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Thanks for making the code available. Always interesting to hear how other people do things.
As you mention Ubuntu, I assume fcombine does not run under Windows.
For us heathens still using Windows, do you know if that archive can be used in a Windows WSL2 instance? Under W10 WSL2 there is a simple Linux command line environment*, but I believe W11 WSL2 instances have a full graphical interface. Have you used fcombine under that?
Finally, what language is the code in? The mention of libcfitsio kinda suggests C. Just curious as to how you work out interframe offsets and rotations – my own code for that works but isn’t elegant or especially fast.
*I run my astrometry.NET installation under it using Ubuntu installed on a Windows laptop via WSL2 – though Windows gave me a choice of which Linux.