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.
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