infrastructure-doctor

# Doctor Module Repository-level "doctor mode": a diagnostic engine plus an automated, audited resolution engine. The doctor never leaves the patient worse off — every mutation is snapshotted before it runs and can be reversed by a single `undo` command. ## Quick start ```bash # Diagnose only (read-only). uv run python -m infrastructure.doctor # Same, JSON for an agent. uv run python -m infrastructure.doctor --json diagnose # Show what would be fixed (no changes). uv run python -m infrastructure.doctor fix --plan # Apply the safest set of fixes. uv run python -m infrastructure.doctor fix --apply # Allow `uv sync` and other moderate-therapy fixes. uv run python -m infrastructure.doctor fix --apply --moderate # Allow radical fixes (e.g. delete orphan output directories — still backed up). uv run python -m infrastructure.doctor fix --apply --aggressive # Reverse the most recent applied, reversible action. uv run python -m infrastructure.doctor undo --last # Reverse one specific action (see `history`). uv run python -m infrastructure.doctor undo --action-id <id> # Inspect the journal. uv run python -m infrastructure.doctor history # Agent-facing capability manifest. uv run python -m infrastructure.doctor capabilities # Stable-text robot manual. uv run python -m infrastructure.doctor robot-docs ``` ## Safety contract Every fix flows through `infrastructure.doctor.safety.mutate(plan, state)`. That function is the **only** code in this module that writes to the filesy...