Cut video (possibly directly to mp4)

ffmpeg -ss 00:01:00 -to 00:02:00 -i ./in.mkv -c copy out.mkv

Cut external subs

ffmpeg -i in.srt -ss 01:00 -to 02:00 out.srt

Burn subs into video

ffmpeg -i out.mkv -vf subtitles=out.srt -c:a copy -y final.mkv

Convert mkv to desired format

ffmpeg -i final.mkv -codec copy final_mp4.mp4

Convert flv to mp4

ffmpeg -i final.mkv -c:v libx264 -crf 19 -strict experimental final_mp4.mp4

Todo

• Map audio/video/subs to output piece - https://superuser.com/questions/639402/convert-specific-video-and-audio-track-only-with-ffmpeg
• Concat pieces - https://stackoverflow.com/questions/7333232/how-to-concatenate-two-mp4-files-using-ffmpeg