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The usefulness of the search feature in the IDE is limited by the fact that at half the search hits are for build products, not source files. So when I go looking for something I need to update I have to be very careful to only open source files, never build files. The Search dialog should at least have an option to skip over unsharable (~ unversioned) files.
While annoying, does not prevent use of the search feature.
Alternate UI would to grey out labels of nodes representing unversioned files.
I will use the approach of greying out labels of nodes representing unversioned files.
I just found that I fixed this together with implementation of search&replace over multiple files (issue #18237). The file in which graying of unsharable files is enabled is utilities/src/org/netbeans/modules/search/NodeRenderer.java. The first milestone with this bug fixed is NetBeans 6.0 M5.