GNU Astronomy Utilities manual

4.2.2 Configuration file precedence

The parameter values in all the programs of Gnuastro will be filled in the following order. Such that if a parameter is assigned a value in an earlier step, any value for that parameter in a later step will be ignored.

1. Command line options, for this particular execution.
2. Current directory, for all executions in the directory from which any of the utilities is run (./.gnuastro/).
3. The user’s home directory, for all the executions of a particular user: ($HOME/.local/etc/, see below). It is only read if --onlydirconf is not called, see Operating modes.
4. In a system wide directory for any user on that computer (prefix/etc/, see Installation directory for the value of prefix). It is only read if --onlydirconf is not called, see Operating modes.

The basic idea behind setting this progressive state of checking for parameter values is that separate users of a computer or separate folders in a user’s file system might need different values for some parameters and the same values for others. For example raw telescope images usually have their main image extension in the second FITS extension, while processed FITS images usually only have one extension. If your system wide default input extension is 0 (the first), then when you want to work with the former group of data you have to explicitly mention it to the programs every time. With this progressive state of default values to check, you can set different default values for the different directories that you would like to run Gnuastro in for your different purposes, so you won’t have to worry about this issue any more.

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GNU Astronomy Utilities manual, November 2015.