1.3.0 to 1.3.1 is pretty straightforward. I'm not aware of any changes to the default contents of the ./fuel/applications directory so I'd just extract 1.3.1 into a temporary directory, delete it's ./fuel/applications directory and copy the whole thing over your 1.3 install. The release notes should tell what's changed so you can work out what files are effected.
Make sure you take a backup first and remember to reset your file permissions afterwards.
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Make sure you take a backup first and remember to reset your file permissions afterwards.