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/Cargo.lock

@@ -861,6 +861,7 @@ dependencies = [
  "codex-otel",
  "codex-protocol",
  "codex-rmcp-client",
+ "codex-utils-string",
  "core_test_support",
  "dirs",
  "dunce",
@@ -1254,6 +1255,10 @@ dependencies = [
  "tokio",
 ]
 
+[[package]]
+name = "codex-utils-string"
+version = "0.0.0"
+
 [[package]]
 name = "color-eyre"
 version = "0.6.5"