Migra os 8 comandos restantes (doctor, setup, providers, config, status,
logs, update, provider) de parseArgs manual para a API do Commander.
Cada arquivo exporta register<Nome>(program) e run*Command(opts = {}).
Deleta bin/cli/index.mjs (substituído por commands/registry.mjs).
Remove dependência de bin/cli/args.mjs em todos os comandos migrados.
Corrige CWE-310 em doctor.mjs: authTagLength explícito no createDecipheriv.
Hide admin password entry during setup, make doctor degrade to warnings
when source-only runtime checks are unavailable, and improve stop
behavior by attempting graceful shutdown before force killing ports.
Also use SQLite's backup API for safer snapshots under WAL, align CLI
key writes with the current provider_connections schema, and include
follow-on compatibility fixes for GLM provider detection, stream error
sanitization, and auth-aware test coverage.
