In case anyone finds this post via Google, the answer is to configure the maven-war-plugin to explicitly set the manifest location:
Code:
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<configuration>
<supportedProjectTypes>
<supportedProjectType>bundle</supportedProjectType>
<supportedProjectType>war</supportedProjectType>
</supportedProjectTypes>
</configuration>
<executions>
<execution>
<id>bundle-manifest</id>
<phase>process-classes</phase>
<goals>
<goal>manifest</goal>
</goals>
<configuration>
<!-- config and instructions here -->
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<archive>
<manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>
</archive>
</configuration>
</plugin>