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/core/src/lib.rs

@@ -57,7 +57,6 @@ pub mod default_client;
 pub mod model_family;
 mod openai_model_info;
 mod openai_tools;
-pub mod plan_tool;
 pub mod project_doc;
 mod rollout;
 pub(crate) mod safety;
@@ -65,7 +64,7 @@ pub mod seatbelt;
 pub mod shell;
 pub mod spawn;
 pub mod terminal;
-mod tool_apply_patch;
+mod tools;
 pub mod turn_diff_tracker;
 pub use rollout::ARCHIVED_SESSIONS_SUBDIR;
 pub use rollout::INTERACTIVE_SESSION_SOURCES;