calls to DirectoryScanner.setBasedir(String) fail in embedded environment

when the user declares a resource with relative path, eg.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.0</version>
<configuration>
<webResources>
<resource>
<!-- this is relative to the pom.xml directory -->
<directory>resource/files</directory>
<filtering>true</filtering>
<excludes>
<exclude>**/*bak</exclude>
</excludes>
</resource>
</webResources>
</configuration>
</plugin>

then the build fails to process the resource correctly. I've traced that back to the DirectoryScanner.setBasedir(String) method which will not construct a path relative to the pom file, but to the directory where the IDE was started.