If you are looking to combine MP4 files from the command line here is the easiest solution. First you need to use the following command to install the program.

sudo apt-get install gpac

Once installed you will be able to run the following command to join the files.

MP4Box -cat part1.mp4 -cat part2.mp4 -new joinedfile.mp4

You should now be able to combine MP4 files from the command line, and pretty quick at that.