chore: refactor tool handling (#4510)

# Tool System Refactor

- Centralizes tool definitions and execution in `core/src/tools/*`:
specs (`spec.rs`), handlers (`handlers/*`), router (`router.rs`),
registry/dispatch (`registry.rs`), and shared context (`context.rs`).
One registry now builds the model-visible tool list and binds handlers.
- Router converts model responses to tool calls; Registry dispatches
with consistent telemetry via `codex-rs/otel` and unified error
handling. Function, Local Shell, MCP, and experimental `unified_exec`
all flow through this path; legacy shell aliases still work.
- Rationale: reduce per‑tool boilerplate, keep spec/handler in sync, and
make adding tools predictable and testable.

Example: `read_file`
- Spec: `core/src/tools/spec.rs` (see `create_read_file_tool`,
registered by `build_specs`).
- Handler: `core/src/tools/handlers/read_file.rs` (absolute `file_path`,
1‑indexed `offset`, `limit`, `L#: ` prefixes, safe truncation).
- E2E test: `core/tests/suite/read_file.rs` validates the tool returns
the requested lines.

## Next steps:
- Decompose `handle_container_exec_with_params` 
- Add parallel tool calls

codex-rs/exec/src/event_processor_with_human_output.rs

@@ -1,7 +1,6 @@
 use codex_common::elapsed::format_duration;
 use codex_common::elapsed::format_elapsed;
 use codex_core::config::Config;
-use codex_core::plan_tool::UpdatePlanArgs;
 use codex_core::protocol::AgentMessageEvent;
 use codex_core::protocol::AgentReasoningRawContentEvent;
 use codex_core::protocol::BackgroundEventEvent;
@@ -35,6 +34,8 @@ use crate::event_processor::CodexStatus;
 use crate::event_processor::EventProcessor;
 use crate::event_processor::handle_last_message;
 use codex_common::create_config_summary_entries;
+use codex_protocol::plan_tool::StepStatus;
+use codex_protocol::plan_tool::UpdatePlanArgs;
 
 /// This should be configurable. When used in CI, users may not want to impose
 /// a limit so they can see the full transcript.
@@ -456,7 +457,6 @@ impl EventProcessor for EventProcessorWithHumanOutput {
 
                 // Pretty-print the plan items with simple status markers.
                 for item in plan {
-                    use codex_core::plan_tool::StepStatus;
                     match item.status {
                         StepStatus::Completed => {
                             ts_println!(self, "  {} {}", "✓".style(self.green), item.step);

codex-rs/exec/src/event_processor_with_jsonl_output.rs

@@ -31,8 +31,6 @@ use crate::exec_events::TurnStartedEvent;
 use crate::exec_events::Usage;
 use crate::exec_events::WebSearchItem;
 use codex_core::config::Config;
-use codex_core::plan_tool::StepStatus;
-use codex_core::plan_tool::UpdatePlanArgs;
 use codex_core::protocol::AgentMessageEvent;
 use codex_core::protocol::AgentReasoningEvent;
 use codex_core::protocol::Event;
@@ -48,6 +46,8 @@ use codex_core::protocol::SessionConfiguredEvent;
 use codex_core::protocol::TaskCompleteEvent;
 use codex_core::protocol::TaskStartedEvent;
 use codex_core::protocol::WebSearchEndEvent;
+use codex_protocol::plan_tool::StepStatus;
+use codex_protocol::plan_tool::UpdatePlanArgs;
 use tracing::error;
 use tracing::warn;
 

codex-rs/exec/src/lib.rs

@@ -171,7 +171,7 @@ pub async fn run_main(cli: Cli, codex_linux_sandbox_exe: Option<PathBuf>) -> any
         codex_linux_sandbox_exe,
         base_instructions: None,
         include_plan_tool: Some(include_plan_tool),
-        include_apply_patch_tool: None,
+        include_apply_patch_tool: Some(true),
         include_view_image_tool: None,
         show_raw_agent_reasoning: oss.then_some(true),
         tools_web_search_request: None,