Add require_xxx_source methods to DataFile to avoid 'require' semantic in create_xxx_source methods (applying suggestions)

Refactor write_file on AgipdCorrections to create indexes using the DataFile instead of copying them from the raw data. For compatibility, it still copies some xtdf groups

1.Plot agipd single module geometry for correct and darks
2.Fix sorting dark runs
3.Fix reading a single module which doesnt start at 0