Another Reason To Jailbreak The iPhone

Possibly. You would need to read the information put out by the jailbreak authors, and see what their recommended procedure is.
 
There are three classes of Apps.

1. Appstore Apps. These are downloaded from the Appstore and are synced with iTunes.
2. Cracked Apps. I won't mention anything more about these except to say that they also sync with iTunes, but because they don't have a valid Apple signature you can't get updated versions. It is certainly possible some future version of iTunes might detect these and do "something" resulting in anything from a stern warning, to a bill for the pirated apps, to a summons to appear in court.
3. Cydia Apps a.k.a. Jailbreak Apps. After you jailbreak the device, you can use the Cydia installer to download and install various things directly on the phone. Cydia uses a variation of the Debian apt-get packaging system, and iTunes is not involved at all. There is not a copy of the app anywhere on your actual computer, unless you work out copying it yourself using winscp or some other method.
 
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Thanks again Pepper. One other question. What if you need to restore your iPhone, and you have apps that you downloaded from Cydia? Do you just go back and redownload the apps again from Cydia?
 
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Yes.

There is an "AptBackup" utility you can install that claims to store your list of Cydia apps and that gets backed up with iTunes. So if you have restore the phone, you would then jailbreak it, download AptBackup, and run its restore function which downloads everything else.

That's how it's supposed to work. I've never actually tested it. :)
 
Yes.

There is an "AptBackup" utility you can install that claims to store your list of Cydia apps and that gets backed up with iTunes. So if you have restore the phone, you would then jailbreak it, download AptBackup, and run its restore function which downloads everything else.

That's how it's supposed to work. I've never actually tested it. :)

AptBackup, from Cydia?
 
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Downloaded AptBackup. From what I can see it just backs up the App store apps only. Not ones from other sources. Which brings me to my next question. How do you delete apps on a jailbroke phone? I don't see the little red x on the icons now when I make them wiggle.
 
Read the notes on AptBackup again. It backs up the list of non-appstore stuff.

To delete something, cydia has a management section where you can work with the installed packages.
 
I had cydia apps on my old 3g and used aptbackup. I got a 3G S and jailbroke and ran aptbackup and all but one of my jailbroke apps came back.
 
The only one that didn't for me was Cyntact. Truweather, winterboard, 5 column, a few dialer backgrounds and voipover3g among others restored. The voipover3g did not work at the time, but it does now. As a matter of fact after restoring, only the base apple apps and my cydia apps were left on my phone, I had to re-sync with itunes to get my apple apps back even though they were there before I restored with apt backup.
 

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