Move scatter functions to biopet extensions

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

.../main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala

...src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala

.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

.../nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala

...a/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala

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

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

...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

...sasc/biopet/extensions/gatk/broad/BamGatherFunction.scala

.../lumc/sasc/biopet/extensions/gatk/broad/CatVariants.scala

...sasc/biopet/extensions/gatk/broad/CatVariantsGather.scala

...lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

...c/sasc/biopet/extensions/gatk/broad/CombineVariants.scala

.../biopet/extensions/gatk/broad/ContigScatterFunction.scala

...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

...mc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala