I cleaned my NB sources from the command line and rebuilt them.  Coming back to
NetBeans later I find the following NPE has been thrown.

Annotation: Root: C:\space\newnbsrc\classfile\src File:
file:/C:/space/newnbsrc/classfile/src/org/netbeans/modules/classfile/ClassFile.java
Bootpath:
ClassPath[Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/resources.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/rt.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/sunrsasign.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/jsse.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/jce.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/charsets.jar!/],
Entry[file:/C:/Program%20Files/Java/jdk1.6.0/jre/classes/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/dnsns.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/localedata.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/sunjce_provider.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/sunmscapi.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/sunpkcs11.jar!/]]
Classpath: ClassPath[] Sourcepath:
ClassPath[Entry[file:/C:/space/newnbsrc/classfile/src/]]
Annotation: Root: C:\space\newnbsrc\classfile\src File:
file:/C:/space/newnbsrc/classfile/src/org/netbeans/modules/classfile/ClassFile.java
Bootpath:
ClassPath[Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/resources.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/rt.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/sunrsasign.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/jsse.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/jce.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/charsets.jar!/],
Entry[file:/C:/Program%20Files/Java/jdk1.6.0/jre/classes/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/dnsns.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/localedata.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/sunjce_provider.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/sunmscapi.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/sunpkcs11.jar!/]]
Classpath: ClassPath[] Sourcepath:
ClassPath[Entry[file:/C:/space/newnbsrc/classfile/src/]]
java.lang.NullPointerException
	at com.sun.tools.javac.comp.Enter.visitTopLevel(Enter.java:257)
	at com.sun.tools.javac.tree.JCTree$JCCompilationUnit.accept(JCTree.java:444)
	at com.sun.tools.javac.comp.Enter.classEnter(Enter.java:236)
	at com.sun.tools.javac.comp.Enter.classEnter(Enter.java:250)
	at com.sun.tools.javac.comp.Enter.complete(Enter.java:509)
	at com.sun.tools.javac.main.JavaCompiler.complete(JavaCompiler.java:664)
	at com.sun.tools.javac.jvm.ClassReader.fillIn(ClassReader.java:1884)
	at
org.netbeans.modules.java.source.usages.SymbolClassReader.fillInImpl(SymbolClassReader.java:154)
	at
org.netbeans.modules.java.source.usages.SymbolClassReader.fillIn(SymbolClassReader.java:133)
	at com.sun.tools.javac.jvm.ClassReader.complete(ClassReader.java:1791)
	at com.sun.tools.javac.code.Symbol.complete(Symbol.java:386)
	at com.sun.tools.javac.code.Symbol$ClassSymbol.complete(Symbol.java:764)
	at com.sun.tools.javac.jvm.ClassReader.loadClass(ClassReader.java:1966)
	at com.sun.tools.javac.comp.Resolve.loadClass(Resolve.java:842)
	at com.sun.tools.javac.comp.Resolve.findGlobalType(Resolve.java:901)
	at com.sun.tools.javac.comp.Resolve.findType(Resolve.java:957)
	at com.sun.tools.javac.comp.Resolve.findIdent(Resolve.java:986)
	at com.sun.tools.javac.comp.Resolve.resolveIdent(Resolve.java:1179)
	at com.sun.tools.javac.comp.Attr.visitIdent(Attr.java:1724)
	at com.sun.tools.javac.tree.JCTree$JCIdent.accept(JCTree.java:1551)
	at com.sun.tools.javac.comp.Attr.attribTree(Attr.java:368)
	at com.sun.tools.javac.comp.Attr.attribType(Attr.java:398)
	at com.sun.tools.javac.comp.Attr.visitTypeArray(Attr.java:2406)
	at com.sun.tools.javac.tree.JCTree$JCArrayTypeTree.accept(JCTree.java:1679)
	at com.sun.tools.javac.comp.Attr.attribTree(Attr.java:368)
	at com.sun.tools.javac.comp.Attr.attribType(Attr.java:398)
	at com.sun.tools.javac.comp.MemberEnter.visitVarDef(MemberEnter.java:630)
	at com.sun.tools.javac.tree.JCTree$JCVariableDecl.accept(JCTree.java:695)
	at com.sun.tools.javac.comp.MemberEnter.memberEnter(MemberEnter.java:391)
	at com.sun.tools.javac.comp.MemberEnter.memberEnter(MemberEnter.java:403)
	at com.sun.tools.javac.comp.MemberEnter.finishClass(MemberEnter.java:414)
	at com.sun.tools.javac.comp.MemberEnter.finish(MemberEnter.java:1050)
	at com.sun.tools.javac.comp.MemberEnter.complete(MemberEnter.java:1017)
	at com.sun.tools.javac.code.Symbol.complete(Symbol.java:386)
	at com.sun.tools.javac.code.Symbol$ClassSymbol.complete(Symbol.java:764)
	at com.sun.tools.javac.comp.Enter.complete(Enter.java:516)
	at com.sun.tools.javac.comp.Enter.main(Enter.java:494)
	at com.sun.tools.javac.main.JavaCompiler.enterTrees(JavaCompiler.java:824)
	at com.sun.tools.javac.api.JavacTaskImpl.enter(JavacTaskImpl.java:347)
	at com.sun.tools.javac.api.JavacTaskImpl.enterTrees(JavacTaskImpl.java:379)
	at
org.netbeans.modules.java.source.usages.RepositoryUpdater.batchCompile(RepositoryUpdater.java:1424)
	at
org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker.updateFolder(RepositoryUpdater.java:1030)
	at
org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker.scanRoots(RepositoryUpdater.java:902)
	at
org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker.access$1500(RepositoryUpdater.java:610)
	at
org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker$1.run(RepositoryUpdater.java:699)
	at
org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker$1.run(RepositoryUpdater.java:633)
	at
org.netbeans.modules.java.source.usages.ClassIndexManager.writeLock(ClassIndexManager.java:49)
	at
org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker.run(RepositoryUpdater.java:633)
	at
org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker.run(RepositoryUpdater.java:610)
	at org.netbeans.api.java.source.JavaSource$CompilationJob.run(JavaSource.java:1107)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
[catch] at java.lang.Thread.run(Thread.java:619)
Caused by: Root: C:\space\newnbsrc\classfile\src File:
file:/C:/space/newnbsrc/classfile/src/org/netbeans/modules/classfile/ClassFile.java
Bootpath:
ClassPath[Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/resources.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/rt.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/sunrsasign.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/jsse.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/jce.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/charsets.jar!/],
Entry[file:/C:/Program%20Files/Java/jdk1.6.0/jre/classes/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/dnsns.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/localedata.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/sunjce_provider.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/sunmscapi.jar!/],
Entry[jar:file:/C:/Program%20Files/Java/jdk1.6.0/jre/lib/ext/sunpkcs11.jar!/]]
Classpath: ClassPath[] Sourcepath:
ClassPath[Entry[file:/C:/space/newnbsrc/classfile/src/]]