Partition Configuration to avoid reinstalling applications after update

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http://askubuntu.com – The major bane when I update Ubuntu (which is way more frequent than Windows) is that I lose all installed application. To be precise I do a lot of Maple, Matlab, Geogebra & for all of those I install Java platform which too isnt very straightforward plus the license management things, which really give me craps. I don't install application in /home (to be made available to all users) thus a separate /home partition is meaningless. Can we circumvent this problem somehow such that Java dependent applications along with JDK doesn't blow away after update, may be by a separate partition (jus (HowTos)