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/common/Cargo.toml

@@ -10,6 +10,7 @@ workspace = true
 clap = { workspace = true, features = ["derive", "wrap_help"], optional = true }
 codex-core = { workspace = true }
 codex-protocol = { workspace = true }
+codex-app-server-protocol = { workspace = true }
 serde = { workspace = true, optional = true }
 toml = { workspace = true, optional = true }
 

codex-rs/common/src/model_presets.rs

@@ -1,5 +1,5 @@
+use codex_app_server_protocol::AuthMode;
 use codex_core::protocol_config_types::ReasoningEffort;
-use codex_protocol::mcp_protocol::AuthMode;
 
 /// A simple preset pairing a model slug with a reasoning effort.
 #[derive(Debug, Clone, Copy)]