Your proposal of a command line switch for kstars would be perfectly acceptable, if it can launch quickly (on my machine, kstars does not launch quickly), and if it's easy to associate .fits files with a program that needs a command line switch (without having to resort to a shell script). The second requirement can easily be satisfied by making a symlink (or hard link) of fitsviewer to the kstars executable, then when kstars starts up, it can check to see if it was launched as kstars, or as fitsviewer.

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