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How can I backup my Pythonista directory (.py and data files) the easiest way?

There are several programs to access the filesystem of your iOS device (OK, just partly, but enough to backup your Pythonista directory).

I use PhoneView for the Mac but there are other solutions like iFunbox for Mac and Windows (which is free).

Dropbox Sync

As ccc said, you can the entire Pythonista file system to your Dropbox account quite easily, though it takes some setup the first time around. You can find the scripts to do so in the link ccc provided.