Native library part of git repo

.gitignore

@@ -3,7 +3,6 @@
 /*.bed
 *~
 /*.vcf
-/*.vcf.idx
 /*.txt
 /*.csh
 /.*
@@ -25,54 +24,5 @@ dump/
 lib/
 out/
 /atlassian-ide-plugin.xml
-kg_tmp/
-maven-ant-tasks-2.1.3.jar
-null-sequenceGraph.25.0.0.raw_readthreading_graph.dot
-null-sequenceGraph.25.0.1.cleaned_readthreading_graph.dot
-null-sequenceGraph.25.0.1.initial_seqgraph.dot
-null-sequenceGraph.3.0.0.raw_readthreading_graph.dot
-null-sequenceGraph.3.0.1.cleaned_readthreading_graph.dot
-null-sequenceGraph.3.0.1.initial_seqgraph.dot
-org/
-package-list
-resources/
-velocity.log
-perf
-verify
 maven-metadata-local.xml
 dependency-reduced-pom.xml
-private/gatk-private/private/
-private/gatk-private/public/
-private/gatk-private/target/
-private/na12878kb-utils/public/
-private/na12878kb-utils/target/
-private/queue-private/private/
-private/queue-private/public/
-private/queue-private/target/
-private/scala/
-private/testdata
-protected/gatk-protected/private/
-protected/gatk-protected/public/
-protected/gatk-protected/target/
-public/external-example/target/
-public/gatk-framework/private/
-public/gatk-framework/public/
-public/gatk-framework/target/
-public/gatk-package/private/
-public/gatk-package/public/
-public/gatk-package/target/
-public/gatk-queue-extgen/public/
-public/gatk-queue-extgen/target/
-public/gsalib/public/
-public/gsalib/target/
-public/queue-framework/private/
-public/queue-framework/public/
-public/queue-framework/target/
-public/queue-package/private/
-public/queue-package/public/
-public/queue-package/target/
-public/scala/
-public/sting-utils/public/
-public/sting-utils/target/
-public/testdata
-target/