M1+M2: gateway core loop + agent transparency

M1 (gateway core loop / text round-trip):
- WS server (ws_server.py): bind, hello auth (constant-time), hello.ack, heartbeat, connection registry
- pairing.py: token generation, pairing store, QR payload
- adapter.py: send() -> message frame; inbound message.send -> MessageEvent -> handle_message
- app: Connect screen, GatewayClient (connect + reconnect), ChatScreen send/render, SecureStore (Android/Desktop)
- tests/ws_probe.py: probe harness driving a real turn

M2 (streaming + reasoning + tools + commentary):
- protocol.py: M2 frame types (message.start/update/stop, tool.start/progress/end, commentary)
- adapter.py: per-chat turn-state machine; classify outbound into frames; _split_reasoning; tool-line parsing
- reasoning in streaming: capture via on_stream_delta hook (kind=reasoning, gated by plugins.stream_reasoning_deltas) with a FIFO barrier, attach to message.stop
- app: live streaming bubble, ReasoningBlock (collapse + copy), ToolCard (Everything/Truncated/Nothing), dimmed commentary, typing
- docs/14-milestones.md: M1/M2 marked done; reasoning note corrected

app/desktopApp/src/main/kotlin/iris/desktop/Main.kt

@@ -3,9 +3,11 @@ package iris.desktop
 import androidx.compose.ui.window.Window
 import androidx.compose.ui.window.application
 import iris.IrisApp
+import iris.platform.DesktopSecureStore
 
 fun main() = application {
+    val store = DesktopSecureStore()
     Window(onCloseRequest = ::exitApplication, title = "Iris") {
-        IrisApp()
+        IrisApp(store)
     }
 }