.md | Test suite, fixtures, running tests | | 5Z-KNOWN-ISSUES.md | Known issues & workarounds |