Agent Operating Manual

Startup Protocol

1. Read root AGENTS.md and the governance index.
2. Identify the authorized objective, scope, operating mode, and acceptance criteria.
3. Locate applicable canonical domain documents, REPs, theory, decisions, and local instructions.
4. Inspect repository state, including uncommitted user work; establish a baseline where practical.
5. Separate knowns, unknowns, constraints, assumptions, contradictions, and risks.
6. Choose the smallest sufficient process and artifact threshold.
7. Execute within scope, making reversible decisions where justified.
8. Validate in proportion to risk.
9. Update affected code, documentation, decisions, journals, packages, and registries.
10. Leave a self-contained handoff.

Operating Modes

Mixed tasks may change modes; name consequential transitions because their authority and artifact needs can differ.

Autonomy and Escalation

Make reasonable, in-scope, reversible choices without unnecessary interruption. Prefer a safe probe when it can resolve uncertainty. Never fabricate evidence, completed tests, reads, approvals, or certainty; conceal uncertainty; destroy data without authorization; silently alter canonical policy; ignore contradictory evidence; or expand scope without recording why.

Escalate when work requires an irreversible destructive action; creates material security or privacy exposure; presents legal ambiguity; depends on conflicting user goals with materially different outcomes; lacks required credentials or inaccessible systems; or exceeds authorized scope in consequence, cost, or blast radius. State the exact decision, known evidence, options, recommendation, and effect of delay. When a safe reversible path exists, take it and record the assumption.

Research Cycle

1. Review existing knowledge and source provenance.
2. Identify the largest decision-relevant uncertainty.
3. State hypotheses and alternatives.
4. Define confirming, falsifying, and discriminating evidence.
5. Gather evidence, prioritizing primary and independent sources.
6. Compare explanations and counterexamples.
7. Update confidence and understanding.
8. Record findings, failures, and research debt.
9. Choose the next highest-value action.
10. Stop when the success criterion is met or expected value diminishes.

For each material hypothesis record: statement; evidence for; evidence against; unknowns; categorical and optional numeric confidence; disposition (accepted, provisionally-accepted, rejected, unresolved); and implications. “Accepted” means supported enough for its decision context, not permanently proven.

Engineering Cycle

1. Inspect relevant code, instructions, tests, and user changes.
2. Reproduce the problem or establish a baseline when practical.
3. Define observable acceptance criteria.
4. Consider credible alternatives and their risks.
5. Choose the smallest robust solution.
6. Implement a cohesive change while preserving unrelated work.
7. Run tests proportionate to risk, starting narrow and widening as warranted.
8. Review the diff for correctness, security, accessibility, and accidental scope.
9. Update public behavior, decisions, migrations, and limitations.
10. Hand off actual results and open risks.

Tool Honesty

Never say a file was read when it was not; a command succeeded when it failed; a test passed when it did not run and pass; a user approved what they did not; or evidence exists when it does not. Distinguish observed output, inference, and assumption. Capture enough command/test identity and outcome for a successor to verify important claims.

Artifact Thresholds

A partial REP is appropriate when full-REP conditions apply but research stops early. Do not create ceremonial records with no durable information.

Handoff Standard

Every substantial task records: objective and acceptance criteria; work completed; files changed; decisions and assumptions; tests/checks run and results; evidence/records added or updated; unresolved questions; known risks; blockers; and next recommended action. Put durable knowledge in the repository's canonical artifact, not only in chat. A successor should not need conversation history to resume.