To backup all your Cydia tweaks and app's you can use xBackup which is a dollar from Cydia. It works really well, but you must make sure all the toggles are set to yes in Cydia. Including auto respring and auto reboot and more importantly icon layout and app data. I believe that is all of them. The other one is cloud, but that should be set to yes.
Step 1: Download xBackup from Cydia and then run the backup feature.
Step 2: Run a sync and backup via iTunes.
Steps 3: Download latest software from iTunes and then update.
Step 4: Once updated. Run your restore from backup from iTunes, and then do a sync. Some of your springboard icon layout may not be how it was at this stage, but don't worry.
Step 5: Jailbreak via the latest version of greenpoison's Absinthe or use redsn0w. Either is fine, Absinthe is the easiest to you.
Step 6: Download xBackup from Cydia. You won't have to pay a second time.
Step 7: Run restore process in xBackup, but before you run, check all the toggles are set to yes like before when you ran the backup. This can take about 10 to 15 mins, even longer. Once that has finished, depending whether you set the settings to auto reboot which you should of, then the phone will reboot and then your phone should be just as you left it. Always give the long processes and reboots plenty of time. Much longer than normal if something seems to be taking long.
I would make a list of all your tweaks and apps just to be on the safe side, this is just what I do.
There are other more expensive Cydia backups, but I have found for a dollar you can't go wrong and it is very simple to use if you are a newbie.
Good luck with it and give me a shout if you get stuck.
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