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/app-server/src/fuzzy_file_search.rs

@@ -4,8 +4,8 @@ use std::path::PathBuf;
 use std::sync::Arc;
 use std::sync::atomic::AtomicBool;
 
+use codex_app_server_protocol::FuzzyFileSearchResult;
 use codex_file_search as file_search;
-use codex_protocol::mcp_protocol::FuzzyFileSearchResult;
 use tokio::task::JoinSet;
 use tracing::warn;