Refine default orchestration flow and documentation
- 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
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