Comment 5 for bug 353080

I've got the same issue. Right after starting Netbeans 6.5 in 9.04 I get this stacktrace and finding imports automatic is impossible and makes it (almost) impossible to code. Also tried to remove the profile folder imported from 6.1 but same issue, just that it crashes at another jar file.

So it sure does look like the same as http://www.netbeans.org/issues/show_bug.cgi?id=160498 .

*** Stacktrace ***
Annotation: While scanning: jar:file:/usr/lib/jvm/java-6-openjdk/jre/lib/rt.jar!/
Annotation: While scanning: jar:file:/usr/lib/jvm/java-6-openjdk/jre/lib/rt.jar!/
While scanning: jar:file:/usr/lib/jvm/java-6-openjdk/jre/lib/rt.jar!/
While scanning: jar:file:/usr/lib/jvm/java-6-openjdk/jre/lib/rt.jar!/
Caused: org.apache.lucene.store.AlreadyClosedException: this Directory is closed
 at org.apache.lucene.store.Directory.ensureOpen(Directory.java:220)
 at org.apache.lucene.store.FSDirectory.list(FSDirectory.java:320)
 at org.netbeans.modules.java.source.usages.LuceneIndex.clear(Unknown Source)
 at org.netbeans.modules.java.source.usages.BinaryAnalyser.start(Unknown Source)
 at org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker.scanRoots(Unknown Source)
 at org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker.access$2700(Unknown Source)
 at org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker$1.run(Unknown Source)
 at org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker$1.run(Unknown Source)
 at org.netbeans.modules.java.source.usages.ClassIndexManager.writeLock(Unknown Source)
 at org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker.run(Unknown Source)
 at org.netbeans.modules.java.source.usages.RepositoryUpdater$CompileWorker.run(Unknown Source)
 at org.netbeans.api.java.source.JavaSource$CompilationJob.run(Unknown Source)
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
 at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
 at java.util.concurrent.FutureTask.run(FutureTask.java:166)
 at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
 at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
[catch] at java.lang.Thread.run(Thread.java:636)