m2eclipse supports this. First, add the path to your build path:
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>${project.build.directory}/generated-sources/java/</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
Second, add support for that to m2e:
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<versionRange>[1.0,)</versionRange>
<goals>
<goal>parse-version</goal>
<goal>add-source</goal>
<goal>maven-version</goal>
<goal>add-resource</goal>
<goal>add-test-resource</goal>
<goal>add-test-source</goal>
</goals>
</pluginExecutionFilter>
<action>
<execute>
<runOnConfiguration>true</runOnConfiguration>
<runOnIncremental>true</runOnIncremental>
</execute>
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
</plugins>
</pluginManagement>
The second step might not be necessary, if your eclipse installation has installed the "org.eclipse.m2e.discovery.lifecyclemapping.buildhelper.xml" plugin. This plugin is available via Window -> Preferences -> Maven -> Discovery. Currently, that does not work here at Eclipse Kepler, therefore, I fetched the JAR (linked from the xml shown in the Catalog URL) and extracted the fragments from org.eclipse.m2e.discovery.lifecyclemapping.buildhelper.xml
by hand.