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/tests/event_processor_with_json_output.rs

@@ -37,6 +37,9 @@ use codex_exec::exec_events::TurnFailedEvent;
 use codex_exec::exec_events::TurnStartedEvent;
 use codex_exec::exec_events::Usage;
 use codex_exec::exec_events::WebSearchItem;
+use codex_protocol::plan_tool::PlanItemArg;
+use codex_protocol::plan_tool::StepStatus;
+use codex_protocol::plan_tool::UpdatePlanArgs;
 use mcp_types::CallToolResult;
 use pretty_assertions::assert_eq;
 use std::path::PathBuf;
@@ -115,10 +118,6 @@ fn web_search_end_emits_item_completed() {
 
 #[test]
 fn plan_update_emits_todo_list_started_updated_and_completed() {
-    use codex_core::plan_tool::PlanItemArg;
-    use codex_core::plan_tool::StepStatus;
-    use codex_core::plan_tool::UpdatePlanArgs;
-
     let mut ep = EventProcessorWithJsonOutput::new(None);
 
     // First plan update => item.started (todo_list)
@@ -339,10 +338,6 @@ fn mcp_tool_call_failure_sets_failed_status() {
 
 #[test]
 fn plan_update_after_complete_starts_new_todo_list_with_new_id() {
-    use codex_core::plan_tool::PlanItemArg;
-    use codex_core::plan_tool::StepStatus;
-    use codex_core::plan_tool::UpdatePlanArgs;
-
     let mut ep = EventProcessorWithJsonOutput::new(None);
 
     // First turn: start + complete