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Thank you very much for all the info.

My problem is that when I run "wadsmoosh.exe" it doesn't output a 'doom_complete.pk3' file at all... (I'm using Windows 10. I've run the .exe as admin.)

I've no clue how to check MD5 sums, and I don't really understand how to read the log deep enough so as to discover the issue, but that's ok, I'll eventually figure it out.

Edit: Fixed! I re-dl'ed Master Levels and used those fresh installs for WadSmoosh and it generated the 'doom_complete.pk3' as intended.
And the sky errors have been fixed as well!
Thanks again for the help!

Could you share what you did to fix that?

I'm having the same problem (skies in some of these wads, like ACHRON22, not loading).

For the life of me I can't figure out how to fix it.

It's suspicious that, when I run "wadsmoosh.exe", the output is a "pk3" folder, and not a file... I can pack it up into a .zip file and then rename it to .pk3, but, maybe the mistake is somewhere around that?

I'm completely stumped at this point. Any help would be greatly appreciated.