test(app-server): cover thread turn context updates

Document `thread/turnContext/update` more clearly in the protocol and
README, including that it updates the live defaults used by later
thread-scoped operations.

Add a focused app-server regression test that updates a loaded
thread's cwd and verifies `thread/read` reflects the new value.

codex-rs/app-server-protocol/schema/json/v2/ThreadTurnContextUpdateParams.json

@@ -336,6 +336,7 @@
       "type": "object"
     }
   },
+  "description": "Parameters for `thread/turnContext/update`. Each field is optional; only supplied fields override the thread's defaults for subsequent turns and thread-scoped operations (e.g. shell commands).",
   "properties": {
     "approvalPolicy": {
       "anyOf": [