You can update a HUBzero 1.3.1 instance to a newer revision of HUBzero 1.3.1 through a relatively simple command line process

First update the hubzero-cms-1.3.1 package

# apt-get update
# apt-get upgrade

Then update you HUBzero instance

# hzcms update

The "hzcms update" step is what copies the latest version of the HUBzero CMS 1.3.1 source code into your installed instance and updates the database schema as appropriate. It also fixes any other issues it detects.