You are changing your argument... You were originally talking about security and whatever you define as a "clean system" not about stability and robustness and

You are changing your argument... You were originally talking about security and whatever you define as a "clean system" not about stability and robustness and on that regard my point remains valid: Binary packages are not intrinsically more secure that plain text scripts that you can easily audit. If you feel safer because you are executing by hand a bunch of commands that can be automated with a script that's ok. In my case I rather spend that time doing something more productive.