Move CLI command implementations out of index.ts

[chubes4]

Goal

Make packages/cli/src/index.ts a CLI bootstrap plus command wiring surface, not a container for command implementation.

Current Problem

The command router exists, but index.ts still contains many command handlers and support functions. This keeps CLI behavior harder to scan, review, and extend.

Target Shape

• index.ts owns bootstrap, shared setup, and exports only minimal CLI entry points.
• Command implementations live under focused modules, likely packages/cli/src/commands/.
• Existing helper modules (recipe-*, agent-sandbox, runtime-command-wrappers, output) remain the lower-level building blocks.

Candidate Slices

• commands/recipe.ts
• commands/recipe-run.ts
• commands/schema.ts
• commands/run.ts
• commands/boot.ts
• commands/list.ts or equivalent for discovery/registry output

Acceptance Criteria

• index.ts is materially smaller and readable as CLI bootstrap/orchestration.
• Command behavior, option parsing, JSON output, and help/unknown-command behavior remain unchanged.
• Build and focused CLI command/recipe smokes pass.

AI assistance

• AI assistance: Yes
• Tool(s): OpenCode (openai/gpt-5.5)
• Used for: Drafting this tracker from the current architecture cleanup state.

[chubes4]

Closed after the CLI command extraction landed: packages/cli/src/index.ts is now a small bootstrap/router surface and command implementations live under packages/cli/src/commands/. Verified in the final transfer-readiness pass.