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If one changes VisibilityQuery (e.g. using Tools > Options > Miscellaneous > Files), this change is ignored. IDE restart helps.
Tomas and I discussed this offline and the problem is that the indexing infrastructure crawls through files that are not filtered out by VisibilityQuery and indexes them. If for some reason VQ is changed, the set of files 'visible' for indexing changes as well and the indexes need to be updated. That is the files that have not previously been indexed have to be indexed now and the files that has been indexed, but are not visible now have to be dropped from the indexes. This will somehow have to be added to RepositoryUpdater.
This issue partly blocks issue #168464.
Unfortunately the VisibilityQuery was not designed with performance in mind. The RepositoryUpdater (FileObjectCrawler) will need to ask VisibilityQuery with every file object. I can add it into FOC and enable it by cmd line option. But definitely nothing what should be enabled by default.
Fixed jet-main 1a3ec6ee2d92
Integrated into 'main-golden', will be available in build *201104090401* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main/rev/1a3ec6ee2d92 User: Tomas Zezula <tzezula@netbeans.org> Log: #168460:Changes in VisibilityQuery are ignored