Yes the tutorial is unfortunately very simple and doesn't really explain the why behind each macro.
The manuals for the autotools are unfortunately not too good for the learner. There seems to be a wealth of documentation targeted at the beginner and advanced user, but a gaping hole in the middle where everyone has to pretty much figure things out on their own.
The tutorial makes two programs from one c file each whereas you want one program from multiple c files. in which case you will only have the one _PROGRAMS macro which is followed by a whitespace delimited list of your c files and headers.
This'll get you started but there's a lot more that the autotools do that makes life easier provided you can find somewhere that explains it. Some of the macros in this tutorial are really dated (even for writing at the time of gtk+2.10) and there is much better ways of organising your project. pkgconfig provides an excellent interface for dependency checking and at some point you will probably want to add gnome documentation support, provide instructions for accessing the files through the desktop menus and possibly have runtime translations of your buttons etc. Your best best is to have a look at some examples done by others. They most likely will not do things the best way or sometimes be downright wrong (my stuff included:
https://github.com/pchilds) but you should be able to pick up common themes which are hopefully good practice rather than not.
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