chore: rework tools execution workflow (#5278)

Re-work the tool execution flow. Read `orchestrator.rs` to understand
the structure

codex-rs/core/src/tools/runtimes/mod.rs

@@ -0,0 +1,38 @@
+/*
+Module: runtimes
+
+Concrete ToolRuntime implementations for specific tools. Each runtime stays
+small and focused and reuses the orchestrator for approvals + sandbox + retry.
+*/
+use crate::sandboxing::CommandSpec;
+use crate::tools::sandboxing::ToolError;
+use std::collections::HashMap;
+use std::path::Path;
+
+pub mod apply_patch;
+pub mod shell;
+pub mod unified_exec;
+
+/// Shared helper to construct a CommandSpec from a tokenized command line.
+/// Validates that at least a program is present.
+pub(crate) fn build_command_spec(
+    command: &[String],
+    cwd: &Path,
+    env: &HashMap<String, String>,
+    timeout_ms: Option<u64>,
+    with_escalated_permissions: Option<bool>,
+    justification: Option<String>,
+) -> Result<CommandSpec, ToolError> {
+    let (program, args) = command
+        .split_first()
+        .ok_or_else(|| ToolError::Rejected("command args are empty".to_string()))?;
+    Ok(CommandSpec {
+        program: program.clone(),
+        args: args.to_vec(),
+        cwd: cwd.to_path_buf(),
+        env: env.clone(),
+        timeout_ms,
+        with_escalated_permissions,
+        justification,
+    })
+}