feat: add Atlas native app UX overhaul

Docs/ADR/ADR-002-Protocol-and-Adapters.md

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+# ADR-002: Structured Protocol and Adapter Layer
+
+## Status
+
+Accepted
+
+## Context
+
+Existing upstream capabilities are terminal-oriented and not suitable as a direct contract for a native GUI.
+
+## Decision
+
+- Define a structured local JSON protocol.
+- Wrap reusable upstream logic behind adapters.
+- Keep UI components unaware of script or terminal output format.
+
+## Consequences
+
+- Faster GUI iteration
+- Safer schema evolution
+- Additional adapter maintenance cost