fix: separate codex mcp into codex mcp-server and codex app-server (#4471)

This is a very large PR with some non-backwards-compatible changes.

Historically, `codex mcp` (or `codex mcp serve`) started a JSON-RPC-ish
server that had two overlapping responsibilities:

- Running an MCP server, providing some basic tool calls.
- Running the app server used to power experiences such as the VS Code
extension.

This PR aims to separate these into distinct concepts:

- `codex mcp-server` for the MCP server
- `codex app-server` for the "application server"

Note `codex mcp` still exists because it already has its own subcommands
for MCP management (`list`, `add`, etc.)

The MCP logic continues to live in `codex-rs/mcp-server` whereas the
refactored app server logic is in the new `codex-rs/app-server` folder.
Note that most of the existing integration tests in
`codex-rs/mcp-server/tests/suite` were actually for the app server, so
all the tests have been moved with the exception of
`codex-rs/mcp-server/tests/suite/mod.rs`.

Because this is already a large diff, I tried not to change more than I
had to, so `codex-rs/app-server/tests/common/mcp_process.rs` still uses
the name `McpProcess` for now, but I will do some mechanical renamings
to things like `AppServer` in subsequent PRs.

While `mcp-server` and `app-server` share some overlapping functionality
(like reading streams of JSONL and dispatching based on message types)
and some differences (completely different message types), I ended up
doing a bit of copypasta between the two crates, as both have somewhat
similar `message_processor.rs` and `outgoing_message.rs` files for now,
though I expect them to diverge more in the near future.

One material change is that of the initialize handshake for `codex
app-server`, as we no longer use the MCP types for that handshake.
Instead, we update `codex-rs/protocol/src/mcp_protocol.rs` to add an
`Initialize` variant to `ClientRequest`, which takes the `ClientInfo`
object we need to update the `USER_AGENT_SUFFIX` in
`codex-rs/app-server/src/message_processor.rs`.

One other material change is in
`codex-rs/app-server/src/codex_message_processor.rs` where I eliminated
a use of the `send_event_as_notification()` method I am generally trying
to deprecate (because it blindly maps an `EventMsg` into a
`JSONNotification`) in favor of `send_server_notification()`, which
takes a `ServerNotification`, as that is intended to be a custom enum of
all notification types supported by the app server. So to make this
update, I had to introduce a new variant of `ServerNotification`,
`SessionConfigured`, which is a non-backwards compatible change with the
old `codex mcp`, and clients will have to be updated after the next
release that contains this PR. Note that
`codex-rs/app-server/tests/suite/list_resume.rs` also had to be update
to reflect this change.

I introduced `codex-rs/utils/json-to-toml/src/lib.rs` as a small utility
crate to avoid some of the copying between `mcp-server` and
`app-server`.

codex-rs/app-server/tests/suite/archive_conversation.rs

@@ -0,0 +1,105 @@
+use std::path::Path;
+
+use app_test_support::McpProcess;
+use app_test_support::to_response;
+use codex_core::ARCHIVED_SESSIONS_SUBDIR;
+use codex_protocol::mcp_protocol::ArchiveConversationParams;
+use codex_protocol::mcp_protocol::ArchiveConversationResponse;
+use codex_protocol::mcp_protocol::NewConversationParams;
+use codex_protocol::mcp_protocol::NewConversationResponse;
+use mcp_types::JSONRPCResponse;
+use mcp_types::RequestId;
+use tempfile::TempDir;
+use tokio::time::timeout;
+
+const DEFAULT_READ_TIMEOUT: std::time::Duration = std::time::Duration::from_secs(10);
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn archive_conversation_moves_rollout_into_archived_directory() {
+    let codex_home = TempDir::new().expect("create temp dir");
+    create_config_toml(codex_home.path()).expect("write config.toml");
+
+    let mut mcp = McpProcess::new(codex_home.path())
+        .await
+        .expect("spawn mcp process");
+    timeout(DEFAULT_READ_TIMEOUT, mcp.initialize())
+        .await
+        .expect("initialize timeout")
+        .expect("initialize request");
+
+    let new_request_id = mcp
+        .send_new_conversation_request(NewConversationParams {
+            model: Some("mock-model".to_string()),
+            ..Default::default()
+        })
+        .await
+        .expect("send newConversation");
+    let new_response: JSONRPCResponse = timeout(
+        DEFAULT_READ_TIMEOUT,
+        mcp.read_stream_until_response_message(RequestId::Integer(new_request_id)),
+    )
+    .await
+    .expect("newConversation timeout")
+    .expect("newConversation response");
+
+    let NewConversationResponse {
+        conversation_id,
+        rollout_path,
+        ..
+    } = to_response::<NewConversationResponse>(new_response)
+        .expect("deserialize newConversation response");
+
+    assert!(
+        rollout_path.exists(),
+        "expected rollout path {} to exist",
+        rollout_path.display()
+    );
+
+    let archive_request_id = mcp
+        .send_archive_conversation_request(ArchiveConversationParams {
+            conversation_id,
+            rollout_path: rollout_path.clone(),
+        })
+        .await
+        .expect("send archiveConversation");
+    let archive_response: JSONRPCResponse = timeout(
+        DEFAULT_READ_TIMEOUT,
+        mcp.read_stream_until_response_message(RequestId::Integer(archive_request_id)),
+    )
+    .await
+    .expect("archiveConversation timeout")
+    .expect("archiveConversation response");
+
+    let _: ArchiveConversationResponse =
+        to_response::<ArchiveConversationResponse>(archive_response)
+            .expect("deserialize archiveConversation response");
+
+    let archived_directory = codex_home.path().join(ARCHIVED_SESSIONS_SUBDIR);
+    let archived_rollout_path =
+        archived_directory.join(rollout_path.file_name().unwrap_or_else(|| {
+            panic!("rollout path {} missing file name", rollout_path.display())
+        }));
+
+    assert!(
+        !rollout_path.exists(),
+        "expected rollout path {} to be moved",
+        rollout_path.display()
+    );
+    assert!(
+        archived_rollout_path.exists(),
+        "expected archived rollout path {} to exist",
+        archived_rollout_path.display()
+    );
+}
+
+fn create_config_toml(codex_home: &Path) -> std::io::Result<()> {
+    let config_toml = codex_home.join("config.toml");
+    std::fs::write(config_toml, config_contents())
+}
+
+fn config_contents() -> &'static str {
+    r#"model = "mock-model"
+approval_policy = "never"
+sandbox_mode = "read-only"
+"#
+}