IDE Updates delete all the libraries I have installed, can this be prevented?

So I just updated from IDE 1.6.1 to 1.6.4 and although the dialog states what I took to mean my libraries would stay intact, they in fact are all deleted (libraries I manually installed). I recall this happened the last time I updated (I'm fairly new so have only updated twice), however this time is much more inconvenient as I had many more libraries installed. While I have really enjoy the Arduino and feel it is fairly polished and user friendly hardware, this seems fairly poor and archaic way of handling software updates. Fortunately I recently installed my libraries on another computer so I can copy them back, but I was wondering if there was a way to prevent my libraries from being deleted. My fear is as I have an increased number of libraries, some of which I have had to manually update to work, I will forget to sync to another computer or back them up and then update, only to find they are deleted and worse I can no longer find the libraries I was using online.

If you install libraries to your sketchbook/libraries folder then they should not be deleted when you update. If you install them to the Arduino/libraries folder then they will be deleted.