Avoid corrupting $set-ed arrays when transaction error occurs

lib/plugins/trackTransaction.js

@@ -85,7 +85,7 @@ function mergeAtomics(destination, source) {
     destination.$addToSet = (destination.$addToSet || []).concat(source.$addToSet);
   }
   if (source.$set != null) {
-    destination.$set = Object.assign(destination.$set || {}, source.$set);
+    destination.$set = Array.isArray(source.$set) ? [...source.$set] : Object.assign({}, source.$set);
   }
 
   return destination;

test/docs/transactions.test.js

@@ -397,6 +397,62 @@ describe('transactions', function() {
     assert.equal(docs[0].name, 'test');
   });
 
+  it('handles resetting array state with $set atomic (gh-13698)', async function() {
+    db.deleteModel(/Test/);
+    const subItemSchema = new mongoose.Schema(
+      {
+        name: { type: String, required: true }
+      },
+      { _id: false }
+    );
+
+    const itemSchema = new mongoose.Schema(
+      {
+        name: { type: String, required: true },
+        subItems: { type: [subItemSchema], required: true }
+      },
+      { _id: false }
+    );
+
+    const schema = new mongoose.Schema({
+      items: { type: [itemSchema], required: true }
+    });
+
+    const Test = db.model('Test', schema);
+
+    const { _id } = await Test.create({
+      items: [
+        { name: 'test1', subItems: [{ name: 'x1' }] },
+        { name: 'test2', subItems: [{ name: 'x2' }] }
+      ]
+    });
+
+    const doc = await Test.findById(_id).orFail();
+    let attempt = 0;
+
+    await db.transaction(async(session) => {
+      await doc.save({ session });
+
+      if (attempt === 0) {
+        attempt += 1;
+        throw new mongoose.mongo.MongoServerError({
+          message: 'Test transient transaction failures & retries',
+          errorLabels: [mongoose.mongo.MongoErrorLabel.TransientTransactionError]
+        });
+      }
+    });
+
+    const { items } = await Test.findById(_id).orFail();
+    assert.ok(Array.isArray(items));
+    assert.equal(items.length, 2);
+    assert.equal(items[0].name, 'test1');
+    assert.equal(items[0].subItems.length, 1);
+    assert.equal(items[0].subItems[0].name, 'x1');
+    assert.equal(items[1].name, 'test2');
+    assert.equal(items[1].subItems.length, 1);
+    assert.equal(items[1].subItems[0].name, 'x2');
+  });
+
   it('transaction() retains modified status for documents created outside of the transaction then modified inside the transaction (gh-13973)', async function() {
     db.deleteModel(/Test/);
     const Test = db.model('Test', Schema({ status: String }));