feat: add Atlas native app UX overhaul

Docs/ADR/ADR-003-Workspace-State-and-MVP-Command-Expansion.md

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+# ADR-003: Workspace State Persistence and MVP Command Expansion
+
+## Status
+
+Accepted
+
+## Context
+
+Atlas for Mac already had a native shell, worker transport, and upstream-backed adapters for health and Smart Clean dry runs, but several frozen MVP flows still depended on in-memory scaffold state. That left history, recovery, settings, and app uninstall behavior incomplete across launches and weakened the value of the worker boundary.
+
+## Decision
+
+- Persist a local JSON-backed workspace state for MVP.
+- Store the latest workspace snapshot, current Smart Clean plan, and user settings together.
+- Expand the structured worker protocol to cover missing frozen-scope flows: Smart Clean execute, recovery restore, apps list, app uninstall preview/execute, and settings get/set.
+- Keep these flows behind the existing application/protocol/worker boundaries instead of adding direct UI-side mutations.
+
+## Consequences
+
+- History, recovery, app removal, and settings now survive beyond a single process lifetime.
+- The UI can complete more of the MVP through stable worker commands without parsing or mutating raw script state.
+- The protocol surface is larger and must stay synchronized with docs and tests.
+- Local JSON persistence is acceptable for MVP, but future production hardening may require a more robust store.
+
+## Alternatives Considered
+
+- Keep all new flows in memory only — rejected because recovery and settings would reset across launches.
+- Let the UI mutate app/history/settings state directly — rejected because it breaks the worker-first architecture.
+- Introduce a database immediately — rejected because it adds complexity beyond MVP needs.