Align the docs with the reorganized project layout so container setup commands match the paths users actually run. Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-opencode) Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>