Also it may be good to lump together other classpath attributes that are typically specified on source folders... namely:

• inclusions (like exclusions)
• output folder specific to that particular source folder
• other 'custom' classpath attributes

I.e check out the documentation on the JavaCore.newSourceEntry method:
http://help.eclipse.org/indigo/topic/org.eclipse.jdt.doc.isv/reference/api/org/eclipse/jdt/core/JavaCore.html#newSourceEntry(org.eclipse.core.runtime.IPath,%20org.eclipse.core.runtime.IPath[],%20org.eclipse.core.runtime.IPath[],%20org.eclipse.core.runtime.IPath,%20org.eclipse.jdt.core.IClasspathAttribute[])

I guess the most pressing is the exclusions item. I don't yet want to raise separate issues for the other ones, but some of them may be logical/easy to implement at the same time. So I thought I'd at least mention them.

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