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/cli/args.rs

@@ -58,8 +58,8 @@ impl std::fmt::Display for LogLevelArg {
 #[derive(Debug, Parser)]
 #[command(name = "zosstorage", disable_help_subcommand = true)]
 pub struct Cli {
-    /// Path to YAML configuration (mirrors kernel cmdline key 'zosstorage.config=')
-    #[arg(short = 'c', long = "config")]
+    /// DEPRECATED: external YAML configuration is not used at runtime (ADR-0002). Ignored with a warning.
+    #[arg(short = 'c', long = "config", hide = true)]
     pub config: Option<String>,
 
     /// Log level: error, warn, info, debug
@@ -74,7 +74,7 @@ pub struct Cli {
     #[arg(short = 's', long = "fstab", default_value_t = false)]
     pub fstab: bool,
 
-    /// Select topology (overrides config topology)
+    /// Select topology (CLI has precedence over kernel cmdline)
     #[arg(short = 't', long = "topology", value_enum)]
     pub topology: Option<crate::types::Topology>,
 
@@ -82,8 +82,7 @@ pub struct Cli {
     #[arg(short = 'f', long = "force")]
     pub force: bool,
 
-    /// Allow removable devices (e.g., USB sticks) to be considered during discovery
-    /// Overrides config.device_selection.allow_removable when provided
+    /// Include removable devices (e.g., USB sticks) during discovery (default: false)
     #[arg(long = "allow-removable", default_value_t = false)]
     pub allow_removable: bool,
  
@@ -100,7 +99,7 @@ pub struct Cli {
     #[arg(long = "show", default_value_t = false)]
     pub show: bool,
  
-    /// Write detection/planning JSON report to the given path (overrides config.report.path)
+    /// Write detection/planning JSON report to the given path
     #[arg(long = "report")]
     pub report: Option<String>,