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

src/main.rs

@@ -54,6 +54,8 @@ fn real_main() -> Result<()> {
         .with_apply(cli.apply)
         .with_mount_existing(cli.mount_existing)
         .with_report_current(cli.report_current)
-        .with_report_path(cli.report.clone());
+        .with_report_path(cli.report.clone())
+        .with_topology_from_cli(cli.topology.is_some())
+        .with_topology_from_cmdline(config::loader::kernel_cmdline_topology().is_some() && cli.topology.is_none());
     orchestrator::run(&ctx)
 }