Right now, we need a special profile to load myfaces-impl module on eclipse, because myfaces-impl-ee6 module is added on source folders.
Investigating alternative ways to do it, I notice that we can use maven shade plugin to handle myfaces-impl-ee6 module and prevent this condition. The advantage of this plugin is myfaces-impl-ee6 module is this is not added as a source path, but it updates binary and source jar properly.
The only disadvantage is maven-shade-plugin does not play well with felix OSGI bundle plugin. We can't control the execution order of maven plugins, due to http://jira.codehaus.org/browse/MNG-2258, and in this case, bundle plugin is executed before shade plugin.
There is a workaround for this one and is unpack myfaces-impl-ee6 .class files, so it will be taken into account by bundle plugin. Then, maven shade plugin detect the duplicate but does not stop working, replacing the class with the shaded one.