refactor(app-server): simplify permission confirmation flow

Replace the per-method v1 app-server capability with a single
`permissionConfirmations` opt-in. Route both permission request
flows through that capability.

Collapse the separate preset tool feature into
`request_permissions_tool`, and make core apply accepted preset
responses so clients only confirm the user decision.

codex-rs/app-server-protocol/schema/json/codex_app_server_protocol.v2.schemas.json

@@ -5348,15 +5348,10 @@
             "null"
           ]
         },
-        "supportedServerRequests": {
-          "description": "Server request methods this connection knows how to render and answer.",
-          "items": {
-            "$ref": "#/definitions/SupportedServerRequestMethod"
-          },
-          "type": [
-            "array",
-            "null"
-          ]
+        "permissionConfirmations": {
+          "default": false,
+          "description": "Opt into model-initiated permission confirmation requests.",
+          "type": "boolean"
         }
       },
       "type": "object"
@@ -10267,14 +10262,6 @@
         }
       ]
     },
-    "SupportedServerRequestMethod": {
-      "description": "Server-initiated request methods a client can opt into during initialize.",
-      "enum": [
-        "item/permissions/requestApproval",
-        "item/permissionPreset/requestApproval"
-      ],
-      "type": "string"
-    },
     "TerminalInteractionNotification": {
       "$schema": "http://json-schema.org/draft-07/schema#",
       "properties": {