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cvs-lite correctly ignores .nbinitdb and nbproject/private automatically for standard projects. However, they are not ignored for free-form projects. In both cases, these are NetBeans-created files that should not be committed, so they should be ignored in both cases.
Fixed typo in Summary (should be ".nbintdb" (no second "i"))
A bug in freeform's SharabilityQuery implementation (nbproject/private case)? Please evaluate.
What is your build number? The nbproject/private should be marked as NOT_SHARABLE for freeform projects by fix of issue #65545. Please reopen that bug if you have a new build and your nbproject/private is still not ignored. To the .nbintdb: sorry, but I tested both J2SE project and freeform project and for both of them the ".nbintdb" file was not ignored. I think that cvslite itself should handle ".nbintdb".
I'm using NetBeans 5.0-beta from the netbeans.org website, whatever build that is. I'll try it in a newer build, when it becomes available. Regarding the .nbinitdb file, I may have been mistaken in reporting that it works for standard projects. In any case, the correct behavior would be for it to be ignored for both types of projects.
".nbintdb" are owned by vcsgeneric and should not be shared. By design mistake these lies in user's workdir/datadir instead of IDE's userdir. Keeping build-in ignore list backward compatabilty: Checking in CvsVersioningSystem.java; /shared/data/ccvs/repository/javacvs/cvsmodule/src/org/netbeans/modules/versioning/system/cvss/CvsVersioningSystem.java,v <-- CvsVersioningSystem.java new revision: 1.41; previous revision: 1.40 done