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The rsync way given by Thane with Yamaneko additions work great but leave empty directories. For me the final solution was in two steps, first call rsync with full path, then a find command to remove all empty directories: rsync -rvcm --compare-dest=/tmp/org/ /tmp/new/ /tmp/difference/ find /tmp/difference/ -d -type d -empty -exec rmdir {} \; -print ...


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diff has more than one option related to whitespace. However, one is less useful for patches. The manual page gives an obscure hint, referring to both GNU: -B, --ignore-blank-lines ignore changes where lines are all blank -b, --ignore-space-change ignore changes in the amount of white space -w, --ignore-all-space ...


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While the given pathnames do not look quite right (especially the new tree, which someone else has changed), you can keep in mind that the patch program can be told to ignore a given number of levels of directory from the output of diff using the -p option. When applying a patch to files in a different directory than the patch-file shows, you would cd into ...



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