fix: apply_patch shell_serialization tests (#4786)

## Summary
Adds additional shell_serialization tests specifically for apply_patch
and other cases.

## Test Plan
- [x] These are all tests

codex-rs/core/src/executor/runner.rs

@@ -30,19 +30,19 @@ use codex_otel::otel_event_manager::ToolDecisionSource;
 pub(crate) struct ExecutorConfig {
     pub(crate) sandbox_policy: SandboxPolicy,
     pub(crate) sandbox_cwd: PathBuf,
-    codex_linux_sandbox_exe: Option<PathBuf>,
+    pub(crate) codex_exe: Option<PathBuf>,
 }
 
 impl ExecutorConfig {
     pub(crate) fn new(
         sandbox_policy: SandboxPolicy,
         sandbox_cwd: PathBuf,
-        codex_linux_sandbox_exe: Option<PathBuf>,
+        codex_exe: Option<PathBuf>,
     ) -> Self {
         Self {
             sandbox_policy,
             sandbox_cwd,
-            codex_linux_sandbox_exe,
+            codex_exe,
         }
     }
 }
@@ -86,7 +86,14 @@ impl Executor {
                 maybe_translate_shell_command(request.params, session, request.use_shell_profile);
         }
 
-        // Step 1: Normalise parameters via the selected backend.
+        // Step 1: Snapshot sandbox configuration so it stays stable for this run.
+        let config = self
+            .config
+            .read()
+            .map_err(|_| ExecError::rejection("executor config poisoned"))?
+            .clone();
+
+        // Step 2: Normalise parameters via the selected backend.
         let backend = backend_for_mode(&request.mode);
         let stdout_stream = if backend.stream_stdout(&request.mode) {
             request.stdout_stream.clone()
@@ -94,16 +101,9 @@ impl Executor {
             None
         };
         request.params = backend
-            .prepare(request.params, &request.mode)
+            .prepare(request.params, &request.mode, &config)
             .map_err(ExecError::from)?;
 
-        // Step 2: Snapshot sandbox configuration so it stays stable for this run.
-        let config = self
-            .config
-            .read()
-            .map_err(|_| ExecError::rejection("executor config poisoned"))?
-            .clone();
-
         // Step 3: Decide sandbox placement, prompting for approval when needed.
         let sandbox_decision = select_sandbox(
             &request,
@@ -227,7 +227,7 @@ impl Executor {
             sandbox,
             &config.sandbox_policy,
             &config.sandbox_cwd,
-            &config.codex_linux_sandbox_exe,
+            &config.codex_exe,
             stdout_stream,
         )
         .await