I updated both the 1.12 version and the 1.13 version to support the copying and pasting of command blocks. 1.12->1.3 upgrade support has also been added for command blocks.

Make backups, and let me know if you find any bugs or issues with command block copying, since I am not a command block expert.

Note: Old saves will not contain all command block data. If you use command blocks, make sure you copy them with the new version.

To test this update I copied a region using 2.3.3, 2.3.4, and 3.3.0. I then pasted them using 3.3.0. It upgraded them. The version copied in 2.3.3 did not have the correct direction, and it did not have the command. The version copied in 2.3.4 was identical to the one copied in 3.3.0.