[eluser]WanWizard[/eluser]
The point is that when you want to upgrade your system folder to a new version of CI, are you going to remember all changes you have made to the old version? So you can reapply them to the new code?
If not, chances are that your site doesn't work anymore after an upgrade of CI.
To deal with that, you'll need tools to track your changes, i.e. a version control system (Subversion, Git, Mercurial, ...), and you need to know how to perform merge operations, so you can merge your changes with the code of the new CI version.
