chore: remove dead CLI commands (deploy, install, old mcp start)

Remove deploy command (skill disabled), install/uninstall (old plugin
system), mcp start + .mcp.json + run-mcp.cjs (old plugin MCP launcher).
Guard `local` subcommands behind isRunFromMonorepo().

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: cevian