I just noticed that since we are using GNU C Library's Argp for parsing of arguments, we can use the each programs' argp_option array (and the `gal_commonargs_options' in `lib/commonargs.h' for the common options) to look up all the long option names automatically. 

Since the `argp_option' array is statically defined, we can easily get the number of elements in it with ((sizeof options)/(sizeof options[0])) and parse over them to pull out the option names that were not set on the command-line and put them in a list to pass onto the library function as suggested below.

This will make each program's `args.h' the only place where the long option names are mentioned, greatly simplifying the process of reading in options. With the programs essentially shrinking to library calls, this will make the creation of new programs or management of existing ones an order of magnitude more easier than before and most importantly the code will be much more elegant.

I don't have the time to do this now, so if you are up for the challenge, you are most welcome to start working on it, I would be very happy to help ;-).

With the expansion of Gnuastro and its libraries (which will centralize many operations), the number of common options will increase. So it would be much more easier for the gnuastro users to set the values of common options only once for all of Gnuastro's programs (when they want to).

One example maybe that you want your work to be reproducible, and so all the programs must run with the same version fo Gnuastro, and you want them to only use the current directory configuration file. To do this, you have to manually add the two `onlydirconf' and `onlyversion' to the configuration files of all the Gnuastro programs that you use.

This can be buggy and cause errors, for example, during your research (before you publish/release the reproduction pipeline), a new version of Gnuastro comes and you want to use it instead, this step of checking/changing all those configuration files can be hard and a cause of avoiding this update.

There are many other examples like log files, or (later) printing/file formats for programs that output tables.

So here, I am suggesting to add a `gnuastro.conf' configuration file which will only be used in reading common options to all the programs. Its precedence would be lower than the configuration file for that utility in the same directory.

It would also be great if as part of this transition we could also re-write the way each program's configuration files are read, and values are checked. Currently each program does this in its own `ui.c' file and uses macros a lot. There might be better/cleaner ways to do all this in the library so the programs just have to call the appropriate function.

This might be possible with the new root data structure (task #14245), in a similar way to how we read table columns (see `gal_table_read' in the new lib/table.c). In short, each program makes a linked list of `gal_data_t' with the `name' field set to the long option name (short options are only for the command-line). This linked list is passed to the library function along with the program's name (to determine the name of the configuration file).

The library function will then start looking for the directory, user-wide and system-wide configuration files and fill in the option values as they are read from the lines. Every option that is read will be popped from the input linked list (and added to the output linked list) so any future occurance of that option (in lower precedence configuration file) is never checked (since it is no longer in the list that is searched).

This will also remove the need for the `*set' variables in the `uiparams' structure of each program's `main.h' file. Because the options that have been set on the command-line will not be in the linked list that is passed onto the library function for reading configuration files. This can be a good way forward to greatly simplifying the process of option management in Gnuastro's programs and simplifying the life of developers/users :-).