doctor

name	doctor
description	Diagnose Polytropos Codex plugin, agent, skill, prompt, and managed-install state without changing it. Use for setup, upgrades, stale paths, missing skills, or install conflicts.

Diagnose Codex setup safely

Resolve the plugin root before running commands

Set POLYTROPOS_ROOT from this file's real location: in plugin mode, this file is <root>/codex/skills/doctor/SKILL.md, so ascend to <root>; in a managed copied install, use the installer-resolved POLYTROPOS_ROOT="{{POLYTROPOS_ROOT}}". Reject a literal placeholder. Before shelling out, verify $POLYTROPOS_ROOT/data/pricing.codex.json and $POLYTROPOS_ROOT/bin/harness_select.py exist. If proof fails, stop and direct the user to python3 bin/harness_select.py doctor --harness codex; never run a guessed or stale path.

Run the read-only doctor with an explicit Codex home when one is known:

python3 "$POLYTROPOS_ROOT/bin/harness_select.py" doctor --harness codex --repo-root "$POLYTROPOS_ROOT" --codex-home <codex-home>
python3 "$POLYTROPOS_ROOT/bin/harness_select.py" doctor --harness codex --repo-root "$POLYTROPOS_ROOT" --codex-home <codex-home> --json

You may also preview an intended install with install ... --dry-run; preview and doctor must remain byte-read-only. Summarize each component state (install, up-to-date, managed-update, conflict, unmanaged, or skip) and give the exact remedy printed by the engine. Never suggest --force, deleting the Codex home, or overwriting config.toml.

An actual install or --refresh-managed is a write. Show the plan and obtain explicit user authority before running it. Managed refresh is allowed only for unchanged recorded copies; user-edited or unrelated destinations remain conflicts. Remind the user to restart Codex or start a new task after enabling a plugin or changing agents.