Something new, unexpected, and possibly worrying has popped up in iTunes. iTunes now "calls home" to the Apple mothership whenever you restore an iPhone or iPod touch. It tells you that it's "Verifying restore with Apple...", checking your device identifier and the firmware with Apple's new signature server.

Today, TUAW has the pleasure of talking with Jay Freeman, otherwise known as "Saurik", the developer of Cydia. Saurik has constructed a server that duplicates Apple's functionality, ensuring that you'll be able to downgrade your iPhone or iPod in the future, even if you have not jailbroken your device. This topic is for all iPhone users, regardless of whether they use jailbreaking. Please join us with your questions and comments as we hear from Freeman about why this move matters to you. Read on to see the full live chat transcript.

The legendary Dev-Team has done it again. It just released the new version of the Pwnage Tool, a desktop application that's used to create custom firmware packages to jailbreak iPhones and iPod touches.

Jailbreaking is the act of modifying the official firmware in order to run applications not approved by Apple. Chief among those applications, at least for the iPhone crowd, is the SIM unlock that allows the phone to be used on unofficial cell phone service providers.

The Dev-Team has found holes in previous versions of the iPhone OS that allow this code modification and has developed tools to make exploitation easier for the average user to accomplish. Once implemented, the jailbreak process installs an app that acts an unofficial App Store of sorts. The iPhone or iPod touch user can browse and install games, utilities, themes, and general applications. Cydia, one of these installer apps, even has a store with applications for sale.

Traditionally, when Apple releases a new iPhone OS version, that software upgrade breaks any jailbreak and SIM unlock present on the device. And so, you end up with the cat-and-mouse game that Steve Jobs alluded to shortly after the first firmware loophole was exploited and the original iPhone was unlocked.

Well, the mouse has stolen the cheese once again, and the Pwnage Tool released today will jailbreak the latest firmware, version 3.1.*

The big asterisk at the end of that previous sentence is that the Tool will only work on about half of the devices that use the iPhone OS -- only the original iPhone, original iPod touch, and iPhone 3G. The iPod touch line just released, as well as the 2nd generation iPod touch and the iPhone 3GS, cannot be jailbroken at this time. That means if you've already upgraded to 3.1 on your 3GS, you still won't be able to SIM unlock it as of the time of this post.

So, if you want to SIM unlock your iPhone 3G or the original model, Pwnage Tool 3.1 should do the trick. On the 3G, you'll need to use Icy or Cydia to also install the ultrasn0w app that actually performs the software unlock; however the original iPhone should be unlocked without this additional step.

You will need a Mac to run Pwnage Tool 3.1, but a Windows version is expected in the near future. Also expected soon is redsn0w, for both Mac and Windows, that further simplifies the jailbreak process by avoiding the need to create a custom firmware package.

Keep in mind, if you've been waiting for a jailbreak solution before upgrading to the latest firmware, many users have had fairly substantial issues with iPhone 3.1. My fellow TUAW blogger, Josh Carr, has reported that lots of iPhones and iPod touches are working poorly after upgrading. You may wish to hold off and stick with 3.0 or 3.0.1 until a solution is found, either by Apple or some other group of smart people.

But, if you're so inclined, you may find links to download Pwnage Tool 3.1 on the Dev-Team's official blog. Make sure to read the instructions thoroughly, and take heed of all of the warnings. They are there for a reason.

There's no shortage of Twitter apps in the App Store. Even more surprising is the number of GOOD apps that connect to the popular microblogging platform. I like each for a different reason: Tweetie has a clean user interface, TweetDeck offers multiple columns that sync with its desktop counterpart, and TwitterFon has ReadItLater integration. There are countless others that have unique features, and many of us end up with at least a couple on our iDevices.

But I have a new favorite, qTweeter, developed by the folks at Efiko Software. You won't find it in the App Store, though, because this app requires a jailbroken device. Multitasking isn't officially allowed (yet?) on the iPhone OS, yet qTweeter relies on this capability to perform its best trick.

Say you're checking the weather and want to tell everyone of the approaching hurricane. Normally, you would close your weather application, swipe through pages of apps, tap on and wait for your favorite Twitter client to open and load all of the tweets that you really don't care about right now, and finally type your warning to get the heck out of town. By the time you do all of that, the highway is going to be grid-locked with fleeing residents and you'll be stuck boarding up windows and sweeping up the debris!

Instead, you could have just "pulled" qTweeter down from the status bar, typed your tweet, and went back to the app still running in the background.

In fact, per the recent trend, you could have also posted that same message to your Facebook status with just a tap of a checkbox. It's a much quicker way to get your message out of your head and onto the Net, a fact that you'll appreciate as you get older and those thoughts become more fleeting.

As previously reported, users of jailbroken phones and the developers who cater to them now have an avenue for commerce in apps: the Cydia Store. Smoking Apples visits the store and has a solid rundown, noting that Amazon Payments is the only funding source for the moment (PayPal is on the way, says Cydia lead Saurik/Jay Freeman). Users who update to the latest version of Cydia on their phones get the store capability automatically; if your phone isn't already jailbroken, though, you'll have to jailbreak it and install Cydia.

The limited number of apps on the store versus the overwhelming bounty of the official App Store may help users find the apps they truly want, says SA. Freeman has a list of apps queued up for release over the next few weeks before he begins accepting unsolicited submissions.

