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In my opinion it is not goot to mix the physical and logical structure and make the content and settings infrastructure dependent on the logical structure. There is a being written proposal to address this feeling at: http://www.netbeans.org/source/browse/projects/www/proposals/logicalorganisation/fspec.html.diff?r1=1.1&r2=1.1.4 Please evaluate, update, merge and implement that proposal.
This is for me, I guess :-).
The proposal has been merged to trunk and almost all proposed changes has been implemented. However some parts of the porposal are obsoleted by new projects uispec. The main changes in uispec affecting this proposal are that project has just one view but modules can extend it (e.g. plug special nodes which children are then completely controlled by the module), infra provides some children too but they aren't prominent in any way). Also the uispec decreased the levels of settings hierarchy to just two levels - settings on file and default settings on project, thus e.g. organizer doesn't define settings anymore.
Verified