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If I manually apply a patch due to an error when trying to install the patch via SSH, should I update the "applied_patches" file manually also?

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It is not mandatory , but its a good practice so that other dev that might work on project will know that the patch is applied

and can be used to get of list of applied patches like

$ grep -F '|' app/etc/applied.patches.list|cut -f 2,1 -d'|'
2017-06-01 07:28:34 UTC | SUPEE-9765
2017-01-21 22:18:17 UTC | SUPEE-8788
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It is not mandatory , applied_patches for reference any other developer will know that the patch is applied.

Note : Any reporting tool consider the patches applied based on behavior-based identification patterns.

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