[app-server] refactor: split API types into v1 and v2 (#6005)

Makes it easier to figure out which types are defined in the old vs. new
API schema.

codex-rs/app-server-protocol/src/protocol/mod.rs

@@ -0,0 +1,6 @@
+// Module declarations for the app-server protocol namespace.
+// Exposes protocol pieces used by `lib.rs` via `pub use protocol::common::*;`.
+
+pub mod common;
+pub mod v1;
+pub mod v2;