Merge "This change does a number of things: 1 - Modify...

Merge "This change does a number of things: 1 - Modify IntegrityFileManagerTest to use Binary serializer. 2 - Fix a few minor indexing bugs that exist. 3 - Introduce a comprehensive test that verifies that the created indexing file helps to parse the binary file correctly. 4 - Deletes a flaky test that is now covered by the tests in IntegrityFileManager."