Reindexing files with a user-generated manifest file did not work because modifications for generating nightly binaries broke this. Absolute file paths were replaced with filepaths containing placeholders in a pass by reference value and therefore affected other parts of the code. In this case, the code used for reindexing files mentioned in the manifest file. Some files ended up containing placeholders and couldn't be located and reindexed. 2. Use FileUtils method instead of going through deprecated util method.