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)

-- 
Netbeans IDE 6.5 don't autocomplete import statement
https://bugs.launchpad.net/bugs/353080
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