From a40fa7dd8e50a3fc240573dda17bb3014b3f466d Mon Sep 17 00:00:00 2001
From: patrick-schultz <pschultz@broadinstitute.org>
Date: Tue, 17 Dec 2024 13:56:01 -0500
Subject: [PATCH] move mill modules into subdirectory

---
 build.yaml                                    |  20 +++++++++---------
 hail/build.mill                               |   3 +++
 .../java/is/hail/annotations/Memory.java      |   0
 .../src/dist/scripts/Plot_gq20bydp.R          |   0
 .../src/main/c/ApproximateQuantiles_test.cpp  |   0
 hail/{ => modules}/src/main/c/Decoder.cpp     |   0
 hail/{ => modules}/src/main/c/Encoder.cpp     |   0
 hail/{ => modules}/src/main/c/FS.cpp          |   0
 hail/{ => modules}/src/main/c/Logging.cpp     |   0
 hail/{ => modules}/src/main/c/Makefile        |   0
 hail/{ => modules}/src/main/c/NativeBoot.cpp  |   0
 .../src/main/c/NativeCodeSuite.cpp            |   0
 .../src/main/c/NativeLongFunc.cpp             |   0
 .../{ => modules}/src/main/c/NativeModule.cpp |   0
 hail/{ => modules}/src/main/c/NativePtr.cpp   |   0
 .../{ => modules}/src/main/c/NativeStatus.cpp |   0
 hail/{ => modules}/src/main/c/ObjectArray.cpp |   0
 .../src/main/c/PartitionIterators.cpp         |   0
 hail/{ => modules}/src/main/c/README.md       |   0
 hail/{ => modules}/src/main/c/Region.cpp      |   0
 hail/{ => modules}/src/main/c/Region_test.cpp |   0
 hail/{ => modules}/src/main/c/Upcalls.cpp     |   0
 hail/{ => modules}/src/main/c/cache-tests.cpp |   0
 hail/{ => modules}/src/main/c/ibs.cpp         |   0
 hail/{ => modules}/src/main/c/ibs.h           |   0
 hail/{ => modules}/src/main/c/test.cpp        |   0
 .../src/main/c/testutils/style.css            |   0
 .../src/main/c/testutils/test-reporter.xslt   |   0
 .../src/main/c/testutils/unit-tests.cpp       |   0
 .../hail/expr/ir/MatrixWriterConstants.java   |   0
 .../java/is/hail/io/compress/BGzipCodec.java  |   0
 .../is/hail/io/compress/BGzipCodecGZ.java     |   0
 .../is/hail/io/compress/BGzipCodecTbi.java    |   0
 .../is/hail/io/compress/BGzipConstants.java   |   0
 .../is/hail/io/compress/BGzipInputStream.java |   0
 .../hail/io/compress/BGzipOutputStream.java   |   0
 .../io/compress/ComposableBGzipCodec.java     |   0
 .../compress/ComposableBGzipOutputStream.java |   0
 .../main/java/is/hail/io/fs/Positioned.java   |   0
 .../src/main/java/is/hail/io/fs/Seekable.java |   0
 .../com.azure.core.http.HttpClientProvider    |   0
 ...sv.relaxng_datatype.DatatypeLibraryFactory |   0
 .../com.ctc.wstx.stax.WstxInputFactory        |   0
 .../com.fasterxml.jackson.core.JsonFactory    |   0
 .../com.fasterxml.jackson.core.ObjectCodec    |   0
 .../com.fasterxml.jackson.databind.Module     |   0
 .../io.micrometer.context.ContextAccessor     |   0
 ...ure.com.azure.core.http.HttpClientProvider |   0
 .../services/javax.xml.stream.XMLEventFactory |   0
 .../services/javax.xml.stream.XMLInputFactory |   0
 .../javax.xml.stream.XMLOutputFactory         |   0
 ...tax2.validation.XMLValidationSchemaFactory |   0
 ....validation.XMLValidationSchemaFactory.dtd |   0
 ...idation.XMLValidationSchemaFactory.relaxng |   0
 ....validation.XMLValidationSchemaFactory.w3c |   0
 ...ockhound.integration.BlockHoundIntegration |   0
 .../src/main/resources/include/README         |   0
 .../include/hail/ApproximateQuantiles.h       |   0
 .../resources/include/hail/ArrayBuilder.h     |   0
 .../main/resources/include/hail/ArraySorter.h |   0
 .../src/main/resources/include/hail/Decoder.h |   0
 .../src/main/resources/include/hail/Encoder.h |   0
 .../src/main/resources/include/hail/FS.h      |   0
 .../src/main/resources/include/hail/Logging.h |   0
 .../src/main/resources/include/hail/NDArray.h |   0
 .../resources/include/hail/NativeMethod.h     |   0
 .../resources/include/hail/NativeModule.h     |   0
 .../main/resources/include/hail/NativeObj.h   |   0
 .../main/resources/include/hail/NativePtr.h   |   0
 .../resources/include/hail/NativeStatus.h     |   0
 .../main/resources/include/hail/ObjectArray.h |   0
 .../main/resources/include/hail/Ordering.h    |   0
 .../include/hail/PartitionIterators.h         |   0
 .../src/main/resources/include/hail/Region.h  |   0
 .../main/resources/include/hail/RegionPool.h  |   0
 .../main/resources/include/hail/SparkUtils.h  |   0
 .../src/main/resources/include/hail/Upcalls.h |   0
 .../src/main/resources/include/hail/Utils.h   |   0
 .../src/main/resources/include/hail/hail.h    |   0
 .../src/main/resources/log4j.properties       |   0
 .../src/main/resources/reference/canfam3.json |   0
 .../src/main/resources/reference/grch37.json  |   0
 .../src/main/resources/reference/grch38.json  |   0
 .../src/main/resources/reference/grcm38.json  |   0
 .../src/main/scala/is/hail/HailContext.scala  |   0
 .../main/scala/is/hail/HailFeatureFlags.scala |   0
 .../is/hail/annotations/Annotation.scala      |   0
 .../is/hail/annotations/BroadcastValue.scala  |   0
 .../is/hail/annotations/ChunkCache.scala      |   0
 .../hail/annotations/ExtendedOrdering.scala   |   0
 .../hail/annotations/JoinedRegionValue.scala  |   0
 .../hail/annotations/OrderedRVIterator.scala  |   0
 .../scala/is/hail/annotations/Region.scala    |   0
 .../is/hail/annotations/RegionMemory.scala    |   0
 .../is/hail/annotations/RegionPool.scala      |   0
 .../is/hail/annotations/RegionValue.scala     |   0
 .../hail/annotations/RegionValueBuilder.scala |   0
 .../is/hail/annotations/UnsafeOrdering.scala  |   0
 .../scala/is/hail/annotations/UnsafeRow.scala |   0
 .../is/hail/annotations/UnsafeUtils.scala     |   0
 .../is/hail/annotations/ValueVisitor.scala    |   0
 .../annotations/WritableRegionValue.scala     |   0
 .../scala/is/hail/annotations/package.scala   |   0
 .../scala/is/hail/asm4s/AsmFunction.scala     |   0
 .../scala/is/hail/asm4s/ClassBuilder.scala    |   0
 .../src/main/scala/is/hail/asm4s/Code.scala   |   0
 .../scala/is/hail/asm4s/CodeBuilder.scala     |   0
 .../scala/is/hail/asm4s/GenericTypeInfo.scala |   0
 .../scala/is/hail/asm4s/HailClassLoader.scala |   0
 .../main/scala/is/hail/asm4s/package.scala    |   0
 .../main/scala/is/hail/backend/Backend.scala  |   0
 .../scala/is/hail/backend/BackendServer.scala |   0
 .../scala/is/hail/backend/BackendUtils.scala  |   0
 .../is/hail/backend/ExecuteContext.scala      |   0
 .../is/hail/backend/ExecutionCache.scala      |   0
 .../is/hail/backend/HailStateManager.scala    |   0
 .../is/hail/backend/HailTaskContext.scala     |   0
 .../is/hail/backend/local/LocalBackend.scala  |   0
 .../scala/is/hail/backend/service/Main.scala  |   0
 .../hail/backend/service/ServiceBackend.scala |   0
 .../is/hail/backend/service/Worker.scala      |   0
 .../is/hail/backend/spark/SparkBackend.scala  |   0
 .../backend/spark/SparkBlockMatrixCache.scala |   0
 .../main/scala/is/hail/check/Arbitrary.scala  |   0
 .../src/main/scala/is/hail/check/Gen.scala    |   0
 .../src/main/scala/is/hail/check/Prop.scala   |   0
 .../compatibility/LegacyBufferSpecs.scala     |   0
 .../LegacyEncodedTypeParser.scala             |   0
 .../hail/compatibility/LegacyRVDSpecs.scala   |   0
 .../is/hail/cxx/RegionValueIterator.scala     |   0
 .../experimental/ExperimentalFunctions.scala  |   0
 .../scala/is/hail/experimental/package.scala  |   0
 .../scala/is/hail/expr/AnnotationImpex.scala  |   0
 .../src/main/scala/is/hail/expr/NatBase.scala |   0
 .../src/main/scala/is/hail/expr/Parser.scala  |   0
 .../main/scala/is/hail/expr/Validate.scala    |   0
 .../expr/ir/AbstractMatrixTableSpec.scala     |   0
 .../is/hail/expr/ir/AbstractTableSpec.scala   |   0
 .../main/scala/is/hail/expr/ir/AggOp.scala    |   0
 .../scala/is/hail/expr/ir/ArraySorter.scala   |   0
 .../main/scala/is/hail/expr/ir/BaseIR.scala   |   0
 .../main/scala/is/hail/expr/ir/BinaryOp.scala |   0
 .../scala/is/hail/expr/ir/BinarySearch.scala  |   0
 .../main/scala/is/hail/expr/ir/Binds.scala    |   0
 .../scala/is/hail/expr/ir/BlockMatrixIR.scala |   0
 .../is/hail/expr/ir/BlockMatrixWriter.scala   |   0
 .../main/scala/is/hail/expr/ir/Casts.scala    |   0
 .../main/scala/is/hail/expr/ir/Children.scala |   0
 .../scala/is/hail/expr/ir/ComparisonOp.scala  |   0
 .../scala/is/hail/expr/ir/Compilable.scala    |   0
 .../main/scala/is/hail/expr/ir/Compile.scala  |   0
 .../is/hail/expr/ir/CompileAndEvaluate.scala  |   0
 .../is/hail/expr/ir/ComputeUsesAndDefs.scala  |   0
 .../src/main/scala/is/hail/expr/ir/Copy.scala |   0
 .../is/hail/expr/ir/DeprecatedIRBuilder.scala |   0
 .../is/hail/expr/ir/DistinctlyKeyed.scala     |   0
 .../src/main/scala/is/hail/expr/ir/Emit.scala |   0
 .../is/hail/expr/ir/EmitClassBuilder.scala    |   0
 .../is/hail/expr/ir/EmitCodeBuilder.scala     |   0
 .../hail/expr/ir/EmitStreamDistribute.scala   |   0
 .../src/main/scala/is/hail/expr/ir/Env.scala  |   0
 .../main/scala/is/hail/expr/ir/Exists.scala   |   0
 .../hail/expr/ir/ExtractIntervalFilters.scala |   0
 .../scala/is/hail/expr/ir/FoldConstants.scala |   0
 .../scala/is/hail/expr/ir/ForwardLets.scala   |   0
 .../hail/expr/ir/ForwardRelationalLets.scala  |   0
 .../scala/is/hail/expr/ir/FreeVariables.scala |   0
 .../scala/is/hail/expr/ir/GenericLines.scala  |   0
 .../is/hail/expr/ir/GenericTableValue.scala   |   0
 .../src/main/scala/is/hail/expr/ir/IR.scala   |   0
 .../scala/is/hail/expr/ir/IRBuilder.scala     |   0
 .../main/scala/is/hail/expr/ir/IRSize.scala   |   0
 .../scala/is/hail/expr/ir/IRTraversal.scala   |   0
 .../is/hail/expr/ir/InTailPosition.scala      |   0
 .../scala/is/hail/expr/ir/InferPType.scala    |   0
 .../scala/is/hail/expr/ir/InferType.scala     |   0
 .../scala/is/hail/expr/ir/Interpret.scala     |   0
 .../scala/is/hail/expr/ir/Interpretable.scala |   0
 .../scala/is/hail/expr/ir/IsConstant.scala    |   0
 .../main/scala/is/hail/expr/ir/IsPure.scala   |   0
 .../hail/expr/ir/LiftRelationalValues.scala   |   0
 .../scala/is/hail/expr/ir/LowerMatrixIR.scala |   0
 .../ir/LowerOrInterpretNonCompilable.scala    |   0
 .../is/hail/expr/ir/LoweringAnalyses.scala    |   0
 .../main/scala/is/hail/expr/ir/MapIR.scala    |   0
 .../main/scala/is/hail/expr/ir/MatrixIR.scala |   0
 .../scala/is/hail/expr/ir/MatrixValue.scala   |   0
 .../scala/is/hail/expr/ir/MatrixWriter.scala  |   0
 .../main/scala/is/hail/expr/ir/Mentions.scala |   0
 .../is/hail/expr/ir/NativeReaderOptions.scala |   0
 .../scala/is/hail/expr/ir/NestingDepth.scala  |   0
 .../is/hail/expr/ir/NormalizeNames.scala      |   0
 .../is/hail/expr/ir/NumericPrimitives.scala   |   0
 .../main/scala/is/hail/expr/ir/Optimize.scala |   0
 .../main/scala/is/hail/expr/ir/Param.scala    |   0
 .../main/scala/is/hail/expr/ir/Parser.scala   |   0
 .../main/scala/is/hail/expr/ir/Pretty.scala   |   0
 ...rimitiveTypeToIRIntermediateClassTag.scala |   0
 .../is/hail/expr/ir/PruneDeadFields.scala     |   0
 .../main/scala/is/hail/expr/ir/Random.scala   |   0
 .../scala/is/hail/expr/ir/RefEquality.scala   |   0
 .../scala/is/hail/expr/ir/Requiredness.scala  |   0
 .../is/hail/expr/ir/RewriteBottomUp.scala     |   0
 .../is/hail/expr/ir/RewriteTopDown.scala      |   0
 .../main/scala/is/hail/expr/ir/Scope.scala    |   0
 .../main/scala/is/hail/expr/ir/Simplify.scala |   0
 .../expr/ir/SpecializedArrayBuilders.scala    |   0
 .../is/hail/expr/ir/StringTableReader.scala   |   0
 .../main/scala/is/hail/expr/ir/Subst.scala    |   0
 .../src/main/scala/is/hail/expr/ir/Sym.scala  |   0
 .../main/scala/is/hail/expr/ir/TableIR.scala  |   0
 .../scala/is/hail/expr/ir/TableValue.scala    |   0
 .../scala/is/hail/expr/ir/TableWriter.scala   |   0
 .../scala/is/hail/expr/ir/TypeCheck.scala     |   0
 .../main/scala/is/hail/expr/ir/UnaryOp.scala  |   0
 .../scala/is/hail/expr/ir/ValueReader.scala   |   0
 .../scala/is/hail/expr/ir/ValueWriter.scala   |   0
 .../is/hail/expr/ir/add-ir-checklist.txt      |   0
 .../is/hail/expr/ir/agg/AggregatorState.scala |   0
 .../is/hail/expr/ir/agg/AppendOnlyBTree.scala |   0
 .../expr/ir/agg/ApproxCDFAggregator.scala     |   0
 .../expr/ir/agg/ApproxCDFStateManager.scala   |   0
 .../ArrayElementLengthCheckAggregator.scala   |   0
 .../expr/ir/agg/CallStatsAggregator.scala     |   0
 .../hail/expr/ir/agg/CollectAggregator.scala  |   0
 .../expr/ir/agg/CollectAsSetAggregator.scala  |   0
 .../is/hail/expr/ir/agg/CountAggregator.scala |   0
 .../hail/expr/ir/agg/DensifyAggregator.scala  |   0
 .../expr/ir/agg/DownsampleAggregator.scala    |   0
 .../scala/is/hail/expr/ir/agg/Extract.scala   |   0
 .../is/hail/expr/ir/agg/FoldAggregator.scala  |   0
 .../hail/expr/ir/agg/GroupedAggregator.scala  |   0
 .../expr/ir/agg/ImputeTypeAggregator.scala    |   0
 .../ir/agg/LinearRegressionAggregator.scala   |   0
 .../hail/expr/ir/agg/MonoidAggregator.scala   |   0
 .../ir/agg/NDArrayMultiplyAddAggregator.scala |   0
 .../expr/ir/agg/NDArraySumAggregator.scala    |   0
 .../expr/ir/agg/PrevNonNullAggregator.scala   |   0
 .../ir/agg/ReservoirSampleAggregator.scala    |   0
 .../hail/expr/ir/agg/StagedAggregator.scala   |   0
 .../hail/expr/ir/agg/StagedArrayBuilder.scala |   0
 .../expr/ir/agg/StagedBlockLinkedList.scala   |   0
 .../is/hail/expr/ir/agg/TakeAggregator.scala  |   0
 .../hail/expr/ir/agg/TakeByAggregator.scala   |   0
 .../ir/analyses/ComputeMethodSplits.scala     |   0
 .../analyses/ControlFlowPreventsSplit.scala   |   0
 .../expr/ir/analyses/ParentPointers.scala     |   0
 .../hail/expr/ir/analyses/SemanticHash.scala  |   0
 .../ir/functions/ApproxCDFFunctions.scala     |   0
 .../expr/ir/functions/ArrayFunctions.scala    |   0
 .../expr/ir/functions/CallFunctions.scala     |   0
 .../expr/ir/functions/DictFunctions.scala     |   0
 .../is/hail/expr/ir/functions/Functions.scala |   0
 .../expr/ir/functions/GenotypeFunctions.scala |   0
 .../hail/expr/ir/functions/GetElement.scala   |   0
 .../expr/ir/functions/IntervalFunctions.scala |   0
 .../expr/ir/functions/LocusFunctions.scala    |   0
 .../expr/ir/functions/MathFunctions.scala     |   0
 .../ir/functions/MatrixWriteBlockMatrix.scala |   0
 .../expr/ir/functions/NDArrayFunctions.scala  |   0
 .../ir/functions/RandomSeededFunctions.scala  |   0
 .../functions/ReferenceGenomeFunctions.scala  |   0
 .../ir/functions/RelationalFunctions.scala    |   0
 .../hail/expr/ir/functions/SetFunctions.scala |   0
 .../expr/ir/functions/StringFunctions.scala   |   0
 .../TableCalculateNewPartitions.scala         |   0
 .../expr/ir/functions/UtilFunctions.scala     |   0
 .../ir/lowering/CanLowerEfficiently.scala     |   0
 .../expr/ir/lowering/EvalRelationalLets.scala |   0
 .../is/hail/expr/ir/lowering/IRState.scala    |   0
 .../ir/lowering/LowerAndExecuteShuffles.scala |   0
 .../expr/ir/lowering/LowerBlockMatrixIR.scala |   0
 .../ir/lowering/LowerDistributedSort.scala    |   0
 .../hail/expr/ir/lowering/LowerTableIR.scala  |   0
 .../ir/lowering/LowerTableIRHelpers.scala     |   0
 .../is/hail/expr/ir/lowering/LowerToCDA.scala |   0
 .../hail/expr/ir/lowering/LoweringPass.scala  |   0
 .../expr/ir/lowering/LoweringPipeline.scala   |   0
 .../expr/ir/lowering/RVDToTableStage.scala    |   0
 .../scala/is/hail/expr/ir/lowering/Rule.scala |   0
 .../ir/lowering/TableStageDependency.scala    |   0
 .../hail/expr/ir/ndarrays/EmitNDArray.scala   |   0
 .../expr/ir/orderings/BinaryOrdering.scala    |   0
 .../hail/expr/ir/orderings/CallOrdering.scala |   0
 .../hail/expr/ir/orderings/CodeOrdering.scala |   0
 .../expr/ir/orderings/IntervalOrdering.scala  |   0
 .../expr/ir/orderings/IterableOrdering.scala  |   0
 .../expr/ir/orderings/LocusOrdering.scala     |   0
 .../expr/ir/orderings/PrimitiveOrdering.scala |   0
 .../expr/ir/orderings/StringOrdering.scala    |   0
 .../expr/ir/orderings/StructOrdering.scala    |   0
 .../main/scala/is/hail/expr/ir/package.scala  |   0
 .../is/hail/expr/ir/streams/EmitStream.scala  |   0
 .../hail/expr/ir/streams/StagedMinHeap.scala  |   0
 .../is/hail/expr/ir/streams/StreamUtils.scala |   0
 .../src/main/scala/is/hail/expr/package.scala |   0
 .../is/hail/io/AbstractBinaryReader.scala     |   0
 .../main/scala/is/hail/io/BufferSpecs.scala   |   0
 .../scala/is/hail/io/ByteArrayReader.scala    |   0
 .../src/main/scala/is/hail/io/CodecSpec.scala |   0
 .../src/main/scala/is/hail/io/Decoder.scala   |   0
 .../scala/is/hail/io/DoubleInputBuffer.scala  |   0
 .../is/hail/io/ElasticsearchConnector.scala   |   0
 .../src/main/scala/is/hail/io/Encoder.scala   |   0
 .../scala/is/hail/io/FileWriteMetadata.scala  |   0
 .../is/hail/io/HadoopFSDataBinaryReader.scala |   0
 .../main/scala/is/hail/io/IndexBTree.scala    |   0
 .../is/hail/io/IndexedBinaryBlockReader.scala |   0
 .../is/hail/io/IndexedBinaryInputFormat.scala |   0
 .../main/scala/is/hail/io/InputBuffers.scala  |   0
 .../main/scala/is/hail/io/MemoryBuffer.scala  |   0
 .../main/scala/is/hail/io/OutputBuffers.scala |   0
 .../hail/io/RichContextRDDRegionValue.scala   |   0
 .../src/main/scala/is/hail/io/Spec.scala      |   0
 .../scala/is/hail/io/TypedCodecSpec.scala     |   0
 .../is/hail/io/avro/AvroPartitionReader.scala |   0
 .../hail/io/avro/AvroSchemaSerializer.scala   |   0
 .../is/hail/io/avro/AvroTableReader.scala     |   0
 .../avro/UnsafeAvroTableReaderOptions.scala   |   0
 .../is/hail/io/bgen/BgenRDDPartitions.scala   |   0
 .../scala/is/hail/io/bgen/BgenSettings.scala  |   0
 .../main/scala/is/hail/io/bgen/LoadBgen.scala |   0
 .../is/hail/io/bgen/StagedBGENReader.scala    |   0
 .../is/hail/io/compress/BGzipLineReader.scala |   0
 .../main/scala/is/hail/io/compress/LZ4.scala  |   0
 .../scala/is/hail/io/fs/AzureStorageFS.scala  |   0
 .../src/main/scala/is/hail/io/fs/FS.scala     |   0
 .../scala/is/hail/io/fs/GoogleStorageFS.scala |   0
 .../main/scala/is/hail/io/fs/HadoopFS.scala   |   0
 .../src/main/scala/is/hail/io/fs/README       |   0
 .../main/scala/is/hail/io/fs/RouterFS.scala   |   0
 .../is/hail/io/fs/TerraAzureStorageFS.scala   |   0
 .../main/scala/is/hail/io/fs/package.scala    |   0
 .../scala/is/hail/io/gen/ExportBGEN.scala     |   0
 .../main/scala/is/hail/io/gen/ExportGen.scala |   0
 .../io/hadoop/ByteArrayOutputFormat.scala     |   0
 .../is/hail/io/hadoop/BytesOnlyWritable.scala |   0
