You can store the commands directly in the message file (messX.dat, mess35X.dat). This is the cleanest way, but it needs a lot of work to find the commands again, for example, when the user chooses to delete a command.
When users write commands themselves, your program might also find and manipulate a user-written command, which may or may not be your intention.
The big advantage of this method is that it works with every Maketurn program.