Currently this method will find all the files that haven been
 updated since the last hash. This is then used to find out
 which packages will need to be regenered. We should not try to
 regenerate files that have been deleted, this causes a file does
 not exist error when running the generator.

 The provided flag restricts to files that:
   - (A) Added
   - (C) Copied
   - (M) Modified
   - (R) Renamed