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Archetype: Command-line tool

Maturity: draft. Structure is stable; examples are being expanded.

You have this archetype if your tool runs in a terminal. Example in our ecosystem: nemar-cli. The job here is mostly usage: an agent can already run shell commands, so help it run yours correctly.

Why it matters

An agent driving a terminal discovers a command-line tool the way a person does: by running --help and reading the output. If your help text is clear, complete, and stable, the agent succeeds. If it is thin or inconsistent, the agent guesses and fails.

Do these, in order of value

  1. Write excellent --help. Every subcommand, every flag, with a one-line purpose and at least one example. Treat --help as the primary interface for both people and agents.

  2. Ship a machine-readable help form. A stable --version and, ideally, a structured dump such as mytool --help=json or a documented mytool schema command that prints the command tree as JSON. This lets an agent enumerate capabilities without scraping prose. The tools agents already lean on set the precedent: gh, docker, and kubectl all offer --output json.

  3. Add an AGENTS.md at the repo root. Install command, the three or four commands that matter most, a worked end-to-end example, and the common failure modes. See templates/AGENTS.md.

  4. Use meaningful exit codes and predictable output. Non-zero on failure, a --json output mode for anything an agent might parse, and errors that state what went wrong and how to fix it.

  5. Keep an examples cookbook in the docs: real invocations for real tasks, copy-pasteable.

  6. Optional but powerful: wrap the tool in a Model Context Protocol (MCP) server. This turns your subcommands into callable tools an agent can invoke directly, with typed arguments, instead of composing raw shell strings.

Precedent and specifics

  • Describe inputs and outputs, not just the command's existence, using the Bioschemas ComputationalTool and FormalParameter profiles.
  • Wrapping as MCP need not be a rewrite; the MCPmed "breadcrumbs" pattern wraps an existing tool.

Minimum viable setup

Great --help on every subcommand, plus an AGENTS.md with a worked example.

Pitfalls

  • Do not let --help and the docs disagree.
  • Do not print progress or logs to stdout that a --json consumer will choke on; use stderr.
  • Do not require interactive prompts with no non-interactive flag; agents cannot answer them.