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I've set up a cron job to automatically open the app at 7 in the morning every day (and to minimise all other apps would be nice but I can't find anything to do it). I'll also set up the same functionality on my iPhone (jailbroken devices can do this with Activator).

Maybe this would work for you.

Could wmctl on Linux allow you to minimise apps

Possibly, but I run OSX.

Your reply did make me take another crack at it and I got it to work. The script if anyone is interested: http://pastebin.com/pC9VTzjv. It does do some specific-to-me things to close apps I usually have open that did not want to minimise.

It's important to remember that you don't have to review all your "due" cards at once. Just open it up and do one card per deck. Maybe you'll do more as you get going or if the next card after the first is easy. It accumulates, but over time as you actually memorize things you'll whittle the due set down as every card starts becoming "due" months into the future.

Don't study too many cards then. Nobody is saying that you have to finish all the dues.