extract version 4 to a new directory
it will ask if you want to import your stuff from 3.2
after that, you're done
optionally remove your 3.2 directory
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Current using SQL Developer version 3.2.09.
OS: SUSE Linux 11
How to upgrade from version 3.2 to version 4?
The documentation is your friend.
All of that is explained fully in the Oracle documentation.
Oracle makes their documentation available for FREE download. The Sql Developer Installation Guide covers nothing BUT how to install and upgrade the product.
The user guide is also available