 .../scala/is/hail/io/index/IndexReader.scala  |   0
 .../scala/is/hail/io/index/IndexWriter.scala  |   0
 .../hail/io/index/InternalNodeBuilder.scala   |   0
 .../is/hail/io/index/LeafNodeBuilder.scala    |   0
 .../is/hail/io/index/StagedIndexReader.scala  |   0
 .../src/main/scala/is/hail/io/package.scala   |   0
 .../scala/is/hail/io/plink/ExportPlink.scala  |   0
 .../scala/is/hail/io/plink/LoadPlink.scala    |   0
 .../is/hail/io/reference/FASTAReader.scala    |   0
 .../scala/is/hail/io/reference/LiftOver.scala |   0
 .../scala/is/hail/io/tabix/TabixReader.scala  |   0
 .../main/scala/is/hail/io/vcf/ExportVCF.scala |   0
 .../main/scala/is/hail/io/vcf/LoadVCF.scala   |   0
 .../is/hail/io/vcf/TabixReadVCFIterator.scala |   0
 .../is/hail/kryo/HailKryoRegistrator.scala    |   0
 .../src/main/scala/is/hail/linalg/BLAS.scala  |   0
 .../scala/is/hail/linalg/BlockMatrix.scala    |   0
 .../is/hail/linalg/GridPartitioner.scala      |   0
 .../main/scala/is/hail/linalg/LAPACK.scala    |   0
 .../is/hail/linalg/LinalgCodeUtils.scala      |   0
 .../main/scala/is/hail/linalg/RowMatrix.scala |   0
 .../scala/is/hail/linalg/RowPartitioner.scala |   0
 .../src/main/scala/is/hail/lir/Blocks.scala   |   0
 .../src/main/scala/is/hail/lir/CFG.scala      |   0
 .../src/main/scala/is/hail/lir/Emit.scala     |   0
 .../scala/is/hail/lir/InitializeLocals.scala  |   0
 .../src/main/scala/is/hail/lir/Liveness.scala |   0
 .../src/main/scala/is/hail/lir/Locals.scala   |   0
 .../src/main/scala/is/hail/lir/PST.scala      |   0
 .../src/main/scala/is/hail/lir/Pretty.scala   |   0
 .../scala/is/hail/lir/SimplifyControl.scala   |   0
 .../scala/is/hail/lir/SplitLargeBlocks.scala  |   0
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 .../scala/is/hail/utils/BitVectorSuite.scala  |   0
 .../BufferedAggregatorIteratorSuite.scala     |   0
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 .../is/hail/utils/PartitionCountsSuite.scala  |   0
 .../scala/is/hail/utils/RichArraySuite.scala  |   0
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 .../utils/SpillingCollectIteratorSuite.scala  |   0
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 .../scala/is/hail/utils/UnionFindSuite.scala  |   0
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 .../prettyPrint/PrettyPrintWriterSuite.scala  |   0
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 4377 files changed, 13 insertions(+), 10 deletions(-)
 rename hail/{ => modules}/src/debug/java/is/hail/annotations/Memory.java (100%)
 rename hail/{ => modules}/src/dist/scripts/Plot_gq20bydp.R (100%)
 rename hail/{ => modules}/src/main/c/ApproximateQuantiles_test.cpp (100%)
 rename hail/{ => modules}/src/main/c/Decoder.cpp (100%)
 rename hail/{ => modules}/src/main/c/Encoder.cpp (100%)
 rename hail/{ => modules}/src/main/c/FS.cpp (100%)
 rename hail/{ => modules}/src/main/c/Logging.cpp (100%)
 rename hail/{ => modules}/src/main/c/Makefile (100%)
 rename hail/{ => modules}/src/main/c/NativeBoot.cpp (100%)
 rename hail/{ => modules}/src/main/c/NativeCodeSuite.cpp (100%)
 rename hail/{ => modules}/src/main/c/NativeLongFunc.cpp (100%)
 rename hail/{ => modules}/src/main/c/NativeModule.cpp (100%)
 rename hail/{ => modules}/src/main/c/NativePtr.cpp (100%)
 rename hail/{ => modules}/src/main/c/NativeStatus.cpp (100%)
 rename hail/{ => modules}/src/main/c/ObjectArray.cpp (100%)
 rename hail/{ => modules}/src/main/c/PartitionIterators.cpp (100%)
 rename hail/{ => modules}/src/main/c/README.md (100%)
 rename hail/{ => modules}/src/main/c/Region.cpp (100%)
 rename hail/{ => modules}/src/main/c/Region_test.cpp (100%)
 rename hail/{ => modules}/src/main/c/Upcalls.cpp (100%)
 rename hail/{ => modules}/src/main/c/cache-tests.cpp (100%)
 rename hail/{ => modules}/src/main/c/ibs.cpp (100%)
 rename hail/{ => modules}/src/main/c/ibs.h (100%)
 rename hail/{ => modules}/src/main/c/test.cpp (100%)
 rename hail/{ => modules}/src/main/c/testutils/style.css (100%)
 rename hail/{ => modules}/src/main/c/testutils/test-reporter.xslt (100%)
 rename hail/{ => modules}/src/main/c/testutils/unit-tests.cpp (100%)
 rename hail/{ => modules}/src/main/java/is/hail/expr/ir/MatrixWriterConstants.java (100%)
 rename hail/{ => modules}/src/main/java/is/hail/io/compress/BGzipCodec.java (100%)
 rename hail/{ => modules}/src/main/java/is/hail/io/compress/BGzipCodecGZ.java (100%)
 rename hail/{ => modules}/src/main/java/is/hail/io/compress/BGzipCodecTbi.java (100%)
 rename hail/{ => modules}/src/main/java/is/hail/io/compress/BGzipConstants.java (100%)
 rename hail/{ => modules}/src/main/java/is/hail/io/compress/BGzipInputStream.java (100%)
 rename hail/{ => modules}/src/main/java/is/hail/io/compress/BGzipOutputStream.java (100%)
 rename hail/{ => modules}/src/main/java/is/hail/io/compress/ComposableBGzipCodec.java (100%)
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 rename hail/{ => modules}/src/main/resources/META-INF/services/com.azure.core.http.HttpClientProvider (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/com.ctc.wstx.shaded.msv.relaxng_datatype.DatatypeLibraryFactory (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/com.ctc.wstx.stax.WstxInputFactory (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/com.fasterxml.jackson.core.JsonFactory (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/com.fasterxml.jackson.core.ObjectCodec (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/com.fasterxml.jackson.databind.Module (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/io.micrometer.context.ContextAccessor (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/is.hail.shadedazure.com.azure.core.http.HttpClientProvider (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/javax.xml.stream.XMLEventFactory (100%)
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 rename hail/{ => modules}/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.dtd (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.relaxng (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.w3c (100%)
 rename hail/{ => modules}/src/main/resources/META-INF/services/reactor.blockhound.integration.BlockHoundIntegration (100%)
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 rename hail/{ => modules}/src/main/scala/is/hail/cxx/RegionValueIterator.scala (100%)
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 rename hail/{ => modules}/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala (100%)
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 rename hail/{ => modules}/src/main/scala/is/hail/expr/ir/streams/StagedMinHeap.scala (100%)
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 rename hail/{ => modules}/src/main/scala/is/hail/expr/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/AbstractBinaryReader.scala (100%)
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 rename hail/{ => modules}/src/main/scala/is/hail/io/ByteArrayReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/CodecSpec.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/Decoder.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/DoubleInputBuffer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/ElasticsearchConnector.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/Encoder.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/FileWriteMetadata.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/HadoopFSDataBinaryReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/IndexBTree.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/IndexedBinaryBlockReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/IndexedBinaryInputFormat.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/InputBuffers.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/MemoryBuffer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/OutputBuffers.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/RichContextRDDRegionValue.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/Spec.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/TypedCodecSpec.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/avro/AvroPartitionReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/avro/AvroSchemaSerializer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/avro/AvroTableReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/avro/UnsafeAvroTableReaderOptions.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/bgen/BgenSettings.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/bgen/LoadBgen.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/bgen/StagedBGENReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/compress/BGzipLineReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/compress/LZ4.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/fs/AzureStorageFS.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/fs/FS.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/fs/GoogleStorageFS.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/fs/HadoopFS.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/fs/README (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/fs/RouterFS.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/fs/TerraAzureStorageFS.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/fs/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/gen/ExportBGEN.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/gen/ExportGen.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/hadoop/ByteArrayOutputFormat.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/hadoop/BytesOnlyWritable.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/index/IndexReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/index/IndexWriter.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/index/InternalNodeBuilder.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/index/LeafNodeBuilder.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/index/StagedIndexReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/plink/ExportPlink.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/plink/LoadPlink.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/reference/FASTAReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/reference/LiftOver.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/tabix/TabixReader.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/vcf/ExportVCF.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/vcf/LoadVCF.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/io/vcf/TabixReadVCFIterator.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/kryo/HailKryoRegistrator.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/linalg/BLAS.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/linalg/BlockMatrix.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/linalg/GridPartitioner.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/linalg/LAPACK.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/linalg/LinalgCodeUtils.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/linalg/RowMatrix.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/linalg/RowPartitioner.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/Blocks.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/CFG.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/Emit.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/InitializeLocals.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/Liveness.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/Locals.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/PST.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/Pretty.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/SimplifyControl.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/SplitLargeBlocks.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/SplitMethod.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/X.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/lir/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/FilterPartitions.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/ForceCount.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/IBD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/IBSFFI.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/LinearRegression.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/LocalLDPrune.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/LocalWhitening.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/LogisticRegression.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/MatrixExportEntriesByCol.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/NPartitions.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/Nirvana.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/PCA.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/PCRelate.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/PoissonRegression.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/Skat.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/methods/VEP.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/misc/BGZipBlocks.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/rvd/AbstractRVDSpec.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/rvd/KeyedRVD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/rvd/PartitionBoundOrdering.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/rvd/RVD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/rvd/RVDContext.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/rvd/RVDPartitionInfo.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/rvd/RVDPartitioner.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/rvd/RVDType.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/services/BatchClient.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/services/BatchConfig.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/services/DeployConfig.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/services/JSONLogLayout.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/services/NettyProxy.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/services/README (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/services/oauth2.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/services/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/services/requests.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/services/tls/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/sparkextras/BlockedRDD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/sparkextras/ContextPairRDDFunctions.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/sparkextras/ContextRDD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/sparkextras/IndexReadRDD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/sparkextras/MapPartitionsWithValueRDD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/sparkextras/MultiWayZipPartitionsRDD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/sparkextras/OriginUnionRDD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/sparkextras/ReorderedPartitionsRDD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/sparkextras/RepartitionedOrderedRDD2.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/stats/GeneralizedChiSquaredDistribution.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/stats/LeveneHaldane.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/stats/LinearMixedModel.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/stats/LinearRegressionModel.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/stats/LogisticRegressionModel.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/stats/PoissonRegressionModel.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/stats/RegressionUtils.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/stats/eigSymD.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/stats/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/BaseType.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/Box.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/MapTypes.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/TypeWithRequiredness.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EBaseStruct.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EBinary.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EBlockMatrixNDArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EBoolean.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EContainer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EFloat32.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EFloat64.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EInt32.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EInt64.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/ENDArrayColumnMajor.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/ENumpyBinaryNDArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/ERNGState.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EStructOfArrays.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EType.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/encoded/EUnsortedSet.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PArrayBackedContainer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PBaseStruct.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PBinary.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PBoolean.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCall.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalBaseStruct.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalBinary.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalCall.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalDict.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalInterval.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalLocus.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalNDArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalSet.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalString.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalStruct.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PCanonicalTuple.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PContainer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PDict.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PField.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PFloat32.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PFloat64.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PInt32.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PInt64.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PInterval.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PIterable.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PLocus.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PNDArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PNumeric.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PPrimitive.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PSet.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PString.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PStruct.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PSubsetStruct.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PTuple.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PType.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PUnrealizable.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/PVoid.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/StoredSTypePType.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/SCode.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/SType.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/SingleCodeSCode.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SInsertFieldsStruct.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaBytes.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaString.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SRNGState.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SStackInterval.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SStackStruct.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SStringPointer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SStructView.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/concrete/SUnreachable.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/SBinary.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/SCall.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/SContainer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/SInterval.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/SLocus.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/SNDArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/SStream.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/SString.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/SVoid.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/interfaces/package.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/primitives/SBoolean.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat32.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat64.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/primitives/SInt32.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/primitives/SInt64.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/physical/stypes/primitives/SPrimitive.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/BlockMatrixType.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/Field.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/MatrixType.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TBaseStruct.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TBinary.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TBoolean.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TCall.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TContainer.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TDict.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TFloat32.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TFloat64.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TInt32.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TInt64.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TIntegral.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TInterval.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TIterable.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TLocus.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TNDArray.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TNumeric.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TRNGState.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TSet.scala (100%)
 rename hail/{ => modules}/src/main/scala/is/hail/types/virtual/TStream.scala (100%)
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 rename hail/{ => modules}/src/test/resources/gvcfs/HG00096.g.vcf.gz.mt/index/part-0-cce3bb95-cfb5-49f4-b53e-0965d8a827cf.idx/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/gvcfs/HG00096.g.vcf.gz.mt/metadata.json.gz (100%)
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 rename hail/{ => modules}/src/test/resources/random_vcfs/0.vcf.bgz (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/entries/rows/parts/part-18-2d6e1f0f-5062-4722-b8e4-c6c84215297b (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/entries/rows/parts/part-19-2dff4095-1c1b-4679-a079-0f8b3dfba161 (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/entries/rows/parts/part-20-42275eb3-6cc3-4682-ae1b-750ca916472b (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/entries/rows/parts/part-21-b780d57c-d980-4635-b2de-ad05e9396b71 (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/entries/rows/parts/part-22-0f507e63-746e-487c-b02e-b4e021e3ac70 (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/entries/rows/parts/part-23-443e84d9-8ca6-4192-9796-e589c2762ecd (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/globals/README.txt (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/globals/rows/metadata.json.gz (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/index/part-00-abc40412-8974-450d-b07e-998169063959.idx/index (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/index/part-00-abc40412-8974-450d-b07e-998169063959.idx/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/index/part-01-a7c2fa85-0ace-4e7e-a3dd-c6fa231030ae.idx/index (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/index/part-02-dd2dfbc3-b8e4-4d7f-b165-900f17f0f288.idx/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/index/part-03-fff07b37-1b36-47c3-ac12-e472c3de8107.idx/index (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/index/part-03-fff07b37-1b36-47c3-ac12-e472c3de8107.idx/metadata.json.gz (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/reference_data/rows/rows/parts/part-21-b780d57c-d980-4635-b2de-ad05e9396b71 (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/entries/rows/parts/part-19-97053c54-2092-4715-92c4-c78e4d4a3293 (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/entries/rows/parts/part-21-acd46275-b0a7-421a-a876-8b118f9092f0 (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/entries/rows/parts/part-22-06299478-4dd6-482f-a12c-ee79266f5c7b (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/entries/rows/parts/part-23-5d25ccaf-9dfd-4d8e-b97c-d990509eb982 (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/globals/README.txt (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/globals/_SUCCESS (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/globals/globals/parts/part-0 (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-00-55129387-976d-4fab-b811-fb49223e81fa.idx/index (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-00-55129387-976d-4fab-b811-fb49223e81fa.idx/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-01-81e01510-13f6-4654-b5af-cf004cee1146.idx/index (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-02-882f8dda-869e-4db0-bb44-0db6949d2d99.idx/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-03-9596e6ff-9116-42f1-93ac-c3f4dd9dc4ec.idx/index (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-04-5d5af87f-2c97-411a-bfa1-70dd8e928247.idx/index (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-04-5d5af87f-2c97-411a-bfa1-70dd8e928247.idx/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-05-e57f9497-2cd1-468b-bfa6-cd4b435d1d11.idx/index (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-08-40a18a67-28b3-44bf-9ab1-7e21d8d1e1fb.idx/index (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-21-acd46275-b0a7-421a-a876-8b118f9092f0.idx/index (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-21-acd46275-b0a7-421a-a876-8b118f9092f0.idx/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-22-06299478-4dd6-482f-a12c-ee79266f5c7b.idx/index (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-23-5d25ccaf-9dfd-4d8e-b97c-d990509eb982.idx/index (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/index/part-23-5d25ccaf-9dfd-4d8e-b97c-d990509eb982.idx/metadata.json.gz (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/rows/rows/parts/part-00-55129387-976d-4fab-b811-fb49223e81fa (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/rows/rows/parts/part-09-293c5a2f-cfce-4c70-8585-8a1a8eb0d27d (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/rows/rows/parts/part-11-27f273f6-d3d1-4c90-8bf7-9afd0f21edbf (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/rows/rows/parts/part-14-31c709a5-a1e5-4b16-be3b-d099cc1f0b9f (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/rows/rows/parts/part-19-97053c54-2092-4715-92c4-c78e4d4a3293 (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/rows/rows/parts/part-20-5e9bcf6d-c764-41b3-b904-30678c044eb6 (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/rows/rows/parts/part-21-acd46275-b0a7-421a-a876-8b118f9092f0 (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/rows/rows/parts/part-22-06299478-4dd6-482f-a12c-ee79266f5c7b (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_2samples_starts.vds/variant_data/rows/rows/parts/part-23-5d25ccaf-9dfd-4d8e-b97c-d990509eb982 (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_chr22_5_samples.vds/extra_reference_globals.json (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_chr22_5_samples.vds/reference_data/index/part-0-16-0-0-7c066333-b6bd-3457-a7e3-b23a8bb0248f.idx/index (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_chr22_5_samples.vds/reference_data/index/part-0-16-0-0-7c066333-b6bd-3457-a7e3-b23a8bb0248f.idx/metadata.json.gz (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_chr22_5_samples.vds/reference_data/rows/rows/parts/part-0-16-0-0-7c066333-b6bd-3457-a7e3-b23a8bb0248f (100%)
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 rename hail/{ => modules}/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/index/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825.idx/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/_SUCCESS (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/metadata.json.gz (100%)
 rename hail/{ => modules}/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825 (100%)
 rename hail/{ => modules}/src/test/resources/vep_grch38_input_req_indexed_cache.tsv (100%)
 rename hail/{ => modules}/src/test/resources/width_scale_tests/1024.tsv (100%)
 rename hail/{ => modules}/src/test/resources/width_scale_tests/16384.tsv (100%)
 rename hail/{ => modules}/src/test/resources/width_scale_tests/2048.tsv (100%)
 rename hail/{ => modules}/src/test/resources/width_scale_tests/256.tsv (100%)
 rename hail/{ => modules}/src/test/resources/width_scale_tests/3072.tsv (100%)
 rename hail/{ => modules}/src/test/resources/width_scale_tests/4096.tsv (100%)
 rename hail/{ => modules}/src/test/resources/width_scale_tests/512.tsv (100%)
 rename hail/{ => modules}/src/test/resources/width_scale_tests/8192.tsv (100%)
 rename hail/{ => modules}/src/test/resources/x-chromosome.vcf (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/HailContextSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/HailSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/LogTestListener.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/TestUtils.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/TestUtilsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/annotations/AnnotationsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/annotations/ApproxCDFAggregatorSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/annotations/RegionSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/annotations/ScalaToRegionValue.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/annotations/StagedConstructorSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/annotations/UnsafeSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/asm4s/ASM4SSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/asm4s/CodeSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/asm4s/Foo.java (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/backend/ServiceBackendSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ParserSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/Aggregators2Suite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/AggregatorsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/ArrayDeforestationSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/ArrayFunctionsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/BlockMatrixIRSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/CallFunctionsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/DictFunctionsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/DistinctlyKeyedSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/EmitStreamSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/EncodedLiteralSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/FakeTableReader.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/FoldConstantsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/ForwardLetsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/FunctionSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/GenotypeFunctionsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/IRSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/IntervalSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/LiftLiteralsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/LocusFunctionsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/LoweringPipelineSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/MathFunctionsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/MatrixIRSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/MemoryLeakSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/MissingArrayBuilderSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/OrderingSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/PruneSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/RandomSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/RequirednessSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/SetFunctionsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/SimplifySuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/StagedBTreeSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/StagedMinHeapSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/StringFunctionsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/StringLengthSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/StringSliceSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/TableIRSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/TakeByAggregatorSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/TestUtils.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/TrapNodeSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/UtilFunctionsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/agg/DownsampleSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/analyses/SemanticHashSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/expr/ir/table/TableGenSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/io/AvroReaderSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/io/ByteArrayReaderSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/io/IndexBTreeSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/io/IndexSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/io/TabixSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/io/compress/BGzipCodecSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/io/fs/AzureStorageFSSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/io/fs/FSSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/io/fs/FakeFS.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/io/fs/GoogleStorageFSSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/linalg/BlockMatrixSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/linalg/GridPartitionerSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/linalg/RowMatrixSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/linalg/RowPartitionerSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/lir/CompileTimeRequirednessSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/lir/LIRSplitSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/methods/ExprSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/methods/LocalLDPruneSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/methods/MultiArray2Suite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/methods/SkatSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/rvd/RVDPartitionerSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/services/BatchClientSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/stats/FisherExactTestSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/stats/GeneralizedChiSquaredDistributionSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/stats/LeveneHaldaneSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/stats/LogisticRegressionModelSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/stats/StatsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/stats/eigSymDSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/testUtils/AltAllele.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/testUtils/Variant.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/encoded/ETypeSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/physical/PBaseStructSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/physical/PBinarySuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/physical/PCallSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/physical/PContainerTest.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/physical/PIntervalSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/physical/PNDArraySuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/physical/PTypeSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/physical/PhysicalTestUtils.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/types/virtual/TStructSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/ArrayBuilderSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/ArrayStackSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/BinaryHeapSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/BitVectorSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/BufferedAggregatorIteratorSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/FlipbookIteratorSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/GraphSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/HashMethodsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/IntervalSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/PartitionCountsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/RichArraySuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/RichDenseMatrixDoubleSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/RichIndexedRowMatrixSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/RichRDDSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/RowIntervalSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/SemanticVersionSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/SpillingCollectIteratorSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/TreeTraversalSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/UnionFindSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/UtilsSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/variant/GenotypeSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/variant/LocusIntervalSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/variant/ReferenceGenomeSuite.scala (100%)
