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Yup, I got confused and broke something on my side, fixed now.  Thanks!

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.

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After running WadSmoosh, you should have a file named `doom_complete.pk3` alongside the `wadsmoosh.exe` you launched.  That's the real output of WadSmoosh, that `pk3` folder you found is just the working directory where WadSmoosh extracted everything to.

Regarding the skies, double-check the contents of `source_wads`.  I don't recall the exact fault on my side now (its been months) but the issue was that WadSmoosh wasn't finding all the data it needed because I'd messed up a filename.  My exact fault probably isn't the same as your exact fault, anyway, so double-check the names and MD5 sums of all the files (MD5 sums can be found on one of the Doom wiki fan sites).  Better yet, check the log!  That's what clued me in.

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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!