fix(app-server): fix optional bool annotations (#24099)

`#[serde(default)]` wasn't sufficient for our generated TS types to
reflect that clients didn't have to set them. We also need
`skip_serializing_if = "std::ops::Not::not"`. This is already a rule in
our agents.md file.

codex-rs/app-server-protocol/schema/json/ClientRequest.json

@@ -423,7 +423,6 @@
           ]
         },
         "includeLayers": {
-          "default": false,
           "type": "boolean"
         }
       },
@@ -721,8 +720,7 @@
         }
       },
       "required": [
-        "classification",
-        "includeLogs"
+        "classification"
       ],
       "type": "object"
     },
@@ -1034,7 +1032,6 @@
     "GetAccountParams": {
       "properties": {
         "refreshToken": {
-          "default": false,
           "description": "When `true`, requests a proactive token refresh before returning.\n\nIn managed auth mode this triggers the normal refresh-token flow. In external auth mode this flag is ignored. Clients should refresh tokens themselves and call `account/login/start` with `chatgptAuthTokens`.",
           "type": "boolean"
         }
@@ -3424,7 +3421,6 @@
     "ThreadReadParams": {
       "properties": {
         "includeTurns": {
-          "default": false,
           "description": "When true, include turns and their items from rollout history.",
           "type": "boolean"
         },