 rename hail/{ => modules}/src/test/scala/is/hail/variant/vsm/PartitioningSuite.scala (100%)

diff --git a/build.yaml b/build.yaml
index cf1938b499d..4451542cb1b 100644
--- a/build.yaml
+++ b/build.yaml
@@ -832,7 +832,7 @@ steps:
       cd /io/repo/hail
 
       time tar czf test.tar.gz -C python test pytest.ini
-      time tar czf resources.tar.gz -C src/test resources
+      time tar czf resources.tar.gz -C modules/src/test resources
       time tar czf data.tar.gz -C python/hail/docs data
       time TESTNG_SPLITS=5 python3 generate_splits.py
       time tar czf splits.tar.gz testng-splits-*.xml
@@ -965,7 +965,7 @@ steps:
       export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
       export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
       python3 -m hailtop.aiotools.copy 'null' '[
-      {"from": "src/test/resources",
+      {"from": "modules/src/test/resources",
        "to":   "{{ global.test_storage_uri }}/{{ token }}/test/resources"},
       {"from": "python/hail/docs/data",
        "to":   "{{ global.test_storage_uri }}/{{ token }}/doctest/data"}
@@ -976,8 +976,8 @@ steps:
           valueFrom: default_ns.name
         mountPath: /test-gsa-key
     inputs:
-      - from: /repo/hail/src/test/resources
-        to: /io/repo/hail/src/test/resources
+      - from: /repo/hail/modules/src/test/resources
+        to: /io/repo/hail/modules/src/test/resources
       - from: /repo/hail/python/hail/docs/data
         to: /io/repo/hail/python/hail/docs/data
     dependsOn:
@@ -996,8 +996,8 @@ steps:
     script: |
       set -ex
       cd /io
-      mkdir -p src/test
-      tar xzf resources.tar.gz -C src/test
+      mkdir -p modules/src/test
+      tar xzf resources.tar.gz -C modules/src/test
       tar xzf splits.tar.gz
       export HAIL_TEST_SKIP_R=1
       java -cp hail-test.jar:$SPARK_HOME/jars/* org.testng.TestNG -listener is.hail.LogTestListener testng-splits-$HAIL_RUN_IMAGE_SPLIT_INDEX.xml
@@ -3636,8 +3636,8 @@ steps:
     script: |
       set -ex
       cd /io
-      mkdir -p src/test
-      tar xzf resources.tar.gz -C src/test
+      mkdir -p modules/src/test
+      tar xzf resources.tar.gz -C modules/src/test
 
       export HAIL_CLOUD={{ global.cloud }}
       export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
@@ -3696,8 +3696,8 @@ steps:
       export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
 
       cd /io
-      mkdir -p src/test
-      tar xzf resources.tar.gz -C src/test
+      mkdir -p modules/src/test
+      tar xzf resources.tar.gz -C modules/src/test
       java -Xms7500M -Xmx7500M \
            -cp hail-test.jar:$SPARK_HOME/jars/* \
            org.testng.TestNG \
diff --git a/hail/build.mill b/hail/build.mill
index 35f3e2be318..9afdd012661 100644
--- a/hail/build.mill
+++ b/hail/build.mill
@@ -11,6 +11,7 @@ import mill.scalalib.Assembly._
 import mill.scalalib.TestModule.TestNg
 import mill.scalalib.scalafmt.ScalafmtModule
 import mill.util.Jvm
+import os.Path
 
 object Settings {
   val hailMajorMinorVersion = "0.2"
@@ -126,6 +127,8 @@ trait HailScalaModule extends SbtModule with ScalafmtModule with ScalafixModule
 
 object `package` extends RootModule with HailScalaModule { outer =>
 
+  override def millSourcePath: Path = super.millSourcePath / "modules"
+
   object env extends Module {
     def scalaVersion: T[String] = Task.Input {
       val v = T.ctx().env.getOrElse("SCALA_VERSION", "2.12.20")
diff --git a/hail/src/debug/java/is/hail/annotations/Memory.java b/hail/modules/src/debug/java/is/hail/annotations/Memory.java
similarity index 100%
rename from hail/src/debug/java/is/hail/annotations/Memory.java
rename to hail/modules/src/debug/java/is/hail/annotations/Memory.java
diff --git a/hail/src/dist/scripts/Plot_gq20bydp.R b/hail/modules/src/dist/scripts/Plot_gq20bydp.R
similarity index 100%
rename from hail/src/dist/scripts/Plot_gq20bydp.R
rename to hail/modules/src/dist/scripts/Plot_gq20bydp.R
diff --git a/hail/src/main/c/ApproximateQuantiles_test.cpp b/hail/modules/src/main/c/ApproximateQuantiles_test.cpp
similarity index 100%
rename from hail/src/main/c/ApproximateQuantiles_test.cpp
rename to hail/modules/src/main/c/ApproximateQuantiles_test.cpp
diff --git a/hail/src/main/c/Decoder.cpp b/hail/modules/src/main/c/Decoder.cpp
similarity index 100%
rename from hail/src/main/c/Decoder.cpp
rename to hail/modules/src/main/c/Decoder.cpp
diff --git a/hail/src/main/c/Encoder.cpp b/hail/modules/src/main/c/Encoder.cpp
similarity index 100%
rename from hail/src/main/c/Encoder.cpp
rename to hail/modules/src/main/c/Encoder.cpp
diff --git a/hail/src/main/c/FS.cpp b/hail/modules/src/main/c/FS.cpp
similarity index 100%
rename from hail/src/main/c/FS.cpp
rename to hail/modules/src/main/c/FS.cpp
diff --git a/hail/src/main/c/Logging.cpp b/hail/modules/src/main/c/Logging.cpp
similarity index 100%
rename from hail/src/main/c/Logging.cpp
rename to hail/modules/src/main/c/Logging.cpp
diff --git a/hail/src/main/c/Makefile b/hail/modules/src/main/c/Makefile
similarity index 100%
rename from hail/src/main/c/Makefile
rename to hail/modules/src/main/c/Makefile
diff --git a/hail/src/main/c/NativeBoot.cpp b/hail/modules/src/main/c/NativeBoot.cpp
similarity index 100%
rename from hail/src/main/c/NativeBoot.cpp
rename to hail/modules/src/main/c/NativeBoot.cpp
diff --git a/hail/src/main/c/NativeCodeSuite.cpp b/hail/modules/src/main/c/NativeCodeSuite.cpp
similarity index 100%
rename from hail/src/main/c/NativeCodeSuite.cpp
rename to hail/modules/src/main/c/NativeCodeSuite.cpp
diff --git a/hail/src/main/c/NativeLongFunc.cpp b/hail/modules/src/main/c/NativeLongFunc.cpp
similarity index 100%
rename from hail/src/main/c/NativeLongFunc.cpp
rename to hail/modules/src/main/c/NativeLongFunc.cpp
diff --git a/hail/src/main/c/NativeModule.cpp b/hail/modules/src/main/c/NativeModule.cpp
similarity index 100%
rename from hail/src/main/c/NativeModule.cpp
rename to hail/modules/src/main/c/NativeModule.cpp
diff --git a/hail/src/main/c/NativePtr.cpp b/hail/modules/src/main/c/NativePtr.cpp
similarity index 100%
rename from hail/src/main/c/NativePtr.cpp
rename to hail/modules/src/main/c/NativePtr.cpp
diff --git a/hail/src/main/c/NativeStatus.cpp b/hail/modules/src/main/c/NativeStatus.cpp
similarity index 100%
rename from hail/src/main/c/NativeStatus.cpp
rename to hail/modules/src/main/c/NativeStatus.cpp
diff --git a/hail/src/main/c/ObjectArray.cpp b/hail/modules/src/main/c/ObjectArray.cpp
similarity index 100%
rename from hail/src/main/c/ObjectArray.cpp
rename to hail/modules/src/main/c/ObjectArray.cpp
diff --git a/hail/src/main/c/PartitionIterators.cpp b/hail/modules/src/main/c/PartitionIterators.cpp
similarity index 100%
rename from hail/src/main/c/PartitionIterators.cpp
rename to hail/modules/src/main/c/PartitionIterators.cpp
diff --git a/hail/src/main/c/README.md b/hail/modules/src/main/c/README.md
similarity index 100%
rename from hail/src/main/c/README.md
rename to hail/modules/src/main/c/README.md
diff --git a/hail/src/main/c/Region.cpp b/hail/modules/src/main/c/Region.cpp
similarity index 100%
rename from hail/src/main/c/Region.cpp
rename to hail/modules/src/main/c/Region.cpp
diff --git a/hail/src/main/c/Region_test.cpp b/hail/modules/src/main/c/Region_test.cpp
similarity index 100%
rename from hail/src/main/c/Region_test.cpp
rename to hail/modules/src/main/c/Region_test.cpp
diff --git a/hail/src/main/c/Upcalls.cpp b/hail/modules/src/main/c/Upcalls.cpp
similarity index 100%
rename from hail/src/main/c/Upcalls.cpp
rename to hail/modules/src/main/c/Upcalls.cpp
diff --git a/hail/src/main/c/cache-tests.cpp b/hail/modules/src/main/c/cache-tests.cpp
similarity index 100%
rename from hail/src/main/c/cache-tests.cpp
rename to hail/modules/src/main/c/cache-tests.cpp
diff --git a/hail/src/main/c/ibs.cpp b/hail/modules/src/main/c/ibs.cpp
similarity index 100%
rename from hail/src/main/c/ibs.cpp
rename to hail/modules/src/main/c/ibs.cpp
diff --git a/hail/src/main/c/ibs.h b/hail/modules/src/main/c/ibs.h
similarity index 100%
rename from hail/src/main/c/ibs.h
rename to hail/modules/src/main/c/ibs.h
diff --git a/hail/src/main/c/test.cpp b/hail/modules/src/main/c/test.cpp
similarity index 100%
rename from hail/src/main/c/test.cpp
rename to hail/modules/src/main/c/test.cpp
diff --git a/hail/src/main/c/testutils/style.css b/hail/modules/src/main/c/testutils/style.css
similarity index 100%
rename from hail/src/main/c/testutils/style.css
rename to hail/modules/src/main/c/testutils/style.css
diff --git a/hail/src/main/c/testutils/test-reporter.xslt b/hail/modules/src/main/c/testutils/test-reporter.xslt
similarity index 100%
rename from hail/src/main/c/testutils/test-reporter.xslt
rename to hail/modules/src/main/c/testutils/test-reporter.xslt
diff --git a/hail/src/main/c/testutils/unit-tests.cpp b/hail/modules/src/main/c/testutils/unit-tests.cpp
similarity index 100%
rename from hail/src/main/c/testutils/unit-tests.cpp
rename to hail/modules/src/main/c/testutils/unit-tests.cpp
diff --git a/hail/src/main/java/is/hail/expr/ir/MatrixWriterConstants.java b/hail/modules/src/main/java/is/hail/expr/ir/MatrixWriterConstants.java
similarity index 100%
rename from hail/src/main/java/is/hail/expr/ir/MatrixWriterConstants.java
rename to hail/modules/src/main/java/is/hail/expr/ir/MatrixWriterConstants.java
diff --git a/hail/src/main/java/is/hail/io/compress/BGzipCodec.java b/hail/modules/src/main/java/is/hail/io/compress/BGzipCodec.java
similarity index 100%
rename from hail/src/main/java/is/hail/io/compress/BGzipCodec.java
rename to hail/modules/src/main/java/is/hail/io/compress/BGzipCodec.java
diff --git a/hail/src/main/java/is/hail/io/compress/BGzipCodecGZ.java b/hail/modules/src/main/java/is/hail/io/compress/BGzipCodecGZ.java
similarity index 100%
rename from hail/src/main/java/is/hail/io/compress/BGzipCodecGZ.java
rename to hail/modules/src/main/java/is/hail/io/compress/BGzipCodecGZ.java
diff --git a/hail/src/main/java/is/hail/io/compress/BGzipCodecTbi.java b/hail/modules/src/main/java/is/hail/io/compress/BGzipCodecTbi.java
similarity index 100%
rename from hail/src/main/java/is/hail/io/compress/BGzipCodecTbi.java
rename to hail/modules/src/main/java/is/hail/io/compress/BGzipCodecTbi.java
diff --git a/hail/src/main/java/is/hail/io/compress/BGzipConstants.java b/hail/modules/src/main/java/is/hail/io/compress/BGzipConstants.java
similarity index 100%
rename from hail/src/main/java/is/hail/io/compress/BGzipConstants.java
rename to hail/modules/src/main/java/is/hail/io/compress/BGzipConstants.java
diff --git a/hail/src/main/java/is/hail/io/compress/BGzipInputStream.java b/hail/modules/src/main/java/is/hail/io/compress/BGzipInputStream.java
similarity index 100%
rename from hail/src/main/java/is/hail/io/compress/BGzipInputStream.java
rename to hail/modules/src/main/java/is/hail/io/compress/BGzipInputStream.java
diff --git a/hail/src/main/java/is/hail/io/compress/BGzipOutputStream.java b/hail/modules/src/main/java/is/hail/io/compress/BGzipOutputStream.java
similarity index 100%
rename from hail/src/main/java/is/hail/io/compress/BGzipOutputStream.java
rename to hail/modules/src/main/java/is/hail/io/compress/BGzipOutputStream.java
diff --git a/hail/src/main/java/is/hail/io/compress/ComposableBGzipCodec.java b/hail/modules/src/main/java/is/hail/io/compress/ComposableBGzipCodec.java
similarity index 100%
rename from hail/src/main/java/is/hail/io/compress/ComposableBGzipCodec.java
rename to hail/modules/src/main/java/is/hail/io/compress/ComposableBGzipCodec.java
diff --git a/hail/src/main/java/is/hail/io/compress/ComposableBGzipOutputStream.java b/hail/modules/src/main/java/is/hail/io/compress/ComposableBGzipOutputStream.java
similarity index 100%
rename from hail/src/main/java/is/hail/io/compress/ComposableBGzipOutputStream.java
rename to hail/modules/src/main/java/is/hail/io/compress/ComposableBGzipOutputStream.java
diff --git a/hail/src/main/java/is/hail/io/fs/Positioned.java b/hail/modules/src/main/java/is/hail/io/fs/Positioned.java
similarity index 100%
rename from hail/src/main/java/is/hail/io/fs/Positioned.java
rename to hail/modules/src/main/java/is/hail/io/fs/Positioned.java
diff --git a/hail/src/main/java/is/hail/io/fs/Seekable.java b/hail/modules/src/main/java/is/hail/io/fs/Seekable.java
similarity index 100%
rename from hail/src/main/java/is/hail/io/fs/Seekable.java
rename to hail/modules/src/main/java/is/hail/io/fs/Seekable.java
diff --git a/hail/src/main/resources/META-INF/services/com.azure.core.http.HttpClientProvider b/hail/modules/src/main/resources/META-INF/services/com.azure.core.http.HttpClientProvider
similarity index 100%
rename from hail/src/main/resources/META-INF/services/com.azure.core.http.HttpClientProvider
rename to hail/modules/src/main/resources/META-INF/services/com.azure.core.http.HttpClientProvider
diff --git a/hail/src/main/resources/META-INF/services/com.ctc.wstx.shaded.msv.relaxng_datatype.DatatypeLibraryFactory b/hail/modules/src/main/resources/META-INF/services/com.ctc.wstx.shaded.msv.relaxng_datatype.DatatypeLibraryFactory
similarity index 100%
rename from hail/src/main/resources/META-INF/services/com.ctc.wstx.shaded.msv.relaxng_datatype.DatatypeLibraryFactory
rename to hail/modules/src/main/resources/META-INF/services/com.ctc.wstx.shaded.msv.relaxng_datatype.DatatypeLibraryFactory
diff --git a/hail/src/main/resources/META-INF/services/com.ctc.wstx.stax.WstxInputFactory b/hail/modules/src/main/resources/META-INF/services/com.ctc.wstx.stax.WstxInputFactory
similarity index 100%
rename from hail/src/main/resources/META-INF/services/com.ctc.wstx.stax.WstxInputFactory
rename to hail/modules/src/main/resources/META-INF/services/com.ctc.wstx.stax.WstxInputFactory
diff --git a/hail/src/main/resources/META-INF/services/com.fasterxml.jackson.core.JsonFactory b/hail/modules/src/main/resources/META-INF/services/com.fasterxml.jackson.core.JsonFactory
similarity index 100%
rename from hail/src/main/resources/META-INF/services/com.fasterxml.jackson.core.JsonFactory
rename to hail/modules/src/main/resources/META-INF/services/com.fasterxml.jackson.core.JsonFactory
diff --git a/hail/src/main/resources/META-INF/services/com.fasterxml.jackson.core.ObjectCodec b/hail/modules/src/main/resources/META-INF/services/com.fasterxml.jackson.core.ObjectCodec
similarity index 100%
rename from hail/src/main/resources/META-INF/services/com.fasterxml.jackson.core.ObjectCodec
rename to hail/modules/src/main/resources/META-INF/services/com.fasterxml.jackson.core.ObjectCodec
diff --git a/hail/src/main/resources/META-INF/services/com.fasterxml.jackson.databind.Module b/hail/modules/src/main/resources/META-INF/services/com.fasterxml.jackson.databind.Module
similarity index 100%
rename from hail/src/main/resources/META-INF/services/com.fasterxml.jackson.databind.Module
rename to hail/modules/src/main/resources/META-INF/services/com.fasterxml.jackson.databind.Module
diff --git a/hail/src/main/resources/META-INF/services/io.micrometer.context.ContextAccessor b/hail/modules/src/main/resources/META-INF/services/io.micrometer.context.ContextAccessor
similarity index 100%
rename from hail/src/main/resources/META-INF/services/io.micrometer.context.ContextAccessor
rename to hail/modules/src/main/resources/META-INF/services/io.micrometer.context.ContextAccessor
diff --git a/hail/src/main/resources/META-INF/services/is.hail.shadedazure.com.azure.core.http.HttpClientProvider b/hail/modules/src/main/resources/META-INF/services/is.hail.shadedazure.com.azure.core.http.HttpClientProvider
similarity index 100%
rename from hail/src/main/resources/META-INF/services/is.hail.shadedazure.com.azure.core.http.HttpClientProvider
rename to hail/modules/src/main/resources/META-INF/services/is.hail.shadedazure.com.azure.core.http.HttpClientProvider
diff --git a/hail/src/main/resources/META-INF/services/javax.xml.stream.XMLEventFactory b/hail/modules/src/main/resources/META-INF/services/javax.xml.stream.XMLEventFactory
similarity index 100%
rename from hail/src/main/resources/META-INF/services/javax.xml.stream.XMLEventFactory
rename to hail/modules/src/main/resources/META-INF/services/javax.xml.stream.XMLEventFactory
diff --git a/hail/src/main/resources/META-INF/services/javax.xml.stream.XMLInputFactory b/hail/modules/src/main/resources/META-INF/services/javax.xml.stream.XMLInputFactory
similarity index 100%
rename from hail/src/main/resources/META-INF/services/javax.xml.stream.XMLInputFactory
rename to hail/modules/src/main/resources/META-INF/services/javax.xml.stream.XMLInputFactory
diff --git a/hail/src/main/resources/META-INF/services/javax.xml.stream.XMLOutputFactory b/hail/modules/src/main/resources/META-INF/services/javax.xml.stream.XMLOutputFactory
similarity index 100%
rename from hail/src/main/resources/META-INF/services/javax.xml.stream.XMLOutputFactory
rename to hail/modules/src/main/resources/META-INF/services/javax.xml.stream.XMLOutputFactory
diff --git a/hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory b/hail/modules/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory
similarity index 100%
rename from hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory
rename to hail/modules/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory
diff --git a/hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.dtd b/hail/modules/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.dtd
similarity index 100%
rename from hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.dtd
rename to hail/modules/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.dtd
diff --git a/hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.relaxng b/hail/modules/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.relaxng
similarity index 100%
rename from hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.relaxng
rename to hail/modules/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.relaxng
diff --git a/hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.w3c b/hail/modules/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.w3c
similarity index 100%
rename from hail/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.w3c
rename to hail/modules/src/main/resources/META-INF/services/org.codehaus.stax2.validation.XMLValidationSchemaFactory.w3c
diff --git a/hail/src/main/resources/META-INF/services/reactor.blockhound.integration.BlockHoundIntegration b/hail/modules/src/main/resources/META-INF/services/reactor.blockhound.integration.BlockHoundIntegration
similarity index 100%
rename from hail/src/main/resources/META-INF/services/reactor.blockhound.integration.BlockHoundIntegration
rename to hail/modules/src/main/resources/META-INF/services/reactor.blockhound.integration.BlockHoundIntegration
diff --git a/hail/src/main/resources/include/README b/hail/modules/src/main/resources/include/README
similarity index 100%
rename from hail/src/main/resources/include/README
rename to hail/modules/src/main/resources/include/README
diff --git a/hail/src/main/resources/include/hail/ApproximateQuantiles.h b/hail/modules/src/main/resources/include/hail/ApproximateQuantiles.h
similarity index 100%
rename from hail/src/main/resources/include/hail/ApproximateQuantiles.h
rename to hail/modules/src/main/resources/include/hail/ApproximateQuantiles.h
diff --git a/hail/src/main/resources/include/hail/ArrayBuilder.h b/hail/modules/src/main/resources/include/hail/ArrayBuilder.h
similarity index 100%
rename from hail/src/main/resources/include/hail/ArrayBuilder.h
rename to hail/modules/src/main/resources/include/hail/ArrayBuilder.h
diff --git a/hail/src/main/resources/include/hail/ArraySorter.h b/hail/modules/src/main/resources/include/hail/ArraySorter.h
similarity index 100%
rename from hail/src/main/resources/include/hail/ArraySorter.h
rename to hail/modules/src/main/resources/include/hail/ArraySorter.h
diff --git a/hail/src/main/resources/include/hail/Decoder.h b/hail/modules/src/main/resources/include/hail/Decoder.h
similarity index 100%
rename from hail/src/main/resources/include/hail/Decoder.h
rename to hail/modules/src/main/resources/include/hail/Decoder.h
diff --git a/hail/src/main/resources/include/hail/Encoder.h b/hail/modules/src/main/resources/include/hail/Encoder.h
similarity index 100%
rename from hail/src/main/resources/include/hail/Encoder.h
rename to hail/modules/src/main/resources/include/hail/Encoder.h
diff --git a/hail/src/main/resources/include/hail/FS.h b/hail/modules/src/main/resources/include/hail/FS.h
similarity index 100%
rename from hail/src/main/resources/include/hail/FS.h
rename to hail/modules/src/main/resources/include/hail/FS.h
diff --git a/hail/src/main/resources/include/hail/Logging.h b/hail/modules/src/main/resources/include/hail/Logging.h
similarity index 100%
rename from hail/src/main/resources/include/hail/Logging.h
rename to hail/modules/src/main/resources/include/hail/Logging.h
diff --git a/hail/src/main/resources/include/hail/NDArray.h b/hail/modules/src/main/resources/include/hail/NDArray.h
similarity index 100%
rename from hail/src/main/resources/include/hail/NDArray.h
rename to hail/modules/src/main/resources/include/hail/NDArray.h
diff --git a/hail/src/main/resources/include/hail/NativeMethod.h b/hail/modules/src/main/resources/include/hail/NativeMethod.h
similarity index 100%
rename from hail/src/main/resources/include/hail/NativeMethod.h
rename to hail/modules/src/main/resources/include/hail/NativeMethod.h
diff --git a/hail/src/main/resources/include/hail/NativeModule.h b/hail/modules/src/main/resources/include/hail/NativeModule.h
similarity index 100%
rename from hail/src/main/resources/include/hail/NativeModule.h
rename to hail/modules/src/main/resources/include/hail/NativeModule.h
diff --git a/hail/src/main/resources/include/hail/NativeObj.h b/hail/modules/src/main/resources/include/hail/NativeObj.h
similarity index 100%
rename from hail/src/main/resources/include/hail/NativeObj.h
rename to hail/modules/src/main/resources/include/hail/NativeObj.h
diff --git a/hail/src/main/resources/include/hail/NativePtr.h b/hail/modules/src/main/resources/include/hail/NativePtr.h
similarity index 100%
rename from hail/src/main/resources/include/hail/NativePtr.h
rename to hail/modules/src/main/resources/include/hail/NativePtr.h
diff --git a/hail/src/main/resources/include/hail/NativeStatus.h b/hail/modules/src/main/resources/include/hail/NativeStatus.h
similarity index 100%
rename from hail/src/main/resources/include/hail/NativeStatus.h
rename to hail/modules/src/main/resources/include/hail/NativeStatus.h
diff --git a/hail/src/main/resources/include/hail/ObjectArray.h b/hail/modules/src/main/resources/include/hail/ObjectArray.h
similarity index 100%
rename from hail/src/main/resources/include/hail/ObjectArray.h
rename to hail/modules/src/main/resources/include/hail/ObjectArray.h
diff --git a/hail/src/main/resources/include/hail/Ordering.h b/hail/modules/src/main/resources/include/hail/Ordering.h
similarity index 100%
rename from hail/src/main/resources/include/hail/Ordering.h
rename to hail/modules/src/main/resources/include/hail/Ordering.h
diff --git a/hail/src/main/resources/include/hail/PartitionIterators.h b/hail/modules/src/main/resources/include/hail/PartitionIterators.h
similarity index 100%
rename from hail/src/main/resources/include/hail/PartitionIterators.h
rename to hail/modules/src/main/resources/include/hail/PartitionIterators.h
diff --git a/hail/src/main/resources/include/hail/Region.h b/hail/modules/src/main/resources/include/hail/Region.h
similarity index 100%
rename from hail/src/main/resources/include/hail/Region.h
rename to hail/modules/src/main/resources/include/hail/Region.h
diff --git a/hail/src/main/resources/include/hail/RegionPool.h b/hail/modules/src/main/resources/include/hail/RegionPool.h
similarity index 100%
rename from hail/src/main/resources/include/hail/RegionPool.h
rename to hail/modules/src/main/resources/include/hail/RegionPool.h
diff --git a/hail/src/main/resources/include/hail/SparkUtils.h b/hail/modules/src/main/resources/include/hail/SparkUtils.h
similarity index 100%
rename from hail/src/main/resources/include/hail/SparkUtils.h
rename to hail/modules/src/main/resources/include/hail/SparkUtils.h
diff --git a/hail/src/main/resources/include/hail/Upcalls.h b/hail/modules/src/main/resources/include/hail/Upcalls.h
similarity index 100%
rename from hail/src/main/resources/include/hail/Upcalls.h
rename to hail/modules/src/main/resources/include/hail/Upcalls.h
diff --git a/hail/src/main/resources/include/hail/Utils.h b/hail/modules/src/main/resources/include/hail/Utils.h
similarity index 100%
rename from hail/src/main/resources/include/hail/Utils.h
rename to hail/modules/src/main/resources/include/hail/Utils.h
diff --git a/hail/src/main/resources/include/hail/hail.h b/hail/modules/src/main/resources/include/hail/hail.h
similarity index 100%
rename from hail/src/main/resources/include/hail/hail.h
rename to hail/modules/src/main/resources/include/hail/hail.h
diff --git a/hail/src/main/resources/log4j.properties b/hail/modules/src/main/resources/log4j.properties
similarity index 100%
rename from hail/src/main/resources/log4j.properties
rename to hail/modules/src/main/resources/log4j.properties
diff --git a/hail/src/main/resources/reference/canfam3.json b/hail/modules/src/main/resources/reference/canfam3.json
similarity index 100%
rename from hail/src/main/resources/reference/canfam3.json
rename to hail/modules/src/main/resources/reference/canfam3.json
diff --git a/hail/src/main/resources/reference/grch37.json b/hail/modules/src/main/resources/reference/grch37.json
similarity index 100%
rename from hail/src/main/resources/reference/grch37.json
rename to hail/modules/src/main/resources/reference/grch37.json
diff --git a/hail/src/main/resources/reference/grch38.json b/hail/modules/src/main/resources/reference/grch38.json
similarity index 100%
rename from hail/src/main/resources/reference/grch38.json
rename to hail/modules/src/main/resources/reference/grch38.json
diff --git a/hail/src/main/resources/reference/grcm38.json b/hail/modules/src/main/resources/reference/grcm38.json
similarity index 100%
rename from hail/src/main/resources/reference/grcm38.json
rename to hail/modules/src/main/resources/reference/grcm38.json
diff --git a/hail/src/main/scala/is/hail/HailContext.scala b/hail/modules/src/main/scala/is/hail/HailContext.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/HailContext.scala
rename to hail/modules/src/main/scala/is/hail/HailContext.scala
diff --git a/hail/src/main/scala/is/hail/HailFeatureFlags.scala b/hail/modules/src/main/scala/is/hail/HailFeatureFlags.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/HailFeatureFlags.scala
rename to hail/modules/src/main/scala/is/hail/HailFeatureFlags.scala
diff --git a/hail/src/main/scala/is/hail/annotations/Annotation.scala b/hail/modules/src/main/scala/is/hail/annotations/Annotation.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/Annotation.scala
rename to hail/modules/src/main/scala/is/hail/annotations/Annotation.scala
diff --git a/hail/src/main/scala/is/hail/annotations/BroadcastValue.scala b/hail/modules/src/main/scala/is/hail/annotations/BroadcastValue.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/BroadcastValue.scala
rename to hail/modules/src/main/scala/is/hail/annotations/BroadcastValue.scala
diff --git a/hail/src/main/scala/is/hail/annotations/ChunkCache.scala b/hail/modules/src/main/scala/is/hail/annotations/ChunkCache.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/ChunkCache.scala
rename to hail/modules/src/main/scala/is/hail/annotations/ChunkCache.scala
diff --git a/hail/src/main/scala/is/hail/annotations/ExtendedOrdering.scala b/hail/modules/src/main/scala/is/hail/annotations/ExtendedOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/ExtendedOrdering.scala
rename to hail/modules/src/main/scala/is/hail/annotations/ExtendedOrdering.scala
diff --git a/hail/src/main/scala/is/hail/annotations/JoinedRegionValue.scala b/hail/modules/src/main/scala/is/hail/annotations/JoinedRegionValue.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/JoinedRegionValue.scala
rename to hail/modules/src/main/scala/is/hail/annotations/JoinedRegionValue.scala
diff --git a/hail/src/main/scala/is/hail/annotations/OrderedRVIterator.scala b/hail/modules/src/main/scala/is/hail/annotations/OrderedRVIterator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/OrderedRVIterator.scala
rename to hail/modules/src/main/scala/is/hail/annotations/OrderedRVIterator.scala
diff --git a/hail/src/main/scala/is/hail/annotations/Region.scala b/hail/modules/src/main/scala/is/hail/annotations/Region.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/Region.scala
rename to hail/modules/src/main/scala/is/hail/annotations/Region.scala
diff --git a/hail/src/main/scala/is/hail/annotations/RegionMemory.scala b/hail/modules/src/main/scala/is/hail/annotations/RegionMemory.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/RegionMemory.scala
rename to hail/modules/src/main/scala/is/hail/annotations/RegionMemory.scala
diff --git a/hail/src/main/scala/is/hail/annotations/RegionPool.scala b/hail/modules/src/main/scala/is/hail/annotations/RegionPool.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/RegionPool.scala
rename to hail/modules/src/main/scala/is/hail/annotations/RegionPool.scala
diff --git a/hail/src/main/scala/is/hail/annotations/RegionValue.scala b/hail/modules/src/main/scala/is/hail/annotations/RegionValue.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/RegionValue.scala
rename to hail/modules/src/main/scala/is/hail/annotations/RegionValue.scala
diff --git a/hail/src/main/scala/is/hail/annotations/RegionValueBuilder.scala b/hail/modules/src/main/scala/is/hail/annotations/RegionValueBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/RegionValueBuilder.scala
rename to hail/modules/src/main/scala/is/hail/annotations/RegionValueBuilder.scala
diff --git a/hail/src/main/scala/is/hail/annotations/UnsafeOrdering.scala b/hail/modules/src/main/scala/is/hail/annotations/UnsafeOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/UnsafeOrdering.scala
rename to hail/modules/src/main/scala/is/hail/annotations/UnsafeOrdering.scala
diff --git a/hail/src/main/scala/is/hail/annotations/UnsafeRow.scala b/hail/modules/src/main/scala/is/hail/annotations/UnsafeRow.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/UnsafeRow.scala
rename to hail/modules/src/main/scala/is/hail/annotations/UnsafeRow.scala
diff --git a/hail/src/main/scala/is/hail/annotations/UnsafeUtils.scala b/hail/modules/src/main/scala/is/hail/annotations/UnsafeUtils.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/UnsafeUtils.scala
rename to hail/modules/src/main/scala/is/hail/annotations/UnsafeUtils.scala
diff --git a/hail/src/main/scala/is/hail/annotations/ValueVisitor.scala b/hail/modules/src/main/scala/is/hail/annotations/ValueVisitor.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/ValueVisitor.scala
rename to hail/modules/src/main/scala/is/hail/annotations/ValueVisitor.scala
diff --git a/hail/src/main/scala/is/hail/annotations/WritableRegionValue.scala b/hail/modules/src/main/scala/is/hail/annotations/WritableRegionValue.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/WritableRegionValue.scala
rename to hail/modules/src/main/scala/is/hail/annotations/WritableRegionValue.scala
diff --git a/hail/src/main/scala/is/hail/annotations/package.scala b/hail/modules/src/main/scala/is/hail/annotations/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/annotations/package.scala
rename to hail/modules/src/main/scala/is/hail/annotations/package.scala
diff --git a/hail/src/main/scala/is/hail/asm4s/AsmFunction.scala b/hail/modules/src/main/scala/is/hail/asm4s/AsmFunction.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/asm4s/AsmFunction.scala
rename to hail/modules/src/main/scala/is/hail/asm4s/AsmFunction.scala
diff --git a/hail/src/main/scala/is/hail/asm4s/ClassBuilder.scala b/hail/modules/src/main/scala/is/hail/asm4s/ClassBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/asm4s/ClassBuilder.scala
rename to hail/modules/src/main/scala/is/hail/asm4s/ClassBuilder.scala
diff --git a/hail/src/main/scala/is/hail/asm4s/Code.scala b/hail/modules/src/main/scala/is/hail/asm4s/Code.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/asm4s/Code.scala
rename to hail/modules/src/main/scala/is/hail/asm4s/Code.scala
diff --git a/hail/src/main/scala/is/hail/asm4s/CodeBuilder.scala b/hail/modules/src/main/scala/is/hail/asm4s/CodeBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/asm4s/CodeBuilder.scala
rename to hail/modules/src/main/scala/is/hail/asm4s/CodeBuilder.scala
diff --git a/hail/src/main/scala/is/hail/asm4s/GenericTypeInfo.scala b/hail/modules/src/main/scala/is/hail/asm4s/GenericTypeInfo.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/asm4s/GenericTypeInfo.scala
rename to hail/modules/src/main/scala/is/hail/asm4s/GenericTypeInfo.scala
diff --git a/hail/src/main/scala/is/hail/asm4s/HailClassLoader.scala b/hail/modules/src/main/scala/is/hail/asm4s/HailClassLoader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/asm4s/HailClassLoader.scala
rename to hail/modules/src/main/scala/is/hail/asm4s/HailClassLoader.scala
diff --git a/hail/src/main/scala/is/hail/asm4s/package.scala b/hail/modules/src/main/scala/is/hail/asm4s/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/asm4s/package.scala
rename to hail/modules/src/main/scala/is/hail/asm4s/package.scala
diff --git a/hail/src/main/scala/is/hail/backend/Backend.scala b/hail/modules/src/main/scala/is/hail/backend/Backend.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/Backend.scala
rename to hail/modules/src/main/scala/is/hail/backend/Backend.scala
diff --git a/hail/src/main/scala/is/hail/backend/BackendServer.scala b/hail/modules/src/main/scala/is/hail/backend/BackendServer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/BackendServer.scala
rename to hail/modules/src/main/scala/is/hail/backend/BackendServer.scala
diff --git a/hail/src/main/scala/is/hail/backend/BackendUtils.scala b/hail/modules/src/main/scala/is/hail/backend/BackendUtils.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/BackendUtils.scala
rename to hail/modules/src/main/scala/is/hail/backend/BackendUtils.scala
diff --git a/hail/src/main/scala/is/hail/backend/ExecuteContext.scala b/hail/modules/src/main/scala/is/hail/backend/ExecuteContext.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/ExecuteContext.scala
rename to hail/modules/src/main/scala/is/hail/backend/ExecuteContext.scala
diff --git a/hail/src/main/scala/is/hail/backend/ExecutionCache.scala b/hail/modules/src/main/scala/is/hail/backend/ExecutionCache.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/ExecutionCache.scala
rename to hail/modules/src/main/scala/is/hail/backend/ExecutionCache.scala
diff --git a/hail/src/main/scala/is/hail/backend/HailStateManager.scala b/hail/modules/src/main/scala/is/hail/backend/HailStateManager.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/HailStateManager.scala
rename to hail/modules/src/main/scala/is/hail/backend/HailStateManager.scala
diff --git a/hail/src/main/scala/is/hail/backend/HailTaskContext.scala b/hail/modules/src/main/scala/is/hail/backend/HailTaskContext.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/HailTaskContext.scala
rename to hail/modules/src/main/scala/is/hail/backend/HailTaskContext.scala
diff --git a/hail/src/main/scala/is/hail/backend/local/LocalBackend.scala b/hail/modules/src/main/scala/is/hail/backend/local/LocalBackend.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/local/LocalBackend.scala
rename to hail/modules/src/main/scala/is/hail/backend/local/LocalBackend.scala
diff --git a/hail/src/main/scala/is/hail/backend/service/Main.scala b/hail/modules/src/main/scala/is/hail/backend/service/Main.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/service/Main.scala
rename to hail/modules/src/main/scala/is/hail/backend/service/Main.scala
diff --git a/hail/src/main/scala/is/hail/backend/service/ServiceBackend.scala b/hail/modules/src/main/scala/is/hail/backend/service/ServiceBackend.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/service/ServiceBackend.scala
rename to hail/modules/src/main/scala/is/hail/backend/service/ServiceBackend.scala
diff --git a/hail/src/main/scala/is/hail/backend/service/Worker.scala b/hail/modules/src/main/scala/is/hail/backend/service/Worker.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/service/Worker.scala
rename to hail/modules/src/main/scala/is/hail/backend/service/Worker.scala
diff --git a/hail/src/main/scala/is/hail/backend/spark/SparkBackend.scala b/hail/modules/src/main/scala/is/hail/backend/spark/SparkBackend.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/spark/SparkBackend.scala
rename to hail/modules/src/main/scala/is/hail/backend/spark/SparkBackend.scala
diff --git a/hail/src/main/scala/is/hail/backend/spark/SparkBlockMatrixCache.scala b/hail/modules/src/main/scala/is/hail/backend/spark/SparkBlockMatrixCache.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/backend/spark/SparkBlockMatrixCache.scala
rename to hail/modules/src/main/scala/is/hail/backend/spark/SparkBlockMatrixCache.scala
diff --git a/hail/src/main/scala/is/hail/check/Arbitrary.scala b/hail/modules/src/main/scala/is/hail/check/Arbitrary.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/check/Arbitrary.scala
rename to hail/modules/src/main/scala/is/hail/check/Arbitrary.scala
diff --git a/hail/src/main/scala/is/hail/check/Gen.scala b/hail/modules/src/main/scala/is/hail/check/Gen.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/check/Gen.scala
rename to hail/modules/src/main/scala/is/hail/check/Gen.scala
diff --git a/hail/src/main/scala/is/hail/check/Prop.scala b/hail/modules/src/main/scala/is/hail/check/Prop.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/check/Prop.scala
rename to hail/modules/src/main/scala/is/hail/check/Prop.scala
diff --git a/hail/src/main/scala/is/hail/compatibility/LegacyBufferSpecs.scala b/hail/modules/src/main/scala/is/hail/compatibility/LegacyBufferSpecs.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/compatibility/LegacyBufferSpecs.scala
rename to hail/modules/src/main/scala/is/hail/compatibility/LegacyBufferSpecs.scala
diff --git a/hail/src/main/scala/is/hail/compatibility/LegacyEncodedTypeParser.scala b/hail/modules/src/main/scala/is/hail/compatibility/LegacyEncodedTypeParser.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/compatibility/LegacyEncodedTypeParser.scala
rename to hail/modules/src/main/scala/is/hail/compatibility/LegacyEncodedTypeParser.scala
diff --git a/hail/src/main/scala/is/hail/compatibility/LegacyRVDSpecs.scala b/hail/modules/src/main/scala/is/hail/compatibility/LegacyRVDSpecs.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/compatibility/LegacyRVDSpecs.scala
rename to hail/modules/src/main/scala/is/hail/compatibility/LegacyRVDSpecs.scala
diff --git a/hail/src/main/scala/is/hail/cxx/RegionValueIterator.scala b/hail/modules/src/main/scala/is/hail/cxx/RegionValueIterator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/cxx/RegionValueIterator.scala
rename to hail/modules/src/main/scala/is/hail/cxx/RegionValueIterator.scala
diff --git a/hail/src/main/scala/is/hail/experimental/ExperimentalFunctions.scala b/hail/modules/src/main/scala/is/hail/experimental/ExperimentalFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/experimental/ExperimentalFunctions.scala
rename to hail/modules/src/main/scala/is/hail/experimental/ExperimentalFunctions.scala
diff --git a/hail/src/main/scala/is/hail/experimental/package.scala b/hail/modules/src/main/scala/is/hail/experimental/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/experimental/package.scala
rename to hail/modules/src/main/scala/is/hail/experimental/package.scala
diff --git a/hail/src/main/scala/is/hail/expr/AnnotationImpex.scala b/hail/modules/src/main/scala/is/hail/expr/AnnotationImpex.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/AnnotationImpex.scala
rename to hail/modules/src/main/scala/is/hail/expr/AnnotationImpex.scala
diff --git a/hail/src/main/scala/is/hail/expr/NatBase.scala b/hail/modules/src/main/scala/is/hail/expr/NatBase.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/NatBase.scala
rename to hail/modules/src/main/scala/is/hail/expr/NatBase.scala
diff --git a/hail/src/main/scala/is/hail/expr/Parser.scala b/hail/modules/src/main/scala/is/hail/expr/Parser.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/Parser.scala
rename to hail/modules/src/main/scala/is/hail/expr/Parser.scala
diff --git a/hail/src/main/scala/is/hail/expr/Validate.scala b/hail/modules/src/main/scala/is/hail/expr/Validate.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/Validate.scala
rename to hail/modules/src/main/scala/is/hail/expr/Validate.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala b/hail/modules/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/AbstractMatrixTableSpec.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/AbstractTableSpec.scala b/hail/modules/src/main/scala/is/hail/expr/ir/AbstractTableSpec.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/AbstractTableSpec.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/AbstractTableSpec.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/AggOp.scala b/hail/modules/src/main/scala/is/hail/expr/ir/AggOp.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/AggOp.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/AggOp.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/ArraySorter.scala b/hail/modules/src/main/scala/is/hail/expr/ir/ArraySorter.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/ArraySorter.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/ArraySorter.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/BaseIR.scala b/hail/modules/src/main/scala/is/hail/expr/ir/BaseIR.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/BaseIR.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/BaseIR.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/BinaryOp.scala b/hail/modules/src/main/scala/is/hail/expr/ir/BinaryOp.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/BinaryOp.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/BinaryOp.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/BinarySearch.scala b/hail/modules/src/main/scala/is/hail/expr/ir/BinarySearch.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/BinarySearch.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/BinarySearch.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Binds.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Binds.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Binds.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Binds.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/BlockMatrixIR.scala b/hail/modules/src/main/scala/is/hail/expr/ir/BlockMatrixIR.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/BlockMatrixIR.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/BlockMatrixIR.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/BlockMatrixWriter.scala b/hail/modules/src/main/scala/is/hail/expr/ir/BlockMatrixWriter.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/BlockMatrixWriter.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/BlockMatrixWriter.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Casts.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Casts.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Casts.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Casts.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Children.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Children.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Children.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Children.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/ComparisonOp.scala b/hail/modules/src/main/scala/is/hail/expr/ir/ComparisonOp.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/ComparisonOp.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/ComparisonOp.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Compilable.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Compilable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Compilable.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Compilable.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Compile.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Compile.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Compile.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Compile.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/CompileAndEvaluate.scala b/hail/modules/src/main/scala/is/hail/expr/ir/CompileAndEvaluate.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/CompileAndEvaluate.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/CompileAndEvaluate.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/ComputeUsesAndDefs.scala b/hail/modules/src/main/scala/is/hail/expr/ir/ComputeUsesAndDefs.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/ComputeUsesAndDefs.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/ComputeUsesAndDefs.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Copy.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Copy.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Copy.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Copy.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/DeprecatedIRBuilder.scala b/hail/modules/src/main/scala/is/hail/expr/ir/DeprecatedIRBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/DeprecatedIRBuilder.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/DeprecatedIRBuilder.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/DistinctlyKeyed.scala b/hail/modules/src/main/scala/is/hail/expr/ir/DistinctlyKeyed.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/DistinctlyKeyed.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/DistinctlyKeyed.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Emit.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Emit.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Emit.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Emit.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/EmitClassBuilder.scala b/hail/modules/src/main/scala/is/hail/expr/ir/EmitClassBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/EmitClassBuilder.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/EmitClassBuilder.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/EmitCodeBuilder.scala b/hail/modules/src/main/scala/is/hail/expr/ir/EmitCodeBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/EmitCodeBuilder.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/EmitCodeBuilder.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/EmitStreamDistribute.scala b/hail/modules/src/main/scala/is/hail/expr/ir/EmitStreamDistribute.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/EmitStreamDistribute.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/EmitStreamDistribute.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Env.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Env.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Env.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Env.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Exists.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Exists.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Exists.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Exists.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/ExtractIntervalFilters.scala b/hail/modules/src/main/scala/is/hail/expr/ir/ExtractIntervalFilters.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/ExtractIntervalFilters.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/ExtractIntervalFilters.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/FoldConstants.scala b/hail/modules/src/main/scala/is/hail/expr/ir/FoldConstants.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/FoldConstants.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/FoldConstants.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/ForwardLets.scala b/hail/modules/src/main/scala/is/hail/expr/ir/ForwardLets.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/ForwardLets.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/ForwardLets.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/ForwardRelationalLets.scala b/hail/modules/src/main/scala/is/hail/expr/ir/ForwardRelationalLets.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/ForwardRelationalLets.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/ForwardRelationalLets.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/FreeVariables.scala b/hail/modules/src/main/scala/is/hail/expr/ir/FreeVariables.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/FreeVariables.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/FreeVariables.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/GenericLines.scala b/hail/modules/src/main/scala/is/hail/expr/ir/GenericLines.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/GenericLines.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/GenericLines.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/GenericTableValue.scala b/hail/modules/src/main/scala/is/hail/expr/ir/GenericTableValue.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/GenericTableValue.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/GenericTableValue.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/IR.scala b/hail/modules/src/main/scala/is/hail/expr/ir/IR.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/IR.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/IR.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/IRBuilder.scala b/hail/modules/src/main/scala/is/hail/expr/ir/IRBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/IRBuilder.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/IRBuilder.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/IRSize.scala b/hail/modules/src/main/scala/is/hail/expr/ir/IRSize.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/IRSize.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/IRSize.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/IRTraversal.scala b/hail/modules/src/main/scala/is/hail/expr/ir/IRTraversal.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/IRTraversal.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/IRTraversal.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/InTailPosition.scala b/hail/modules/src/main/scala/is/hail/expr/ir/InTailPosition.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/InTailPosition.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/InTailPosition.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/InferPType.scala b/hail/modules/src/main/scala/is/hail/expr/ir/InferPType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/InferPType.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/InferPType.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/InferType.scala b/hail/modules/src/main/scala/is/hail/expr/ir/InferType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/InferType.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/InferType.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Interpret.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Interpret.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Interpret.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Interpret.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Interpretable.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Interpretable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Interpretable.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Interpretable.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/IsConstant.scala b/hail/modules/src/main/scala/is/hail/expr/ir/IsConstant.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/IsConstant.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/IsConstant.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/IsPure.scala b/hail/modules/src/main/scala/is/hail/expr/ir/IsPure.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/IsPure.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/IsPure.