how to configure apache to view hidden (`.`) files?

Somewhere you have an IndexIgnore directive (mods-enabled/autoindex.conf?) that adds dotfiles to the list of files to ignore (mine has .??*) . Once a pattern has been added to the ignore list, it can't be removed.

To amend DerfK's answer: in apache version 2.4 you can, in fact, reset IndexIgnore via a new directive, IndexIgnoreReset