In addition to the src/main/java, I am adding a src/bootstrap directory that I want to include in my build process, in other words, I want maven to compile and include the sources there in my build. How!?
You can use the Build Helper Plugin, e.g:
<project>
...
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>some directory</source>
...
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>