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See issue 191300, if you repeat the same scenario for install as root / update as user, you will end up with enabled all updated features (even if you haven't used it before), which is wrong. Used Full IDE.
*** Bug 191643 has been marked as a duplicate of this bug. ***
I guess the best fix would be to not update module that are not enabled.
*** Bug 119658 has been marked as a duplicate of this bug. ***
ergonomics#d12a45fbf91f
Integrated into 'main-golden', will be available in build *201012290001* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main/rev/d12a45fbf91f User: Jaroslav Tulach <jtulach@netbeans.org> Log: #191657: Offer only enabled modules for update