This bug was originally marked as duplicate of bug 223180, that is already resolved. This bug is still valid, so this seems to be another bug, but it might be related.
Build: NetBeans IDE Dev (Build 20121220-4f53a116c76b)
VM: Java HotSpot(TM) 64-Bit Server VM, 23.3-b01, Java(TM) SE Runtime Environment, 1.7.0_07-b11
OS: Windows 7
Maximum slowness yet reported was 2318 ms, average is 2318
Created attachment 129742 [details]
1 call to
org.netbeans.api.java.classpath.ClassPath$RootsListener.addRoots() 100.0 1,538 ms (100%) 1,538 ms 1
yields one to
org.netbeans.modules.masterfs.filebasedfs.fileobjects.FolderObj.getChildren() 99.39461 1,529 ms (99.4%) 1,529 ms 1
which then touches the disk multiple times
org.netbeans.modules.masterfs.filebasedfs.utils.FileInfo.isDirectory() 81.28346 1,250 ms (81.3%) 1,250 ms 8
Probably won't fix. Especially if it takes just 3s.