try this

Author: Andarist

src/test/integration/git.test.ts

@@ -177,16 +177,23 @@ const makeFileChanges = async (
       "../README.md",
       path.join(repoDirectory, "some-dir", "nested"),
     );
-    await git.add({
-      fs,
-      dir: repoDirectory,
-      filepath: "some-dir/nested",
+    // Use native git CLI for symlink commit - isomorphic-git has inconsistent
+    // oid calculation between git.add/commit and WORKDIR walker for symlinks
+    await new Promise<void>((resolve, reject) => {
+      execFile(
+        "git",
+        ["add", "some-dir/nested"],
+        { cwd: repoDirectory },
+        (error) => (error ? reject(error) : resolve()),
+      );
     });
-    await git.commit({
-      fs,
-      dir: repoDirectory,
-      message: "Add symlink",
-      author: { name: "Test", email: "test@test.com" },
+    await new Promise<void>((resolve, reject) => {
+      execFile(
+        "git",
+        ["commit", "-m", "Add symlink"],
+        { cwd: repoDirectory },
+        (error) => (error ? reject(error) : resolve()),
+      );
     });
 
     if (changegroup === "with-changed-symlink") {