Without going into the actual application, there's no way of clearing badges from the SpringBoard. A feature like this could be very handy and there are already Cydia developers who have designed methods to accomplish this. I however have an alternative solution to how this action can be initiated.
Simply drag up over an icon that has a badge. After that action, the badge will change from a number to an "X" in the middle. Tap that and boom goes the badge. With the badge gone, the content should also be marked as "read" within the application. If you wish to not do that action, simply tap somewhere else.
I feel that this is an intuitive way to go about this and goes along with what I like to call "Apple's Two-Step Action." It accounts for human error (even though a drag up on an icon isn't a common mistake to make) and gives the user a second chance to change his or her mind. Plus, it doesn't conflict with SpringBoard paging, the Notification Center, or any other action that is currently being utilized.
Whatcha' think? :)
P.S. If you're looking for an excellent Twitter client for your iPhone or iPad, definitely give Tweetbot a look!
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