Evernote announced today that it has acquired Cocoa Box, developer of Penultimate, the highly acclaimed digital ink notebook app for the iPad. In a post on the company’s blog, Evernote CEO Phil Libin noted that the handwriting app has been one of the company’s favourites since it was first released two years ago and goes on to announce that Penultimate creator Ben Zotto will be joining Evernote to head up future development on the app;…