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I think this isn't a problem with hypernode-magerun but a problem caused by outdated patch data. tools.hypernode.com aggregates it's patch info from the patches spreadsheet which isn't updated regularly. Both the spreadsheet and https://tools.hypernode.com/patches/community/1.9.1.1 don't show there is a v2 patch and this might be why v1 is not detected.
This is one of the main reasons why I build magepatch as it aggregates it's data from the community driven magento-patches repository. Unfortunately this patch wasn't there either so I just added it and updated my patch index.
I can't update the spreadsheet but we can change the command to check if a newer version of a patch is installed and show a status like "newer version installed". Otherwise the problem should be fixed at the spreadsheet.
Line from applied_patches.list:
But reported by list-patches:
The text was updated successfully, but these errors were encountered: