feat: add Atlas native app UX overhaul

Packages/AtlasApplication/README.md

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+# AtlasApplication
+
+## Responsibility
+
+- Use cases and orchestration interfaces
+- Structured application-layer coordination between the app shell and worker boundary
+
+## Planned Use Cases
+
+- `StartScan`
+- `PreviewPlan`
+- `ExecutePlan`
+- `RestoreItems`
+- `InspectPermissions`
+
+## Current Scaffold
+
+- `AtlasWorkspaceController` turns structured worker responses into app-facing scan, preview, and permission outputs.
+- `AtlasWorkerServing` defines the worker boundary without leaking UI concerns into infrastructure.