sync apps from phone to pc

How can I sync my phone apps that are still on my phone (iphone5) to itunes which shows no apps at all?

Reason/Status:

updated itunes to 11.1 and my phone to ios 7

long story short to update itunes i have to remove everything from my computer (literally uninstall any and all software that is apple) and reinstall it manually. Once that was done it was easy to sync my music library and force itunes to delete all music off phone and resync music again however applications are gone

I'm aware that the applications have to be downloaded and installed but since they are on my phone already how can i avoid that and just sync what i have now instead of manually downloading each app again?

The apps area wasn't even there under library until i actually downloaded some app just to have it show up

under my phone and apps area there's only the 1 app i downloaded on the left and all 40 of my other apps are still shown on the phone on the right and are listed there

What do i do?