M2E and having maven generated source folders as eclipse source folders

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You need to attach the source directory with the build-helper-plugin.

Like so:

 <plugin>
    <groupId>org.codehaus.mojo</groupId>
    <artifactId>build-helper-maven-plugin</artifactId>
    <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>

You will also need to:

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