IOVDbMetaDataTool: keep track of processed files to avoid repeating

This MR makes IOVDbMetaDataTool more robust in MP workflows. Checking only for the first input file incident and skipping first BeginInputFile incident following the FirstInputFile is not enough as in MP BeginInputFile is fired again after fork, so we may end up with processing the input file twice. Instead, I propose to keep the set of the processed files (which was already an unused member variable) since processing the same input twice may lead to incorrect IOV metadata.

addresses ATEAM-1073