Output is written to src/main/webapp instead of target

When using wtp 2.0 support MANIFEST.MF file is written to src/main/webapp/META-INF/MANIFEST.MF for webapplications (packaging WAR). According to the documentation this location is configurable using <manifest/>, which is silently ignored. The issues I have with this is a) that output is written to src/main (which is IMHO against maven conventions) and b) that the output location should be configurable according to docs, but is not.

My configuration in the pom.xml is like this:

<plugin>
  <groupId>org.apache.maven.plugins</groupId>
  <artifactId>maven-eclipse-plugin</artifactId>
  <version>2.5-SNAPSHOT</version>
  <configuration>
    <wtpversion>2.0</wtpversion>
    <wtpmanifest>true</wtpmanifest>
  </configuration>
</plugin>

For some discussion see also this thread on nabble.
A related issue to this one is MECLIPSE-389.