app-server: include filesystem entries in permission requests (#19086)

## Why

`item/permissions/requestApproval` sends a requested permission profile
to app-server clients. The core profile already stores filesystem
permissions as `entries`, but the v2 compatibility conversion used the
legacy `read`/`write` projection whenever possible and left `entries`
unset.

That made the request ambiguous for clients that consume the canonical
v2 shape: `permissions.fileSystem.entries` was missing even though
filesystem access was being requested. A client that rendered or echoed
grants from `entries` could treat the request as having no filesystem
permission entries, then return an empty or incomplete grant. The
app-server intersects responses with the original request, so omitted
filesystem permissions are denied.

## What Changed

- Populate `AdditionalFileSystemPermissions.entries` when converting
legacy read/write roots for request permission payloads, while
preserving `read` and `write` for compatibility.
- Mark `read` and `write` as transitional schema fields in the generated
app-server schema.
- Add regression coverage for the v2 conversion, the app-server
`item/permissions/requestApproval` round trip, and TUI app-server
approval conversion expectations.
- Refresh generated JSON and TypeScript schema fixtures.

## Verification

- `just fmt`
- `cargo test -p codex-app-server-protocol`
- `cargo test -p codex-app-server request_permissions_round_trip`
- `cargo test -p codex-tui
converts_request_permissions_into_granted_permissions`
- `cargo test -p codex-tui
resolves_permissions_and_user_input_through_app_server_request_id`

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

@@ -25,6 +25,7 @@
           ]
         },
         "read": {
+          "description": "This will be removed in favor of `entries`.",
           "items": {
             "$ref": "#/definitions/AbsolutePathBuf"
           },
@@ -34,6 +35,7 @@
           ]
         },
         "write": {
+          "description": "This will be removed in favor of `entries`.",
           "items": {
             "$ref": "#/definitions/AbsolutePathBuf"
           },