These examples (specifically wordCount) are designed to help you quickly get started with Scoobi. Each directory the required files and directory structure to create your own Scoobi application so can be used as a good starting point.
For more information on building and running, see Scoobi's user guide. src/test/scala/com/nicta/scoobi/acceptance is a good spot to look if you're interested in seeing uses of various uses of Scoobi.