Simple app with 3 classes.
com/company/Obj1.java
com/company/Obj2.java
com/company/inner/Obj3.java
build
in pom.xml
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.0.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
<includes>
<include>com/company/inner/*.java</include>
</includes>
</configuration>
</plugin>
</plugins>
</build>
result: 1 class is compiled.
And any combination of includes is working well
or you mean something else?