Ah yes. So
clean is not actually a graql command. It is a shell command. Furthermore, the command:
./graql.sh -f yourAmazingFile.gql
results in the file
yourAmazingFile.gql just getting passed straight to the Grakn Server for processing and the server only interprets valid graql commands, which clean is currently not one of them.
TL/DR: It's a funny limitation we have right now that we should be able to work around. @felix your thoughts on this one?