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netBeans demonstrates some catastrophic performance issues. In particular it often seems to be doing lots of file access with no disc activity. That would appear to be because it is rapidly doing lots of file operations on the same files. These accesses are supposed to be cached. Looking into with jconsole, a likely culprit is org.netbeans.modules.masterfs.filebasedfs.naming.NamingFactory.nameMap. That uses a WeakHashMap with transient Integer keys for a cache. because the use WeakReference, entries of such a map can be removed immediately. Caches should use SoftReferences for keys. (Why there aren't any sensible caches in the Java library, ask Josh.)
I doubt your analysis is correct. Yes, there used to be nameMap, but rather than having problems with WeakReferences, it may just be too big. Anyway nameMap and WeakHashMap were removed in 7.0 and replaced by home made hash table.