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/exec/tests/event_processor_with_json_output.rs

@@ -1,29 +1,3 @@
-use codex_core::protocol::AgentMessageEvent;
-use codex_core::protocol::AgentReasoningEvent;
-use codex_core::protocol::AgentStatus;
-use codex_core::protocol::AskForApproval;
-use codex_core::protocol::CollabAgentSpawnBeginEvent;
-use codex_core::protocol::CollabAgentSpawnEndEvent;
-use codex_core::protocol::CollabWaitingEndEvent;
-use codex_core::protocol::ErrorEvent;
-use codex_core::protocol::Event;
-use codex_core::protocol::EventMsg;
-use codex_core::protocol::ExecCommandBeginEvent;
-use codex_core::protocol::ExecCommandEndEvent;
-use codex_core::protocol::ExecCommandSource;
-use codex_core::protocol::ExecCommandStatus as CoreExecCommandStatus;
-use codex_core::protocol::FileChange;
-use codex_core::protocol::McpInvocation;
-use codex_core::protocol::McpToolCallBeginEvent;
-use codex_core::protocol::McpToolCallEndEvent;
-use codex_core::protocol::PatchApplyBeginEvent;
-use codex_core::protocol::PatchApplyEndEvent;
-use codex_core::protocol::PatchApplyStatus as CorePatchApplyStatus;
-use codex_core::protocol::SandboxPolicy;
-use codex_core::protocol::SessionConfiguredEvent;
-use codex_core::protocol::WarningEvent;
-use codex_core::protocol::WebSearchBeginEvent;
-use codex_core::protocol::WebSearchEndEvent;
 use codex_exec::event_processor_with_jsonl_output::EventProcessorWithJsonOutput;
 use codex_exec::exec_events::AgentMessageItem;
 use codex_exec::exec_events::CollabAgentState;
@@ -63,9 +37,35 @@ use codex_protocol::models::WebSearchAction;
 use codex_protocol::plan_tool::PlanItemArg;
 use codex_protocol::plan_tool::StepStatus;
 use codex_protocol::plan_tool::UpdatePlanArgs;
+use codex_protocol::protocol::AgentMessageEvent;
+use codex_protocol::protocol::AgentReasoningEvent;
+use codex_protocol::protocol::AgentStatus;
+use codex_protocol::protocol::AskForApproval;
 use codex_protocol::protocol::CodexErrorInfo;
+use codex_protocol::protocol::CollabAgentSpawnBeginEvent;
+use codex_protocol::protocol::CollabAgentSpawnEndEvent;
+use codex_protocol::protocol::CollabWaitingEndEvent;
+use codex_protocol::protocol::ErrorEvent;
+use codex_protocol::protocol::Event;
+use codex_protocol::protocol::EventMsg;
+use codex_protocol::protocol::ExecCommandBeginEvent;
+use codex_protocol::protocol::ExecCommandEndEvent;
 use codex_protocol::protocol::ExecCommandOutputDeltaEvent;
+use codex_protocol::protocol::ExecCommandSource;
+use codex_protocol::protocol::ExecCommandStatus as CoreExecCommandStatus;
 use codex_protocol::protocol::ExecOutputStream;
+use codex_protocol::protocol::FileChange;
+use codex_protocol::protocol::McpInvocation;
+use codex_protocol::protocol::McpToolCallBeginEvent;
+use codex_protocol::protocol::McpToolCallEndEvent;
+use codex_protocol::protocol::PatchApplyBeginEvent;
+use codex_protocol::protocol::PatchApplyEndEvent;
+use codex_protocol::protocol::PatchApplyStatus as CorePatchApplyStatus;
+use codex_protocol::protocol::SandboxPolicy;
+use codex_protocol::protocol::SessionConfiguredEvent;
+use codex_protocol::protocol::WarningEvent;
+use codex_protocol::protocol::WebSearchBeginEvent;
+use codex_protocol::protocol::WebSearchEndEvent;
 use pretty_assertions::assert_eq;
 use rmcp::model::Content;
 use serde_json::json;
@@ -118,7 +118,7 @@ fn task_started_produces_turn_started_event() {
     let mut ep = EventProcessorWithJsonOutput::new(None);
     let out = ep.collect_thread_events(&event(
         "t1",
-        EventMsg::TurnStarted(codex_core::protocol::TurnStartedEvent {
+        EventMsg::TurnStarted(codex_protocol::protocol::TurnStartedEvent {
             turn_id: "turn-1".to_string(),
             model_context_window: Some(32_000),
             collaboration_mode_kind: ModeKind::Default,
@@ -312,7 +312,7 @@ fn plan_update_emits_todo_list_started_updated_and_completed() {
     // Task completes => item.completed (same id, latest state)
     let complete = event(
         "p3",
-        EventMsg::TurnComplete(codex_core::protocol::TurnCompleteEvent {
+        EventMsg::TurnComplete(codex_protocol::protocol::TurnCompleteEvent {
             turn_id: "turn-1".to_string(),
             last_agent_message: None,
         }),
@@ -683,7 +683,7 @@ fn plan_update_after_complete_starts_new_todo_list_with_new_id() {
     let _ = ep.collect_thread_events(&start);
     let complete = event(
         "t2",
-        EventMsg::TurnComplete(codex_core::protocol::TurnCompleteEvent {
+        EventMsg::TurnComplete(codex_protocol::protocol::TurnCompleteEvent {
             turn_id: "turn-1".to_string(),
             last_agent_message: None,
         }),
@@ -763,7 +763,7 @@ fn error_event_produces_error() {
     let mut ep = EventProcessorWithJsonOutput::new(None);
     let out = ep.collect_thread_events(&event(
         "e1",
-        EventMsg::Error(codex_core::protocol::ErrorEvent {
+        EventMsg::Error(codex_protocol::protocol::ErrorEvent {
             message: "boom".to_string(),
             codex_error_info: Some(CodexErrorInfo::Other),
         }),
@@ -803,7 +803,7 @@ fn stream_error_event_produces_error() {
     let mut ep = EventProcessorWithJsonOutput::new(None);
     let out = ep.collect_thread_events(&event(
         "e1",
-        EventMsg::StreamError(codex_core::protocol::StreamErrorEvent {
+        EventMsg::StreamError(codex_protocol::protocol::StreamErrorEvent {
             message: "retrying".to_string(),
             codex_error_info: Some(CodexErrorInfo::Other),
             additional_details: None,
@@ -837,7 +837,7 @@ fn error_followed_by_task_complete_produces_turn_failed() {
 
