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I considering doing a complete re-build of my home desktop computer. The only thing that will actually be the same, will be the case. I have a 1 TB external hard drive I want to back up my 200 GB of stuff to. I want to basically be able to "clone" this entire system onto a bigger hard drive of a compltelely different system, with faster CPU, better motherboard, and alot more memory (more than 4 Gigs). The issues are that I am running the 32 bit version of Elementary OS Jupiter, but to have more than 4 gigs of memory, I know you need 64 bit. So I don't think a direct clone would really work. Is there any way to backup all my apps, files, settings, and even my themes and backgrounds from this 32 bit system. And restore them to a new install of a 64 bit system?

Also eOS Jupiter is based on Ubuntu 10.10. I really really don't like how Unity and Gnome 3 are looking right now. Theme wise and system wise. So sticking with eOS Jupiter for now would be very perferable.

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You do not need to run a 64-bit system to use 4GB of RAM. You can use a PAE kernel, or you can run an amd64 kernel with a 32-bit userland. Check if your distribution provides such a kernel (if it doesn't, you can compile one yourself, but you may not care for that).

If you choose to move to a full 64-bit system, you can't clone your system wholesale. You need to reinstall from scratch. But you can save your home directory, which contains all of your user-specific customizations. To copy the system parts, see How do I duplicate a server's packages and configuration to another machine? and How to migrate user settings and data to new machine? (Elementary OS is sufficiently close to Ubuntu that most of the methods should work identically).

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You can use remastersys, specifically its backup function, it will do literally what you ask, it will back up everything, all apps installed, all prefs, the whole lot

check it out here: http://www.geekconnection.org/remastersys/

you can get the latest version, 3.0, from the forums

best of luck

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