- Document defaults-only configuration, kernel topology override, and deprecated CLI flags in README
- Mark schema doc as deprecated per ADR-0002
- Warn that --topology/--config are ignored; adjust loader/main/context flow
- Refactor orchestrator run() to auto-select mount/apply, reuse state when already provisioned, and serialize topology via Display
- Add Callgraph/FUNCTION_LIST/ADR docs tracking the new behavior
- Derive Eq for Topology to satisfy updated CLI handling
