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M-x helm-locate

lists files in hidden folders, that i will never open. How to instruct helm not to look into certain directories for file search & open.

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helm-locate uses linux command locate which uses updatedb to index the file location. To ignore some directories, configure /etc/updatedb.conf as

PRUNEPATHS="EXISTINGPATH NEWPATH"

And run updatedb in shell prompt with sudo permissions to get this change reflected.