fixed bug reading back old file formats

Had to move the call to ‘branchIDListHelper_->updateFromInput’ to before the call to ‘validateFile’ in the constructor since some old file formats were causing ‘branchIDListHelper_->fixBranchListIndexes’ to be called before ‘updateFromInput’. In the old version of the code this worked since calling ‘fixBranchListIndexes’ in the case where the internal map was empty would inject a dummy value (0) into the map which was then used to ‘fix’ the branch. This only worked as long as the Indexes to be fixed was of length 1. Moving the call to ‘updateFromInput’ earlier now guarantees that the structure is properly filled before any call to ‘fixBranchListIndexes’.