     let complete_event = event(
         "e2",
-        EventMsg::TurnComplete(codex_core::protocol::TurnCompleteEvent {
+        EventMsg::TurnComplete(codex_protocol::protocol::TurnCompleteEvent {
             turn_id: "turn-1".to_string(),
             last_agent_message: None,
         }),
@@ -1267,21 +1267,21 @@ fn task_complete_produces_turn_completed_with_usage() {
     let mut ep = EventProcessorWithJsonOutput::new(None);
 
     // First, feed a TokenCount event with known totals.
-    let usage = codex_core::protocol::TokenUsage {
+    let usage = codex_protocol::protocol::TokenUsage {
         input_tokens: 1200,
         cached_input_tokens: 200,
         output_tokens: 345,
         reasoning_output_tokens: 0,
         total_tokens: 0,
     };
-    let info = codex_core::protocol::TokenUsageInfo {
+    let info = codex_protocol::protocol::TokenUsageInfo {
         total_token_usage: usage.clone(),
         last_token_usage: usage,
         model_context_window: None,
     };
     let token_count_event = event(
         "e1",
-        EventMsg::TokenCount(codex_core::protocol::TokenCountEvent {
+        EventMsg::TokenCount(codex_protocol::protocol::TokenCountEvent {
             info: Some(info),
             rate_limits: None,
         }),
@@ -1291,7 +1291,7 @@ fn task_complete_produces_turn_completed_with_usage() {
     // Then TurnComplete should produce turn.completed with the captured usage.
     let complete_event = event(
         "e2",
-        EventMsg::TurnComplete(codex_core::protocol::TurnCompleteEvent {
+        EventMsg::TurnComplete(codex_protocol::protocol::TurnCompleteEvent {
             turn_id: "turn-1".to_string(),
             last_agent_message: Some("done".to_string()),
         }),