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/LiftRelationalValues.scala b/hail/modules/src/main/scala/is/hail/expr/ir/LiftRelationalValues.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/LiftRelationalValues.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/LiftRelationalValues.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/LowerMatrixIR.scala b/hail/modules/src/main/scala/is/hail/expr/ir/LowerMatrixIR.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/LowerMatrixIR.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/LowerMatrixIR.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala b/hail/modules/src/main/scala/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/LoweringAnalyses.scala b/hail/modules/src/main/scala/is/hail/expr/ir/LoweringAnalyses.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/LoweringAnalyses.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/LoweringAnalyses.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/MapIR.scala b/hail/modules/src/main/scala/is/hail/expr/ir/MapIR.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/MapIR.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/MapIR.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/MatrixIR.scala b/hail/modules/src/main/scala/is/hail/expr/ir/MatrixIR.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/MatrixIR.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/MatrixIR.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/MatrixValue.scala b/hail/modules/src/main/scala/is/hail/expr/ir/MatrixValue.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/MatrixValue.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/MatrixValue.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/MatrixWriter.scala b/hail/modules/src/main/scala/is/hail/expr/ir/MatrixWriter.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/MatrixWriter.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/MatrixWriter.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Mentions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Mentions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Mentions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Mentions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/NativeReaderOptions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/NativeReaderOptions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/NativeReaderOptions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/NativeReaderOptions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/NestingDepth.scala b/hail/modules/src/main/scala/is/hail/expr/ir/NestingDepth.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/NestingDepth.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/NestingDepth.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/NormalizeNames.scala b/hail/modules/src/main/scala/is/hail/expr/ir/NormalizeNames.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/NormalizeNames.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/NormalizeNames.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/NumericPrimitives.scala b/hail/modules/src/main/scala/is/hail/expr/ir/NumericPrimitives.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/NumericPrimitives.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/NumericPrimitives.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Optimize.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Optimize.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Optimize.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Optimize.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Param.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Param.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Param.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Param.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Parser.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Parser.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Parser.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Parser.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Pretty.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Pretty.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Pretty.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Pretty.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/PrimitiveTypeToIRIntermediateClassTag.scala b/hail/modules/src/main/scala/is/hail/expr/ir/PrimitiveTypeToIRIntermediateClassTag.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/PrimitiveTypeToIRIntermediateClassTag.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/PrimitiveTypeToIRIntermediateClassTag.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/PruneDeadFields.scala b/hail/modules/src/main/scala/is/hail/expr/ir/PruneDeadFields.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/PruneDeadFields.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/PruneDeadFields.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Random.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Random.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Random.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Random.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/RefEquality.scala b/hail/modules/src/main/scala/is/hail/expr/ir/RefEquality.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/RefEquality.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/RefEquality.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Requiredness.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Requiredness.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Requiredness.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Requiredness.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/RewriteBottomUp.scala b/hail/modules/src/main/scala/is/hail/expr/ir/RewriteBottomUp.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/RewriteBottomUp.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/RewriteBottomUp.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/RewriteTopDown.scala b/hail/modules/src/main/scala/is/hail/expr/ir/RewriteTopDown.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/RewriteTopDown.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/RewriteTopDown.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Scope.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Scope.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Scope.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Scope.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Simplify.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Simplify.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Simplify.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Simplify.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/SpecializedArrayBuilders.scala b/hail/modules/src/main/scala/is/hail/expr/ir/SpecializedArrayBuilders.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/SpecializedArrayBuilders.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/SpecializedArrayBuilders.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/StringTableReader.scala b/hail/modules/src/main/scala/is/hail/expr/ir/StringTableReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/StringTableReader.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/StringTableReader.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Subst.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Subst.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Subst.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Subst.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/Sym.scala b/hail/modules/src/main/scala/is/hail/expr/ir/Sym.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/Sym.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/Sym.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/TableIR.scala b/hail/modules/src/main/scala/is/hail/expr/ir/TableIR.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/TableIR.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/TableIR.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/TableValue.scala b/hail/modules/src/main/scala/is/hail/expr/ir/TableValue.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/TableValue.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/TableValue.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/TableWriter.scala b/hail/modules/src/main/scala/is/hail/expr/ir/TableWriter.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/TableWriter.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/TableWriter.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/TypeCheck.scala b/hail/modules/src/main/scala/is/hail/expr/ir/TypeCheck.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/TypeCheck.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/TypeCheck.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/UnaryOp.scala b/hail/modules/src/main/scala/is/hail/expr/ir/UnaryOp.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/UnaryOp.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/UnaryOp.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/ValueReader.scala b/hail/modules/src/main/scala/is/hail/expr/ir/ValueReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/ValueReader.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/ValueReader.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/ValueWriter.scala b/hail/modules/src/main/scala/is/hail/expr/ir/ValueWriter.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/ValueWriter.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/ValueWriter.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/add-ir-checklist.txt b/hail/modules/src/main/scala/is/hail/expr/ir/add-ir-checklist.txt
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/add-ir-checklist.txt
rename to hail/modules/src/main/scala/is/hail/expr/ir/add-ir-checklist.txt
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/AggregatorState.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/AggregatorState.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/AggregatorState.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/AggregatorState.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/AppendOnlyBTree.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/AppendOnlyBTree.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/AppendOnlyBTree.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/AppendOnlyBTree.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/ApproxCDFAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/ApproxCDFAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/ApproxCDFAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/ApproxCDFAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/ApproxCDFStateManager.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/ApproxCDFStateManager.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/ApproxCDFStateManager.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/ApproxCDFStateManager.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/CallStatsAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/CallStatsAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/CallStatsAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/CallStatsAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/CollectAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/CollectAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/CollectAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/CollectAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/CollectAsSetAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/CollectAsSetAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/CollectAsSetAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/CollectAsSetAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/CountAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/CountAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/CountAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/CountAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/DensifyAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/DensifyAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/DensifyAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/DensifyAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/DownsampleAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/DownsampleAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/DownsampleAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/DownsampleAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/Extract.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/Extract.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/Extract.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/Extract.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/FoldAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/FoldAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/FoldAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/FoldAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/GroupedAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/GroupedAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/GroupedAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/GroupedAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/ImputeTypeAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/ImputeTypeAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/ImputeTypeAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/ImputeTypeAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/LinearRegressionAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/LinearRegressionAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/LinearRegressionAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/LinearRegressionAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/MonoidAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/MonoidAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/MonoidAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/MonoidAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/NDArraySumAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/NDArraySumAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/NDArraySumAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/NDArraySumAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/PrevNonNullAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/PrevNonNullAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/PrevNonNullAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/PrevNonNullAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/StagedAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/StagedAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/StagedAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/StagedAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/StagedArrayBuilder.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/StagedArrayBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/StagedArrayBuilder.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/StagedArrayBuilder.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/StagedBlockLinkedList.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/StagedBlockLinkedList.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/StagedBlockLinkedList.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/StagedBlockLinkedList.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/TakeAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/TakeAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/TakeAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/TakeAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/agg/TakeByAggregator.scala b/hail/modules/src/main/scala/is/hail/expr/ir/agg/TakeByAggregator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/agg/TakeByAggregator.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/agg/TakeByAggregator.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/analyses/ComputeMethodSplits.scala b/hail/modules/src/main/scala/is/hail/expr/ir/analyses/ComputeMethodSplits.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/analyses/ComputeMethodSplits.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/analyses/ComputeMethodSplits.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/analyses/ControlFlowPreventsSplit.scala b/hail/modules/src/main/scala/is/hail/expr/ir/analyses/ControlFlowPreventsSplit.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/analyses/ControlFlowPreventsSplit.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/analyses/ControlFlowPreventsSplit.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/analyses/ParentPointers.scala b/hail/modules/src/main/scala/is/hail/expr/ir/analyses/ParentPointers.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/analyses/ParentPointers.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/analyses/ParentPointers.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/analyses/SemanticHash.scala b/hail/modules/src/main/scala/is/hail/expr/ir/analyses/SemanticHash.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/analyses/SemanticHash.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/analyses/SemanticHash.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/ApproxCDFFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/ApproxCDFFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/ApproxCDFFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/ApproxCDFFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/ArrayFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/ArrayFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/ArrayFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/ArrayFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/CallFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/CallFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/CallFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/CallFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/DictFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/DictFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/DictFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/DictFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/Functions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/Functions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/Functions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/Functions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/GenotypeFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/GenotypeFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/GenotypeFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/GenotypeFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/GetElement.