A user could not override system-wide settings in their ~/.my.cnf,
because the DEFAULT_SYSCONFDIR was being searched last.  Also, in
some configurations (especially when the --sysconfdir compile-time
option is set to /etc or /etc/mysql), the system-wide my.cnf file
was read multiple times, causing confusion and potential problems.

Rearrange default directories to conform to the manual and logic.
Move --sysconfdir=<path> (DEFAULT_SYSCONFDIR) from the last default
directory to the middle of the list.  $HOME/.my.cnf should be last,
so the user is able to override the system-wide settings.

Change init_default_directories() to remove duplicates from the
list.