FreshStart lets you cleanup your system folder by removing files from the system folder and placing them in subfolders. The main use for system cleanup is to move INIT files to subfolders of the system; FreshStart will do this automatically for you if the Cleanup System option is selected in the options dialog.

When FreshStart looks for INITs, it searches in the system folder, and three subfolders of the system folder. These subfolders, named "Startup Documents", "Control Panel Documents", and "Chooser Documents", are automatically created and maintained by FreshStart when the Cleanup System option is selected, or can be created and maintained by hand. If the "Control Panel Documents" and "Chooser Documents" folder exist, the Control Panel and Chooser will look in these folders ONLY for the files they use. This restriction should be lifted in a future version of FreshStart.

If you have enabled system cleanup, at each boot FreshStart will search the system folder for INIT files and move them to an appropriate folder. It will not search the subfolders to ensure that the files in these folders are in the right place; you can place startup documents in the Control Panel folder, for example. If FreshStart detects a file in the target folder with the same name as the file in system folder, it will prompt you at boot time for which file to use. The other file will be deleted.

Certain INITs should not be moved out of the system folder, due to bugs/incompatabilities in their code. These INITs are generally special cased (see the list of incompatabilities), but you might have an INIT I'm not aware of. If you have an INIT that does not function properly with system folder cleanup, try turning the cleanup off and leaving the INIT in the system folder. If this works, please let me know so I can properly handle the INIT in the future.