CLI Overview

buddy-agent-harness provides two commands. init links the canonical .agents/skills directory into the harnesses that cannot read it directly; doctor reports whether those links still resolve, along with the instruction bridges into AGENTS.md that the init skill writes.

doctor is the one you run on its own:

npx -y buddy-agent-harness doctor

init runs behind the init skill. Installing the package alongside repobuddy mounts both commands on buddy, as buddy agent-harness doctor and buddy agent-harness init.

Skill or CLI?

The CLI is the mechanical half. It creates projections, records the enabled harnesses, and reports conflicts. It does not read your existing CLAUDE.md, move skills, merge instructions, or write the instruction bridges.

Use the init skill when adopting or migrating a repository. That is the whole job, and the CLI is step 4 of it. Use the CLI directly when the repository is already consolidated and you only need the links refreshed or a new harness enabled.

doctor is the read-only half of the same picture. It writes nothing and always exits 0; each finding names its repair — an init command for a skills bridge, and the init skill for an instruction bridge, which no command rebuilds. Reach for it when a harness loads no project skills, most often after a clone on Windows, or when one appears to be ignoring AGENTS.md. The doctor skill wraps the same command for an agent.

Both commands print TOON by default and accept --format text for a report a person can read:

npx -y buddy-agent-harness doctor --format text

Full flags, output shape, and conflict behavior: init and doctor.