fix: eliminate runtime dependency on patch(1) for apply_patch (#718)

When processing an `apply_patch` tool call, we were already computing
the new file content in order to compute the unified diff. Before this
PR, we were shelling out to `patch(1)` to apply the unified diff once
the user accepted the change, but this updates the code to just retain
the new file content and use it to write the file when the user accepts.
This simplifies deployment because it no longer assumes `patch(1)` is on
the host.

Note this change is internal to the Codex agent and does not affect
`protocol.rs`.

codex-rs/core/src/codex.rs

@@ -3,8 +3,6 @@ use std::collections::HashSet;
 use std::io::Write;
 use std::path::Path;
 use std::path::PathBuf;
-use std::process::Command;
-use std::process::Stdio;
 use std::sync::Arc;
 use std::sync::Mutex;
 
@@ -1346,6 +1344,7 @@ fn convert_apply_patch_to_protocol(
             ApplyPatchFileChange::Update {
                 unified_diff,
                 move_path,
+                new_content: _new_content,
             } => FileChange::Update {
                 unified_diff: unified_diff.clone(),
                 move_path: move_path.clone(),
@@ -1400,28 +1399,10 @@ fn apply_changes_from_apply_patch(
                 deleted.push(path.clone());
             }
             ApplyPatchFileChange::Update {
-                unified_diff,
+                unified_diff: _unified_diff,
                 move_path,
+                new_content,
             } => {
-                // TODO(mbolin): `patch` is not guaranteed to be available.
-                // Allegedly macOS provides it, but minimal Linux installs
-                // might omit it.
-                Command::new("patch")
-                    .arg(path)
-                    .arg("-p0")
-                    .stdout(Stdio::null())
-                    .stderr(Stdio::null())
-                    .stdin(Stdio::piped())
-                    .spawn()
-                    .and_then(|mut child| {
-                        let mut stdin = child.stdin.take().unwrap();
-                        stdin.write_all(unified_diff.as_bytes())?;
-                        stdin.flush()?;
-                        // Drop stdin to send EOF.
-                        drop(stdin);
-                        child.wait()
-                    })
-                    .with_context(|| format!("Failed to apply patch to {}", path.display()))?;
                 if let Some(move_path) = move_path {
                     if let Some(parent) = move_path.parent() {
                         if !parent.as_os_str().is_empty() {
@@ -1433,11 +1414,14 @@ fn apply_changes_from_apply_patch(
                             })?;
                         }
                     }
+
                     std::fs::rename(path, move_path)
                         .with_context(|| format!("Failed to rename file {}", path.display()))?;
+                    std::fs::write(move_path, new_content)?;
                     modified.push(move_path.clone());
                     deleted.push(path.clone());
                 } else {
+                    std::fs::write(path, new_content)?;
                     modified.push(path.clone());
                 }
             }