This code will be used to execute commands defined by the user but I want to do it in as safe-a-way as possible.

What do you mean by that? What is "safe"? Should it ask the user if the command is going to remove a file? Should it try to second-guess the user and ask confirmation if the command the user gives may not be what he really wants? Do you first want to make a backup?

Your definition is utterly vague. As safe as possible would be to not do anything - but I doubt that is what you mean. What are you afraid of might happen? What do you want to protect yourself against?