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/Cargo.lock

@@ -165,6 +165,20 @@ version = "1.0.99"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b0674a1ddeecb70197781e945de4b3b8ffb61fa939a5597bcf48503737663100"
 
+[[package]]
+name = "app_test_support"
+version = "0.0.0"
+dependencies = [
+ "anyhow",
+ "assert_cmd",
+ "codex-protocol",
+ "mcp-types",
+ "serde",
+ "serde_json",
+ "tokio",
+ "wiremock",
+]
+
 [[package]]
 name = "arboard"
 version = "3.6.0"
@@ -636,6 +650,36 @@ dependencies = [
  "tracing",
 ]
 
+[[package]]
+name = "codex-app-server"
+version = "0.0.0"
+dependencies = [
+ "anyhow",
+ "app_test_support",
+ "assert_cmd",
+ "base64",
+ "codex-arg0",
+ "codex-common",
+ "codex-core",
+ "codex-file-search",
+ "codex-login",
+ "codex-protocol",
+ "codex-utils-json-to-toml",
+ "core_test_support",
+ "mcp-types",
+ "os_info",
+ "pretty_assertions",
+ "serde",
+ "serde_json",
+ "tempfile",
+ "tokio",
+ "toml",
+ "tracing",
+ "tracing-subscriber",
+ "uuid",
+ "wiremock",
+]
+
 [[package]]
 name = "codex-apply-patch"
 version = "0.0.0"
@@ -685,6 +729,7 @@ dependencies = [
  "assert_cmd",
  "clap",
  "clap_complete",
+ "codex-app-server",
  "codex-arg0",
  "codex-chatgpt",
  "codex-common",
@@ -914,13 +959,11 @@ version = "0.0.0"
 dependencies = [
  "anyhow",
  "assert_cmd",
- "base64",
  "codex-arg0",
  "codex-common",
  "codex-core",
- "codex-file-search",
- "codex-login",
  "codex-protocol",
+ "codex-utils-json-to-toml",
  "core_test_support",
  "mcp-types",
  "mcp_test_support",
@@ -932,10 +975,8 @@ dependencies = [
  "shlex",
  "tempfile",
  "tokio",
- "toml",
  "tracing",
  "tracing-subscriber",
- "uuid",
  "wiremock",
 ]
 
@@ -1104,6 +1145,15 @@ dependencies = [
  "vt100",
 ]
 
+[[package]]
+name = "codex-utils-json-to-toml"
+version = "0.0.0"
+dependencies = [
+ "pretty_assertions",
+ "serde_json",
+ "toml",
+]
+
 [[package]]
 name = "codex-utils-readiness"
 version = "0.0.0"
@@ -3004,7 +3054,6 @@ dependencies = [
  "assert_cmd",
  "codex-core",
  "codex-mcp-server",
- "codex-protocol",
  "mcp-types",
  "os_info",
  "pretty_assertions",