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Netbeans is lacking ability to configure inclusion/exclusion filters per source root. Current functionality of Netbeans is to have a *global* inclusion/exclusion filters. This would be considered a serious limitation when trying to import Eclipse projects. Especially when the project being imported contains source-root-specific inclusion/exclusion filters.
Not solvable in an Eclipse importer, since NB Ant-based projects (intentionally) do not support per-root filters. Could be solved in a direct Eclipse project loader.
Will this be addressed in 6.8?
No, in fact I don't think this will be changed ever, for the reasons already outlined. NB j2seproject's simply do not have interchangeable semantics with Eclipse Java-nature projects; an import can only ever be an approximation to get things started. More serious Eclipse support would require directly opening Eclipse projects from their metadata (the way we do with Maven) - which is certainly an option, but much too big of a project to be considered for 6.8. If you have an application with such distinct source roots that they require separate filters, the better way to manage this in NetBeans is with a set of projects with some interdependencies. Without knowledge of your actual project setup I cannot offer more detailed advice.