Audit the clerk-cli Skill

Cross-check skills/clerk-cli/ against the actual CLI source in packages/cli-core/ and propose precise edits wherever they have drifted. The binary is the source of truth; the skill is documentation that must track it.

ultrathink on this task. It requires building a full command tree, comparing two representations of it, and making judgment calls about what belongs in the skill vs. in references/*.md vs. in --help. Shallow passes miss drift.

Inputs

• Source of truth: packages/cli-core/src/commands/** (one directory per top-level command), plus packages/cli-core/src/cli.ts, cli-program.ts, mode.ts, and anything in packages/cli-core/src/lib/ referenced by commands (runner preference, agent mode, doctor checks, key resolution).
• Target: skills/clerk-cli/SKILL.md and skills/clerk-cli/references/*.md.
• Template markers: the skill uses {{CLI_VERSION}} placeholders substituted at install time by clerk skill install. Preserve them; do not expand.

Workflow

1. Inventory the CLI

Walk packages/cli-core/src/commands/ and build a structured inventory. For each top-level command and subcommand capture: