The option values in all the programs of Gnuastro will be filled in the following order. If an option only takes one value which is given in an earlier step, any value for that option in a later step will be ignored. Note that if the lastconfig option is specified in any step below, no other configuration files will be parsed (see Operating mode options).
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.
Checking the order: You can confirm/check the order of parsing configuration files using the --checkconfig option with any Gnuastro program, see Operating mode options. Just be sure to place this option immediately after the program name, before any other option.
As you see above, there can also be a configuration file containing the common options in all the programs: gnuastro.conf (see Common options). If options specific to one program are specified in this file, there will be unrecognized option errors, or unexpected behavior if the option has different behavior in another program. On the other hand, there is no problem with astprogname.conf containing common options81.
Manipulating the order: You can manipulate this order or add new files with the following two options which are fully described in Operating mode options:
One example of benefiting from these configuration files can be this: 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.
The same can be said about the gnuastro.conf files: by specifying a behavior in this single file, all Gnuastro programs in the respective directory, user, or system-wide steps will behave similarly. For example to keep the input’s directory when no specific output is given (see Automatic output), or to not delete an existing file if it has the same name as a given output (see Input/Output options).
As an example, the --setdirconf and --setusrconf options will also write the common options they have read in their produced astprogname.conf.