The maven-documentation is not very helpful:
Filesets can be filtered, which means the selected files will be used as Velocity templates. They can be non-filtered, which means the selected files will be copied without modification.
So let's take the underneath code. I know that the selected files will be used as Velocity templates and therefore they can be manipulated. How can I manipulate this fileset and how can I use Velocity templates?
<fileSets>
<fileSet filtered="true" packaged="true">
<directory>src/test/java</directory>
<includes>
<include>**/*.java</include>
</includes>
<excludes>
<exclude>AllTest.java</exclude>
</excludes>
</fileSet>
</fileSets>
As you said, if you set filtered to true, then the Velocity engine takes the files and does all the Velocity replacements, including replacing variables given in the $ syntax and evaluating Velocity loops.
The variable values are the properties set in the POM.