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Are configuration files with ~ ending (emacs backup files) interpreted when they are in conf.d directory ?

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Which conf.d directory? Different programs have different rules. Most do skip common backup suffixes, but check their individual documentation. – Gilles Jan 25 '13 at 23:41

They should not be considered, but where to look for configuration files and their names is up to the individual program. Can't give general rules.

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