Reject overlapping EOF patch chunks

codex-rs/apply-patch/src/seek_sequence.rs

@@ -27,7 +27,7 @@ pub(crate) fn seek_sequence(
         return None;
     }
     let search_start = if eof && lines.len() >= pattern.len() {
-        lines.len() - pattern.len()
+        (lines.len() - pattern.len()).max(start)
     } else {
         start
     };

codex-rs/apply-patch/tests/suite/tool.rs

@@ -84,6 +84,26 @@ fn test_apply_patch_cli_applies_multiple_chunks() -> anyhow::Result<()> {
     Ok(())
 }
 
+#[test]
+fn test_apply_patch_cli_rejects_overlapping_end_of_file_chunks() -> anyhow::Result<()> {
+    let tmp = tempdir()?;
+    let target_path = tmp.path().join("overlapping.txt");
+    let expected_target_path = resolved_under(tmp.path(), "overlapping.txt")?;
+    fs::write(&target_path, "one\n")?;
+
+    let patch = "*** Begin Patch\n*** Update File: overlapping.txt\n@@\n-one\n+first\n@@\n-one\n+second\n*** End of File\n*** End Patch";
+
+    run_apply_patch_in_dir(tmp.path(), patch)?
+        .failure()
+        .stderr(format!(
+            "Failed to find expected lines in {}:\none\n",
+            expected_target_path.display()
+        ));
+
+    assert_eq!(fs::read_to_string(target_path)?, "one\n");
+    Ok(())
+}
+
 #[test]
 fn test_apply_patch_cli_preserves_crlf_from_target_file() -> anyhow::Result<()> {
     let patch = "*** Begin Patch\n*** Update File: crlf.txt\n@@\n-one\n+uno\n@@\n two\n+\n+between\n three\n*** End Patch";