Q:

Eclipse overwrites manifest created by maven bundle plugin

I'm using maven-bundle-plugin to generate MANIFEST.MF for OSGi container.  
<build>
    <plugins>
        <plugin>
            <groupId>org.apache.felix</groupId>
            <artifactId>maven-bundle-plugin</artifactId>
            <extensions>true</extensions>
            <configuration>
                <instructions>
                    <Export-Package>com.example.mypackage</Export-Package>
                </instructions>
            </configuration>
            <executions>
                <execution>
                    <id>bundle-manifest</id>
                    <phase>process-classes</phase>
                    <goals>
                        <goal>manifest</goal>
                    </goals>
                </execution>
            </executions>
        </plugin>
    </plugins>
</build>

However, that manifest file got destroyed (overwritten) by Eclipse (4.6.1 Neon) after, f.g Maven/Update Project or Clean/Build. 
Is it possible to make Eclipse somehow aware of the maven plugins, and not destroy their output?  What should I setup to prevent that (mis)behaviour? 
If that issue is not to be fixed with Eclipse, does it work better with IntelliJ, for example?  OSGi support within IDE is quite important for me...

A:

I have to change my answer.  I missed the part that you define the goal manifest.  This is the new and recommended way to use the maven bundle plguin but it requires that you tell the jar plugin to use the existing Manifest. 
        <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-jar-plugin</artifactId>
            <version>2.5</version>
            <configuration>
                <archive>
                    <manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>
                </archive>
            </configuration>
        </plugin>

old answer
I suspect you are using the Eclipse PDE.  The PDE is always working Manifest first.  This means it is incompatible with the maven-bundle-plugin.  
I recommend to use a plain maven build which we use a lot at apache projects like Apache Karaf or Apache Aries.  It lacks the special OSGi support of Eclipse PDE but this sucks anyway. 
You can augment this by using the eclipse plugin bndtools.  Bndtools now provides maven support to a degree.  This means you can now provide maven based OBR indexes for your project and define which bundles to start in a bndrun file.  This allows to directly start and debug your OSGi project in Eclipse.  See the osgi-chat example on how to do it. 
Beware though that bndtools just started with maven support recently.  So the current version 3.3.0 still lacks some of the convenience for maven builds.