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/tools/handlers/shell.rs

@@ -0,0 +1,103 @@
+use async_trait::async_trait;
+use codex_protocol::models::ShellToolCallParams;
+
+use crate::codex::TurnContext;
+use crate::exec::ExecParams;
+use crate::exec_env::create_env;
+use crate::function_tool::FunctionCallError;
+use crate::tools::context::ToolInvocation;
+use crate::tools::context::ToolOutput;
+use crate::tools::context::ToolPayload;
+use crate::tools::handle_container_exec_with_params;
+use crate::tools::registry::ToolHandler;
+use crate::tools::registry::ToolKind;
+
+pub struct ShellHandler;
+
+impl ShellHandler {
+    fn to_exec_params(params: ShellToolCallParams, turn_context: &TurnContext) -> ExecParams {
+        ExecParams {
+            command: params.command,
+            cwd: turn_context.resolve_path(params.workdir.clone()),
+            timeout_ms: params.timeout_ms,
+            env: create_env(&turn_context.shell_environment_policy),
+            with_escalated_permissions: params.with_escalated_permissions,
+            justification: params.justification,
+        }
+    }
+}
+
+#[async_trait]
+impl ToolHandler for ShellHandler {
+    fn kind(&self) -> ToolKind {
+        ToolKind::Function
+    }
+
+    fn matches_kind(&self, payload: &ToolPayload) -> bool {
+        matches!(
+            payload,
+            ToolPayload::Function { .. } | ToolPayload::LocalShell { .. }
+        )
+    }
+
+    async fn handle(
+        &self,
+        invocation: ToolInvocation<'_>,
+    ) -> Result<ToolOutput, FunctionCallError> {
+        let ToolInvocation {
+            session,
+            turn,
+            tracker,
+            sub_id,
+            call_id,
+            tool_name,
+            payload,
+        } = invocation;
+
+        match payload {
+            ToolPayload::Function { arguments } => {
+                let params: ShellToolCallParams =
+                    serde_json::from_str(&arguments).map_err(|e| {
+                        FunctionCallError::RespondToModel(format!(
+                            "failed to parse function arguments: {e:?}"
+                        ))
+                    })?;
+                let exec_params = Self::to_exec_params(params, turn);
+                let content = handle_container_exec_with_params(
+                    tool_name.as_str(),
+                    exec_params,
+                    session,
+                    turn,
+                    tracker,
+                    sub_id.to_string(),
+                    call_id.clone(),
+                )
+                .await?;
+                Ok(ToolOutput::Function {
+                    content,
+                    success: Some(true),
+                })
+            }
+            ToolPayload::LocalShell { params } => {
+                let exec_params = Self::to_exec_params(params, turn);
+                let content = handle_container_exec_with_params(
+                    tool_name.as_str(),
+                    exec_params,
+                    session,
+                    turn,
+                    tracker,
+                    sub_id.to_string(),
+                    call_id.clone(),
+                )
+                .await?;
+                Ok(ToolOutput::Function {
+                    content,
+                    success: Some(true),
+                })
+            }
+            _ => Err(FunctionCallError::RespondToModel(format!(
+                "unsupported payload for shell handler: {tool_name}"
+            ))),
+        }
+    }
+}