Remove duplicated extensions

...ala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala

...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala

...main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala

...umc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala

.../nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala

...sc/biopet/extensions/gatk/broad/GenotypeConcordance.scala

...scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala

...ala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala

...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

...nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala

...c/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala

...pelines/shiva/variantcallers/VarscanCnsSingleSample.scala

...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala