How can I use Arlequin via the command line? I've got a decent knowledge of programming (incl. bash scripting) but I fail to understand how Arlequin works. Could you please help me with a very simple reproducible example on how to use Arlequin via the command line?

As the .zip file comes with its pre-compiled version, I'll just note that I'm on Mac OS X but of course, a reproducible example with Linux (or at worst with Windows) would also be helpful.
For MAC OSX, the executable found in arlsumstat_macosx (arlsumstatmac_64bit) seem to work appropriately. The directory for arlsumstat_macosx does not contain any examples but you can use example files from arlecore_macosx/Example files_linux using this syntax.

The complication is that arlsumstatmac_64bit will look in the current directory for the file arl_run.ars. There is a file with the same name in arlecore_macosx but it is not compatible. So you have to be in the arlsumstat_macosx.

In short, cd to arlsumstat_macosx and do

./arlsumstatmac_64bit path/to/arlecore_macosx/Example\ files_linux/Freqncy/cohen.ars path/to/arlecore_macosx/Example\ files_linux/Freqncy/cohen.arp


, where the .arp file contains the data and the .ars file contains the settings (the description of what you want Arlequin to do).