This page is being written for 1.10 and Maven. Check back for more.
VIVO can be customized in many ways. Most sites customize the interface using themes. See Creating a custom theme. Many sites create ontology extensions to introduce local terminology. See Adding Additional Ontologies to VIVO. Sites can add custom configurations for the Data Distribution API (see Data Distribution API), providing custom APIs returning data you specify in formats you specify at web addresses you specify.
In each case, files distributed with VIVO are replaced or added. The process described here uses a Maven custom installer to replace and add your files to those distributed with VIVO.