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When using rename option in alignmets tool it won't work without alignments file. But it renames filenames right even if it have wrong alignments file given. Does it really need it or is there something going wrong with images with wrong alignments file? Just to be sure before making any damage 
As far as I can remember (and I may be wrong), the rename option does indeed rename based on what is in the PNG header of the image, so no, alignments file is not necessary.
The reason it is still required is that "alignment file" is a required argument for the tool (the tool was created prior to storing information in the png header), and updating it to not be required would be a bit of a pain. It's a nuisance, currently, rather than a critical flaw, so I haven't spent any time on fixing this. One day I will.
This is a long way of saying 'you are correct, and what you are doing is fine'.