Once you have the original game files, copy the updated files from this git over them. Simply cp -r ctp2_data/* ~/ctp2/ctp2_data should do that.
Note, that this is a Windows game, where file names are case-insensitive. This version of CTP2 handles this, and file names can have any case, but the cp command may not overwrite the files that differ in case. If you find a strange behavior or think the files are not up-to-date, check that you don't have 2 copies of a file in different cases (lowercase everything if needed). With the GoG version, no renaming is needed.
If you get the message on the terminal: Failed to load module "atk-bridge". Install at-spi with sudo apt install at-spi.
Continue -> https://github.com/orlovskyjavaprofi/civctp2/blob/master/README.md