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Try to enable JavaEE functionality in a full FoD build with empty userdir. Only part of JavaSE gets enabled. This creates too flexible environment and goes against the original vision as stated at http://wiki.netbeans.org/FitnessForever#Reuse_Existing_Distributions Fix it, so it enables whole JavaSE and behaves the same in other cases (JavaFX, etc.).
The problem happens only if JavaEE is enabled via Tools/Plugins. If JavaEE project is created/opened the whole JavaSE is enabled. CC Dmitrij as this will be autoupdate releated. Btw. I thought the behaviour is tested and indeed it is. Just it tests only the case of created/opened project/file. Not manipulation via Tools/Plugins.
Fixed in ergonomics#efe9ce43de4c Will be available in http://deadlock.netbeans.org/hudson/job/ergonomics/703/ as soon as it finishes. The changed code influences only the Installed tab of Tools/Plugins when "Show Details" is off. Please verify.
Integrated into 'main-golden', will be available in build *200911211401* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main/rev/483df084a7f1 User: Jaroslav Tulach <jtulach@netbeans.org> Log: #177202: Testing whether enabling of J2EE via Tools/Plugins enables all Java SE. Not right now.