Top level project have to have a packaging of "pom". What about plug-ins wanting to make a different top level packaging?

This was already closed WON'T FIX in MNG-1760.

Do you have a specific use case for the inclusion of this?

I am working on creating a maven2 plug-in for Java Plug-in Framework (http://jpf.sourceforge.net/). This framework is inspired by Eclipse. I would like to be able to use maven2 to build applications using this framework. To do this I would like to have a master project (quite like the "pom" packaging, but with different implementations of the validate, install and deploy phases). The modules in the master project would bee the boot module and all the plug-ins needed for a functioning system.

so, this is an aggregating artifact?

I am not sure what you mean by aggregating artifact. What I want to do is to run all the sub projects until the package phase. After that I want to move the packaged sub projects (the boot module and the jpf plug-ins) into the target directory of the master project. So if you run the install phase of the master project you are able to start the jpf application from the target directory.

but do you want to create something at the top level that contains all of those and rebundles them? This is usually how the assembly plugin works, for example.

I think we need to support this, but after more careful consideration of how the module relationship equates to the dependency relationship usually used to build these.

Personally I'm +1 on allowing any project to have a modules section. This used to be allowed in early versions of m2.
That would fix this limitation.

Also, it's no longer a problem with eclipse. Right now you can't add pom.xml projects to eclipse, unless you
specify a workspace somewhere which will link project files.

It might not work to allow this currently, though, because of cyclic dependencies.

Why was this disallowed? I can't seem to find the reason in Jira.