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I'll propose a different workflow (suggested by hasenj): instead of using fdupes to identify duplicate files and perform some post-processing to remove them, you can use Unison to identify and deal with duplicates. You need to run Unison with one of the roots remote, otherwise it doesn't detect identical files. So run unison /home/articles/bibtex.pdf ...


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In my experience fdupes can be inconsistent in the order that it outputs files (I have had my own problems using the --delete option). This should be fairly robust as it doesn't require the files to be in a specific order (as as long as there are always two dupes in different folders): # note no trailing slash source_dir=/home/articles ...



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