Questions on restore and upgrade

[CyberMew]

I am on stock iOS 4.1. If I upgrade via iTunes to 4.2.1, will all my stuff remain intact with an updated iOS, or it will do a clean install of the system with iOS 4.2.1?

Another question, if I have an jailbreak iPhone 3GS, and I backup and restore it on a brand new iPhone 4 with iOS 4.1, will all the old directories and data be moved over as well? I know the normal data like SMSes, etc will be moved over, but if I messed around with the files and folders in the old phone, will it be brought over to my new iPhone 4 as well?

[Simon]

If you do an update then all your itunes stuff will still be there but any jailbreak related stuff will get wiped.

[CyberMew]

So even those jailbreak files/folders, or my personal folders, are not moved during restore?

What about upgrading of iOS versions? Are all files wiped?

[Simon]

A restore wipes everything. A update only wipes jailbreak stuff.