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Looking at the code to understand this, I can confirm that if neither --output or an outFile is specified, then comskip ignores the --output-filename parameter entirely. To work around, you could specify either of these (as @tmm1 suggested).
BTW, if this wasn't intended, then at line 9032, comskip.c needs to build workbasename from the input directory and shortbasename.
attempting to use the command
comskip --ini="myfile.ini" --output-filename="testing" my-video-file.mkv
does not produce testing.edl and testing.txt, it produces my-video-file.edl and my-video-file.txt
Or am I not understanding the purpose of this flag?
Workaround:
ln -s my-video-file.mkv testing.mkv
comskip -ini="myfile.ini" testing.mkv
[ -h testing.mkv ] && rm testing.mkv
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