2

I am looking for a tool that will convert my mkv file to an mp4 file, but is devoid of malware and bloatware.

1

FFMpeg It's a command line program but it can convert a MKV to a MP4 without recompressing the file. Very quick.

The command to do so would be
ffmpeg -i input.mkv -c copy -c:s mov_text output.mp4

If you do some further digging, you can probably find a script to help. Actually, you might look at this Apple.StackExchange answer.

1

I use Permute on a regular basis, although it is subscription based.

If you prefer open source:

Handbrake for GUI.

FFMPG for CLI.

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