chore: remove codex-core public protocol/shell re-exports (#12432)

## Why

`codex-rs/core/src/lib.rs` re-exported a broad set of types and modules
from `codex-protocol` and `codex-shell-command`. That made it easy for
workspace crates to import those APIs through `codex-core`, which in
turn hides dependency edges and makes it harder to reduce compile-time
coupling over time.

This change removes those public re-exports so call sites must import
from the source crates directly. Even when a crate still depends on
`codex-core` today, this makes dependency boundaries explicit and
unblocks future work to drop `codex-core` dependencies where possible.

## What Changed

- Removed public re-exports from `codex-rs/core/src/lib.rs` for:
- `codex_protocol::protocol` and related protocol/model types (including
`InitialHistory`)
  - `codex_protocol::config_types` (`protocol_config_types`)
- `codex_shell_command::{bash, is_dangerous_command, is_safe_command,
parse_command, powershell}`
- Migrated workspace Rust call sites to import directly from:
  - `codex_protocol::protocol`
  - `codex_protocol::config_types`
  - `codex_protocol::models`
  - `codex_shell_command`
- Added explicit `Cargo.toml` dependencies (`codex-protocol` /
`codex-shell-command`) in crates that now import those crates directly.
- Kept `codex-core` internal modules compiling by using `pub(crate)`
aliases in `core/src/lib.rs` (internal-only, not part of the public
API).
- Updated the two utility crates that can already drop a `codex-core`
dependency edge entirely:
  - `codex-utils-approval-presets`
  - `codex-utils-cli`

## Verification

- `cargo test -p codex-utils-approval-presets`
- `cargo test -p codex-utils-cli`
- `cargo check --workspace --all-targets`
- `just clippy`

codex-rs/mcp-server/src/codex_tool_config.rs

@@ -2,9 +2,9 @@
 
 use codex_core::config::Config;
 use codex_core::config::ConfigOverrides;
-use codex_core::protocol::AskForApproval;
 use codex_protocol::ThreadId;
 use codex_protocol::config_types::SandboxMode;
+use codex_protocol::protocol::AskForApproval;
 use codex_utils_json_to_toml::json_to_toml;
 use rmcp::model::JsonObject;
 use rmcp::model::Tool;

codex-rs/mcp-server/src/codex_tool_runner.rs

@@ -13,15 +13,15 @@ use codex_core::CodexThread;
 use codex_core::NewThread;
 use codex_core::ThreadManager;
 use codex_core::config::Config as CodexConfig;
-use codex_core::protocol::AgentMessageEvent;
-use codex_core::protocol::ApplyPatchApprovalRequestEvent;
-use codex_core::protocol::Event;
-use codex_core::protocol::EventMsg;
-use codex_core::protocol::ExecApprovalRequestEvent;
-use codex_core::protocol::Op;
-use codex_core::protocol::Submission;
-use codex_core::protocol::TurnCompleteEvent;
 use codex_protocol::ThreadId;
+use codex_protocol::protocol::AgentMessageEvent;
+use codex_protocol::protocol::ApplyPatchApprovalRequestEvent;
+use codex_protocol::protocol::Event;
+use codex_protocol::protocol::EventMsg;
+use codex_protocol::protocol::ExecApprovalRequestEvent;
+use codex_protocol::protocol::Op;
+use codex_protocol::protocol::Submission;
+use codex_protocol::protocol::TurnCompleteEvent;
 use codex_protocol::user_input::UserInput;
 use rmcp::model::CallToolResult;
 use rmcp::model::Content;

codex-rs/mcp-server/src/exec_approval.rs

@@ -2,10 +2,10 @@ use std::path::PathBuf;
 use std::sync::Arc;
 
 use codex_core::CodexThread;
-use codex_core::protocol::Op;
-use codex_core::protocol::ReviewDecision;
 use codex_protocol::ThreadId;
 use codex_protocol::parse_command::ParsedCommand;
+use codex_protocol::protocol::Op;
+use codex_protocol::protocol::ReviewDecision;
 use rmcp::model::ErrorData;
 use rmcp::model::RequestId;
 use serde::Deserialize;

codex-rs/mcp-server/src/message_processor.rs

@@ -6,9 +6,9 @@ use codex_core::ThreadManager;
 use codex_core::config::Config;
 use codex_core::default_client::USER_AGENT_SUFFIX;
 use codex_core::default_client::get_codex_user_agent;
-use codex_core::protocol::Submission;
 use codex_protocol::ThreadId;
 use codex_protocol::protocol::SessionSource;
+use codex_protocol::protocol::Submission;
 use rmcp::model::CallToolRequestParams;
 use rmcp::model::CallToolResult;
 use rmcp::model::ClientNotification;
@@ -572,7 +572,7 @@ impl MessageProcessor {
         if let Err(e) = codex_arc
             .submit_with_id(Submission {
                 id: request_id_string,
-                op: codex_core::protocol::Op::Interrupt,
+                op: codex_protocol::protocol::Op::Interrupt,
             })
             .await
         {

codex-rs/mcp-server/src/outgoing_message.rs

@@ -2,8 +2,8 @@ use std::collections::HashMap;
 use std::sync::atomic::AtomicI64;
 use std::sync::atomic::Ordering;
 
-use codex_core::protocol::Event;
 use codex_protocol::ThreadId;
+use codex_protocol::protocol::Event;
 use rmcp::model::CustomNotification;
 use rmcp::model::CustomRequest;
 use rmcp::model::ErrorData;
@@ -200,7 +200,7 @@ pub(crate) struct OutgoingNotificationParams {
     pub event: serde_json::Value,
 }
 
-// Additional mcp-specific data to be added to a [`codex_core::protocol::Event`] as notification.params._meta
+// Additional mcp-specific data to be added to a [`codex_protocol::protocol::Event`] as notification.params._meta
 // MCP Spec: https://modelcontextprotocol.io/specification/2025-06-18/basic#meta
 // Typescript Schema: https://github.com/modelcontextprotocol/modelcontextprotocol/blob/0695a497eb50a804fc0e88c18a93a21a675d6b3e/schema/2025-06-18/schema.ts
 #[derive(Debug, Clone, PartialEq, Serialize)]
@@ -231,12 +231,12 @@ mod tests {
     use std::path::PathBuf;
 
     use anyhow::Result;
-    use codex_core::protocol::AskForApproval;
-    use codex_core::protocol::EventMsg;
-    use codex_core::protocol::SandboxPolicy;
-    use codex_core::protocol::SessionConfiguredEvent;
     use codex_protocol::ThreadId;
     use codex_protocol::openai_models::ReasoningEffort;
+    use codex_protocol::protocol::AskForApproval;
+    use codex_protocol::protocol::EventMsg;
+    use codex_protocol::protocol::SandboxPolicy;
+    use codex_protocol::protocol::SessionConfiguredEvent;
     use pretty_assertions::assert_eq;
     use serde_json::json;
     use tempfile::NamedTempFile;

codex-rs/mcp-server/src/patch_approval.rs

@@ -3,10 +3,10 @@ use std::path::PathBuf;
 use std::sync::Arc;
 
 use codex_core::CodexThread;
-use codex_core::protocol::FileChange;
-use codex_core::protocol::Op;
-use codex_core::protocol::ReviewDecision;
 use codex_protocol::ThreadId;
+use codex_protocol::protocol::FileChange;
+use codex_protocol::protocol::Op;
+use codex_protocol::protocol::ReviewDecision;
 use rmcp::model::ErrorData;
 use rmcp::model::RequestId;
 use serde::Deserialize;