For the current (local) and user-wide directories, the configuration files
are stored in the hidden sub-directories named .gnuastro/ and
$HOME/.local/etc/ respectively. Unless you have changed it, the
$HOME environment variable should point to your home directory. You
can check it by running
$ echo $HOME. Each time you run any of
the programs in Gnuastro, this environment variable is read and placed in
the above address. So if you suddenly see that your home configuration
files are not being read, probably you (or some other program) has changed
the value of this environment variable.
Although it might cause confusions like above, this dependence on the HOME environment variable enables you to temporarily use a different directory as your home directory. This can come in handy in complicated situations. To set the user or current directory configuration files based on your command-line input, you can use the --setdirconf or --setusrconf, see Operating mode options.