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/debug-client/src/client.rs

@@ -103,7 +103,7 @@ impl AppServerClient {
                 },
                 capabilities: Some(InitializeCapabilities {
                     experimental_api: true,
-                    supported_server_requests: None,
+                    permission_confirmations: false,
                     opt_out_notification_methods: None,
                 }),
             },