Pengecualian selama debug di NetBeans

Saya memiliki proyek gradle dengan dependensi berikut:

    compile "commons-codec:commons-codec:+"
    compile "commons-io:commons-io:+"
    compile "org.apache.poi:poi:+"
    compile "commons-logging:commons-logging:+"
    compile "net.sourceforge.cssparser:cssparser:+"
    compile "net.sourceforge.htmlunit:htmlunit:+"
    compile "net.sourceforge.htmlunit:htmlunit-core-js:+"
    compile "net.sourceforge.htmlunit:neko-htmlunit:+"
    compile "org.apache.commons:commons-lang3:+"
    compile "org.apache.httpcomponents:httpclient:+"
    compile "org.apache.httpcomponents:httpmime:+"
    compile "org.eclipse.jetty.websocket:websocket-client:+"
    compile "xalan:xalan:+"
    compile "org.apache.poi:poi:+"
    compile "org.apache.poi:poi-ooxml:+"
    compile "org.apache.cassandra:cassandra-all:+"
    compile "org.apache.cassandra:cassandra-thrift:+"
   compile "com.whalin:Memcached-Java-Client:+"
   compile "org.hibernate:hibernate-gradle-plugin:+"
   compile "org.hibernate:hibernate-core:+"
   compile "org.hibernate:hibernate-tools:+"
   compile "org.hibernate:hibernate-entitymanager:+"
   compile "org.hibernate:hibernate:+"
   compile "org.hibernate:hibernate-annotations:+"
   compile "mysql:mysql-connector-java:+"
   compile "org.hibernate:ejb3-persistence:+"
   compile "javax:javaee-api:+"
   compile "javax.persistence:persistence-api:+"
   compile "javassist:javassist:+"

Saya tidak bisa menjalankannya dalam mode debug menggunakan NetBeans IDE, ketika saya mencoba, saya mendapat pengecualian berikut:

18:54:28.174 [main] DEBUG o.h.cfg.annotations.PropertyBinder - Building property year_end
Exception in thread "main" java.lang.NoSuchMethodError: javax.persistence.Table.indexes()[Ljavax/persistence/Index;
    at org.hibernate.cfg.annotations.EntityBinder.processComplementaryTableDefinitions(EntityBinder.java:1106)

Mengapa?

Pertanyaan saya unik karena bukan tentang kompilasi. Program saya dapat dikompilasi dengan baik dengan kode (gradle) berikut:

task compileJar(type: Jar) {
    manifest {
        attributes 'Implementation-Title': 'Applic version 0.9',
            'Implementation-Version': version,
            'Main-Class': 'com.company.runfile'
    }
    baseName = project.name + '-all'
    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
    with jar
    exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA' 
}

Ini menciptakan file jar yang berjalan dengan baik, tapi saya tidak bisa men-debug aplikasi yang sama di NetBeans (juga di Intellij IDEA).