The tools/ide directory contains projects for two versions of NetBeans (5.5 and 6.0). Since they haven't been updated for newer versions of NetBeans, I suppose it means they aren't used much. Also, since there are two of them, NetBeans gets confused as to which of the projects to use, and I have experienced that it often uses a mix of the 5.5 and 6.0 projects for the open source files, which causes problems for navigation and debugging. The problem with having multiple NetBeans projects pointing to the same source is described here: http://wiki.netbeans.org/FaqSourceRootOverlap
To prevent these problems, we should either remove the tools/ide/netbeans directory and let NetBeans users create their own projects (there a pretty good description on the wiki: http://wiki.apache.org/db-derby/BuildingDerby#Using_NetBeans_to_Build_Derby ), or provide an updated project and remove the old ones.
(The project files aren't really tied to a particular version of NetBeans and can be opened by newer versions. But the projects still need to be updated to be usable, I think. For example, they should have project-specific formatting settings (added in NB 6.5, I think) which set tab size to 4, since setting tab size globally to 4 as you would have to with the current projects, only works if Derby is the only project you're working on in NetBeans.)