If the functionality you want and need is uncertain or unlikely to show up in the App Store (*ahem* -- tethering, anyone?), would you jailbreak your phone and buy from the Cydia Store?

While we're pondering the consequences of RIM announcing that programs in the Blackberry "App World" must be at least $2.99US, there are alternatives to the iTunes App Store emerging from the jailbreak side of the iPhone world. The Wall Street Journal reports that Cydia is making the transition from package repository to a full app store. There are also plans for an adult-only app store and a new jailbreak service.

The big question at the moment is how will Apple take this? Apple filed a complaint with the US Copyright Office last month claiming that jailbreaking is illegal. They're not going to take firing a direct salvo at the App Store itself lightly. There is competition for the iTunes Music Store, but Apple could argue that the homegrown app stores infringe on its copyright by using modified versions of its software.

It's not a huge shock that App Store competition is popping up; the only surprise is that it took this long to happen. After all, developers are frustrated that excellent programs such as Podcaster are passed up in favor of the latest, greatest novelty app -- then to make matters worse, those same features turned up in an official iPhone update.

While there are a lot of really terrible apps out there that have no place on the App Store -- I won't even begin to tell you about one adult app pitched to TUAW, we do want to remain a mostly family-friendly site -- there are a lot of good software that get turned down because of Apple's stringent developer's agreement. These developers want an avenue to distribute their programs, and homegrown app stores are one answer.

Cydia's Jay Freeman told the WSJ that he has lined up a lawyer in case Apple comes knocking at the door. He may also want to get in touch with the team that represents Psystar ... just in case.

[via Engadget]

Occipital's ClearCam is another in a long line of photo enhancing apps for the iPhone. ClearCam is going live today on Cydia, so at this point it is only available for jailbroken iPhones. The developer says he hopes a version for all iPhones will make it to the App Store soon.

ClearCam has a couple of interesting modes. Enhanced mode will give you a 4MP image rather than the standard 2 MP image you get now on the iPhone. The magic is done by having the camera take 6 pictures in rapid succession. The software then aligns and enhances the photo and saves it to your camera roll. When you compare the image to a normal one, they look the same, but you can enlarge the image more than a 2MP image, and the noise is noticeably lower. You should be able to see the difference in the gallery image below. That function may not be to Apple's liking, because it breaks the SDK rules of how software can interact with the camera.

In ClearCam's other mode, called QuickShot, it fires off 4 images, figures out which image is best, and throws the bad ones away. I tried using this mode, and it worked as advertised. The results weren't dramatic, but were easy to see. You can contrast this approach with Sudobility's Night Camera app, which uses the accelerometer to determine when your hands have stopped shaking so it can snap a stable longer exposure.

If ClearCam is going to be released through the App Store, it will likely shed the Enhanced mode unless they can get Apple to allow the variance with SDK rules. Occipital is not yet sure about pricing. They say if they have to throw away features, the price will be nominal or free. The feature complete version released through Cydia is free for 15 days, then it's US $9.99.

Click through the gallery below for a look at how ClearCam works.

Those with jailbroken iPhones who use the Cydia package manager discovered a new add-on in the past day or so -- Clippy, from iSpazio, which introduces a method for copy and paste to the iPhone.

According to users, the add-on inserts two buttons into the system keyboard -- one for copying and another for pasting. Those who have tried it out say that it only accepts user-entered text and copies over one line at a time, which can get cumbersome.

Sebastien over at the iPhone Download Blog gives a detailed overview of how the application works. "After installing the application, type any text you want and simply hit the "123″ button on your keyboard to show the copy/paste buttons. Tap "copy" and start selecting the text you want to copy. Tap "copy" again to end the selection. Then tap "paste" to paste this text where you want it to be." This implementation isn't up to Apple's standards for grace and ease, but it seems workable.

My iPhone isn't jailbroken, so I haven't had the chance to try out Clippy. If you've downloaded and had a chance to try out the app, please let us know your impression in the comments.

Thanks to all who submitted this!

We recently got a tip over to this It's Just Poison post about Veency for jailbroken iPhones from Jay "Saurik" Freeman, the author and maintainer of Cydia. Veency provides a VNC remote desktop server for your iPhone, allowing you to connect to the shared screen of your handheld from any VNC client (Apple Remote Desktop, Chicken of the VNC, and more).

I downloaded a copy to my iPhone, rebooted and gave it a whirl to see how well it worked using Chicken of the VNC on my Mac.

From first go, it did what it promised: offering tap-interpretation of my Mac-based mouse clicks as iPhone-sourced finger taps. The current mouse position on the Mac was echoed as a small "x" on the iPhone, so I could always see where the virtual finger was.

After typing his fingers to the bone, overworked iPhone developer Jay "Saurik" Freeman has finally finished his long-awaited Cydia release. As Freeman puts it, the iPhone is a 667MHz computer with 128MB RAM and at least 4GB of flash. So why not use it as a Unix workstation?

Motivated by the relative limitations of the existing BSD subsystem, Freeman decided to port Debian's APT to the iPhone -- tweaking items to work better with the iPhone's relatively messed-up network settings. A UIKit front end, Cydia, provides a GUI for users to select and install programs -- basically Installer.app for fully leaded geeks. Cydia isn't limited to command-line software. It should allow installation of any and all software package types.