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-protocol/Cargo.toml

@@ -0,0 +1,24 @@
+[package]
+edition = "2024"
+name = "codex-app-server-protocol"
+version = { workspace = true }
+
+[lib]
+name = "codex_app_server_protocol"
+path = "src/lib.rs"
+
+[lints]
+workspace = true
+
+[dependencies]
+codex-protocol = { workspace = true }
+paste = { workspace = true }
+serde = { workspace = true, features = ["derive"] }
+serde_json = { workspace = true }
+strum_macros = { workspace = true }
+ts-rs = { workspace = true }
+uuid = { workspace = true, features = ["serde", "v7"] }
+
+[dev-dependencies]
+anyhow = { workspace = true }
+pretty_assertions = { workspace = true }