Build exception: Internal error: (java.io.EOFException) null

This is the log:

2014-01-04 12:19:48,387 [ 162196]   INFO - ij.compiler.impl.CompileDriver - COMPILATION STARTED (BUILD PROCESS)
2014-01-04 12:19:49,646 [ 163455]   INFO - j.compiler.server.BuildManager - BUILDER_PROCESS [stdout]: Build process started. Classpath: /C:/Program Files (x86)/JetBrains/IntelliJ IDEA 13.0/lib/jps-launcher.jar;C:/Program Files/Java/jdk1.7.0_40/lib/tools.jar;/C:/Program Files (x86)/JetBrains/IntelliJ IDEA 13.0/lib/optimizedFileManager.jar;/C:/Program Files (x86)/JetBrains/IntelliJ IDEA 13.0/lib/ecj-4.2.1.jar
2014-01-04 12:19:52,102 [ 165911]   INFO - ij.compiler.impl.CompileDriver - java.io.EOFException
    at java.io.DataInputStream.readFully(DataInputStream.java:197)
    at com.intellij.util.io.IOUtil.readUTFFast(IOUtil.java:131)
    at org.jetbrains.jps.incremental.storage.OneToManyPathsMapping$PathCollectionExternalizer.read(OneToManyPathsMapping.java:96)
    at org.jetbrains.jps.incremental.storage.OneToManyPathsMapping$PathCollectionExternalizer.read(OneToManyPathsMapping.java:84)
    at com.intellij.util.io.PersistentHashMap.doGet(PersistentHashMap.java:427)
    at com.intellij.util.io.PersistentHashMap.get(PersistentHashMap.java:398)
    at org.jetbrains.jps.incremental.storage.AbstractStateStorage.getState(AbstractStateStorage.java:118)
    at org.jetbrains.jps.incremental.storage.OneToManyPathsMapping.getState(OneToManyPathsMapping.java:61)
    at org.jetbrains.jps.incremental.storage.SourceToOutputMappingImpl.getOutputs(SourceToOutputMappingImpl.java:72)
    at org.jetbrains.jps.incremental.IncProjectBuilder.clearOutputFiles(IncProjectBuilder.java:443)
    at org.jetbrains.jps.incremental.IncProjectBuilder.cleanOutputRoots(IncProjectBuilder.java:415)
    at org.jetbrains.jps.incremental.IncProjectBuilder.runBuild(IncProjectBuilder.java:336)
    at org.jetbrains.jps.incremental.IncProjectBuilder.build(IncProjectBuilder.java:184)
    at org.jetbrains.jps.cmdline.BuildRunner.runBuild(BuildRunner.java:129)
    at org.jetbrains.jps.cmdline.BuildSession.runBuild(BuildSession.java:224)
    at org.jetbrains.jps.cmdline.BuildSession.run(BuildSession.java:113)
    at org.jetbrains.jps.cmdline.BuildMain$MyMessageHandler$1.run(BuildMain.java:133)
    at org.jetbrains.jps.service.impl.SharedThreadPoolImpl$1.run(SharedThreadPoolImpl.java:41)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:724)

2014-01-04 12:19:52,108 [ 165917]   INFO - s.impl.stores.FileBasedStorage - Document was not loaded for $PROJECT_CONFIG_DIR$/validation.xml file is null
2014-01-04 12:19:52,154 [ 165963]   INFO - .GenericCompilerPersistentData - Compiler info file doesn't exists: C:\IDE\cache\.IntelliJIdea13\system\compiler\webclient.710e12dd\.caches\jasper_validator\info
2014-01-04 12:19:52,154 [ 165963]   INFO - ler.impl.GenericCompilerRunner - Clearing cache for Jasper Validator
2014-01-04 12:19:52,256 [ 166065]   INFO - lij.compiler.impl.CompilerUtil -     COMPILATION FINISHED (BUILD PROCESS); Errors: 1; warnings: 0 took 3834 ms: 0 min 3sec

I tried to set "clear output directory on rebuild", it seems better, the compilation starts but it is not complete as some files it needs during the build was generated by a previous run of maven install into this directory, so, I need the build to not clear the output directory but doing so, I have the error mentioned above, still, I hope this information could help resolving this issue.

Surprisingly, after setting again "clear output directory on rebuild" to false, re-run a mvn clean install and rebuilt, it works, well I still have issues but nor related to this one, just discover this issue too http://devnet.jetbrains.com/message/5506359#5506359 next time will try the corresponding workaround

yea i'm having the exact same problem. nice feature.