I am suppose do lost of copying and execution other scripts

You mean: Your program is copying other scripts, and executing other scripts? With other scripts, you mean: Other Perl programs?

configuration file which hold all the commands

You mean: There is a file which contains a list of instructions of what other files need to be copied or executed? In this case, one would probably not call this a "configuration file"; a configuration file would typically contain options to configure a program.

Can you decide by yourself how the syntax of the "configuration file" looks like? In this case, you could simply make that file syntactically a Perl program and evaluate it. You would then not have to worry about parsing.