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/Cargo.toml

@@ -3,6 +3,7 @@ members = [
     "backend-client",
     "ansi-escape",
     "app-server",
+    "app-server-protocol",
     "apply-patch",
     "arg0",
     "codex-backend-openapi-models",
@@ -47,6 +48,7 @@ edition = "2024"
 app_test_support = { path = "app-server/tests/common" }
 codex-ansi-escape = { path = "ansi-escape" }
 codex-app-server = { path = "app-server" }
+codex-app-server-protocol = { path = "app-server-protocol" }
 codex-apply-patch = { path = "apply-patch" }
 codex-arg0 = { path = "arg0" }
 codex-chatgpt = { path = "chatgpt" }