fix: remove mcp-types from app server protocol (#4537)

We continue the separation between `codex app-server` and `codex
mcp-server`.

In particular, we introduce a new crate, `codex-app-server-protocol`,
and migrate `codex-rs/protocol/src/mcp_protocol.rs` into it, renaming it
`codex-rs/app-server-protocol/src/protocol.rs`.

Because `ConversationId` was defined in `mcp_protocol.rs`, we move it
into its own file, `codex-rs/protocol/src/conversation_id.rs`, and
because it is referenced in a ton of places, we have to touch a lot of
files as part of this PR.

We also decide to get away from proper JSON-RPC 2.0 semantics, so we
also introduce `codex-rs/app-server-protocol/src/jsonrpc_lite.rs`, which
is basically the same `JSONRPCMessage` type defined in `mcp-types`
except with all of the `"jsonrpc": "2.0"` removed.

Getting rid of `"jsonrpc": "2.0"` makes our serialization logic
considerably simpler, as we can lean heavier on serde to serialize
directly into the wire format that we use now.

codex-rs/exec/tests/event_processor_with_json_output.rs

@@ -52,10 +52,9 @@ fn event(id: &str, msg: EventMsg) -> Event {
 #[test]
 fn session_configured_produces_thread_started_event() {
     let mut ep = EventProcessorWithJsonOutput::new(None);
-    let session_id = codex_protocol::mcp_protocol::ConversationId::from_string(
-        "67e55044-10b1-426f-9247-bb680e5fe0c8",
-    )
-    .unwrap();
+    let session_id =
+        codex_protocol::ConversationId::from_string("67e55044-10b1-426f-9247-bb680e5fe0c8")
+            .unwrap();
     let rollout_path = PathBuf::from("/tmp/rollout.json");
     let ev = event(
         "e1",