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/GetElement.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/GetElement.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/GetElement.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/IntervalFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/IntervalFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/IntervalFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/IntervalFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/LocusFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/LocusFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/LocusFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/LocusFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/MathFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/MathFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/MathFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/MathFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/NDArrayFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/NDArrayFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/NDArrayFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/NDArrayFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/RandomSeededFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/RandomSeededFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/RandomSeededFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/RandomSeededFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/RelationalFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/RelationalFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/RelationalFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/RelationalFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/SetFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/SetFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/SetFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/SetFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/StringFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/StringFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/StringFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/StringFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/functions/UtilFunctions.scala b/hail/modules/src/main/scala/is/hail/expr/ir/functions/UtilFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/functions/UtilFunctions.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/functions/UtilFunctions.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/CanLowerEfficiently.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/CanLowerEfficiently.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/CanLowerEfficiently.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/CanLowerEfficiently.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/EvalRelationalLets.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/EvalRelationalLets.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/EvalRelationalLets.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/EvalRelationalLets.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/IRState.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/IRState.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/IRState.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/IRState.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerDistributedSort.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerDistributedSort.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerDistributedSort.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerDistributedSort.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerTableIR.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerTableIR.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerTableIR.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerTableIR.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LowerToCDA.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerToCDA.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/LowerToCDA.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/LowerToCDA.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LoweringPass.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/LoweringPass.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/LoweringPass.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/LoweringPass.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/LoweringPipeline.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/LoweringPipeline.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/LoweringPipeline.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/LoweringPipeline.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/RVDToTableStage.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/RVDToTableStage.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/RVDToTableStage.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/RVDToTableStage.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/Rule.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/Rule.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/Rule.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/Rule.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/lowering/TableStageDependency.scala b/hail/modules/src/main/scala/is/hail/expr/ir/lowering/TableStageDependency.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/lowering/TableStageDependency.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/lowering/TableStageDependency.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/ndarrays/EmitNDArray.scala b/hail/modules/src/main/scala/is/hail/expr/ir/ndarrays/EmitNDArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/ndarrays/EmitNDArray.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/ndarrays/EmitNDArray.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/BinaryOrdering.scala b/hail/modules/src/main/scala/is/hail/expr/ir/orderings/BinaryOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/orderings/BinaryOrdering.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/orderings/BinaryOrdering.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/CallOrdering.scala b/hail/modules/src/main/scala/is/hail/expr/ir/orderings/CallOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/orderings/CallOrdering.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/orderings/CallOrdering.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/CodeOrdering.scala b/hail/modules/src/main/scala/is/hail/expr/ir/orderings/CodeOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/orderings/CodeOrdering.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/orderings/CodeOrdering.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/IntervalOrdering.scala b/hail/modules/src/main/scala/is/hail/expr/ir/orderings/IntervalOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/orderings/IntervalOrdering.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/orderings/IntervalOrdering.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/IterableOrdering.scala b/hail/modules/src/main/scala/is/hail/expr/ir/orderings/IterableOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/orderings/IterableOrdering.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/orderings/IterableOrdering.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/LocusOrdering.scala b/hail/modules/src/main/scala/is/hail/expr/ir/orderings/LocusOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/orderings/LocusOrdering.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/orderings/LocusOrdering.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/PrimitiveOrdering.scala b/hail/modules/src/main/scala/is/hail/expr/ir/orderings/PrimitiveOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/orderings/PrimitiveOrdering.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/orderings/PrimitiveOrdering.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/StringOrdering.scala b/hail/modules/src/main/scala/is/hail/expr/ir/orderings/StringOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/orderings/StringOrdering.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/orderings/StringOrdering.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/orderings/StructOrdering.scala b/hail/modules/src/main/scala/is/hail/expr/ir/orderings/StructOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/orderings/StructOrdering.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/orderings/StructOrdering.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/package.scala b/hail/modules/src/main/scala/is/hail/expr/ir/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/package.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/package.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/streams/EmitStream.scala b/hail/modules/src/main/scala/is/hail/expr/ir/streams/EmitStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/streams/EmitStream.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/streams/EmitStream.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/streams/StagedMinHeap.scala b/hail/modules/src/main/scala/is/hail/expr/ir/streams/StagedMinHeap.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/streams/StagedMinHeap.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/streams/StagedMinHeap.scala
diff --git a/hail/src/main/scala/is/hail/expr/ir/streams/StreamUtils.scala b/hail/modules/src/main/scala/is/hail/expr/ir/streams/StreamUtils.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/ir/streams/StreamUtils.scala
rename to hail/modules/src/main/scala/is/hail/expr/ir/streams/StreamUtils.scala
diff --git a/hail/src/main/scala/is/hail/expr/package.scala b/hail/modules/src/main/scala/is/hail/expr/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/expr/package.scala
rename to hail/modules/src/main/scala/is/hail/expr/package.scala
diff --git a/hail/src/main/scala/is/hail/io/AbstractBinaryReader.scala b/hail/modules/src/main/scala/is/hail/io/AbstractBinaryReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/AbstractBinaryReader.scala
rename to hail/modules/src/main/scala/is/hail/io/AbstractBinaryReader.scala
diff --git a/hail/src/main/scala/is/hail/io/BufferSpecs.scala b/hail/modules/src/main/scala/is/hail/io/BufferSpecs.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/BufferSpecs.scala
rename to hail/modules/src/main/scala/is/hail/io/BufferSpecs.scala
diff --git a/hail/src/main/scala/is/hail/io/ByteArrayReader.scala b/hail/modules/src/main/scala/is/hail/io/ByteArrayReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/ByteArrayReader.scala
rename to hail/modules/src/main/scala/is/hail/io/ByteArrayReader.scala
diff --git a/hail/src/main/scala/is/hail/io/CodecSpec.scala b/hail/modules/src/main/scala/is/hail/io/CodecSpec.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/CodecSpec.scala
rename to hail/modules/src/main/scala/is/hail/io/CodecSpec.scala
diff --git a/hail/src/main/scala/is/hail/io/Decoder.scala b/hail/modules/src/main/scala/is/hail/io/Decoder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/Decoder.scala
rename to hail/modules/src/main/scala/is/hail/io/Decoder.scala
diff --git a/hail/src/main/scala/is/hail/io/DoubleInputBuffer.scala b/hail/modules/src/main/scala/is/hail/io/DoubleInputBuffer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/DoubleInputBuffer.scala
rename to hail/modules/src/main/scala/is/hail/io/DoubleInputBuffer.scala
diff --git a/hail/src/main/scala/is/hail/io/ElasticsearchConnector.scala b/hail/modules/src/main/scala/is/hail/io/ElasticsearchConnector.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/ElasticsearchConnector.scala
rename to hail/modules/src/main/scala/is/hail/io/ElasticsearchConnector.scala
diff --git a/hail/src/main/scala/is/hail/io/Encoder.scala b/hail/modules/src/main/scala/is/hail/io/Encoder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/Encoder.scala
rename to hail/modules/src/main/scala/is/hail/io/Encoder.scala
diff --git a/hail/src/main/scala/is/hail/io/FileWriteMetadata.scala b/hail/modules/src/main/scala/is/hail/io/FileWriteMetadata.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/FileWriteMetadata.scala
rename to hail/modules/src/main/scala/is/hail/io/FileWriteMetadata.scala
diff --git a/hail/src/main/scala/is/hail/io/HadoopFSDataBinaryReader.scala b/hail/modules/src/main/scala/is/hail/io/HadoopFSDataBinaryReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/HadoopFSDataBinaryReader.scala
rename to hail/modules/src/main/scala/is/hail/io/HadoopFSDataBinaryReader.scala
diff --git a/hail/src/main/scala/is/hail/io/IndexBTree.scala b/hail/modules/src/main/scala/is/hail/io/IndexBTree.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/IndexBTree.scala
rename to hail/modules/src/main/scala/is/hail/io/IndexBTree.scala
diff --git a/hail/src/main/scala/is/hail/io/IndexedBinaryBlockReader.scala b/hail/modules/src/main/scala/is/hail/io/IndexedBinaryBlockReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/IndexedBinaryBlockReader.scala
rename to hail/modules/src/main/scala/is/hail/io/IndexedBinaryBlockReader.scala
diff --git a/hail/src/main/scala/is/hail/io/IndexedBinaryInputFormat.scala b/hail/modules/src/main/scala/is/hail/io/IndexedBinaryInputFormat.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/IndexedBinaryInputFormat.scala
rename to hail/modules/src/main/scala/is/hail/io/IndexedBinaryInputFormat.scala
diff --git a/hail/src/main/scala/is/hail/io/InputBuffers.scala b/hail/modules/src/main/scala/is/hail/io/InputBuffers.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/InputBuffers.scala
rename to hail/modules/src/main/scala/is/hail/io/InputBuffers.scala
diff --git a/hail/src/main/scala/is/hail/io/MemoryBuffer.scala b/hail/modules/src/main/scala/is/hail/io/MemoryBuffer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/MemoryBuffer.scala
rename to hail/modules/src/main/scala/is/hail/io/MemoryBuffer.scala
diff --git a/hail/src/main/scala/is/hail/io/OutputBuffers.scala b/hail/modules/src/main/scala/is/hail/io/OutputBuffers.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/OutputBuffers.scala
rename to hail/modules/src/main/scala/is/hail/io/OutputBuffers.scala
diff --git a/hail/src/main/scala/is/hail/io/RichContextRDDRegionValue.scala b/hail/modules/src/main/scala/is/hail/io/RichContextRDDRegionValue.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/RichContextRDDRegionValue.scala
rename to hail/modules/src/main/scala/is/hail/io/RichContextRDDRegionValue.scala
diff --git a/hail/src/main/scala/is/hail/io/Spec.scala b/hail/modules/src/main/scala/is/hail/io/Spec.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/Spec.scala
rename to hail/modules/src/main/scala/is/hail/io/Spec.scala
diff --git a/hail/src/main/scala/is/hail/io/TypedCodecSpec.scala b/hail/modules/src/main/scala/is/hail/io/TypedCodecSpec.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/TypedCodecSpec.scala
rename to hail/modules/src/main/scala/is/hail/io/TypedCodecSpec.scala
diff --git a/hail/src/main/scala/is/hail/io/avro/AvroPartitionReader.scala b/hail/modules/src/main/scala/is/hail/io/avro/AvroPartitionReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/avro/AvroPartitionReader.scala
rename to hail/modules/src/main/scala/is/hail/io/avro/AvroPartitionReader.scala
diff --git a/hail/src/main/scala/is/hail/io/avro/AvroSchemaSerializer.scala b/hail/modules/src/main/scala/is/hail/io/avro/AvroSchemaSerializer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/avro/AvroSchemaSerializer.scala
rename to hail/modules/src/main/scala/is/hail/io/avro/AvroSchemaSerializer.scala
diff --git a/hail/src/main/scala/is/hail/io/avro/AvroTableReader.scala b/hail/modules/src/main/scala/is/hail/io/avro/AvroTableReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/avro/AvroTableReader.scala
rename to hail/modules/src/main/scala/is/hail/io/avro/AvroTableReader.scala
diff --git a/hail/src/main/scala/is/hail/io/avro/UnsafeAvroTableReaderOptions.scala b/hail/modules/src/main/scala/is/hail/io/avro/UnsafeAvroTableReaderOptions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/avro/UnsafeAvroTableReaderOptions.scala
rename to hail/modules/src/main/scala/is/hail/io/avro/UnsafeAvroTableReaderOptions.scala
diff --git a/hail/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala b/hail/modules/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala
rename to hail/modules/src/main/scala/is/hail/io/bgen/BgenRDDPartitions.scala
diff --git a/hail/src/main/scala/is/hail/io/bgen/BgenSettings.scala b/hail/modules/src/main/scala/is/hail/io/bgen/BgenSettings.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/bgen/BgenSettings.scala
rename to hail/modules/src/main/scala/is/hail/io/bgen/BgenSettings.scala
diff --git a/hail/src/main/scala/is/hail/io/bgen/LoadBgen.scala b/hail/modules/src/main/scala/is/hail/io/bgen/LoadBgen.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/bgen/LoadBgen.scala
rename to hail/modules/src/main/scala/is/hail/io/bgen/LoadBgen.scala
diff --git a/hail/src/main/scala/is/hail/io/bgen/StagedBGENReader.scala b/hail/modules/src/main/scala/is/hail/io/bgen/StagedBGENReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/bgen/StagedBGENReader.scala
rename to hail/modules/src/main/scala/is/hail/io/bgen/StagedBGENReader.scala
diff --git a/hail/src/main/scala/is/hail/io/compress/BGzipLineReader.scala b/hail/modules/src/main/scala/is/hail/io/compress/BGzipLineReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/compress/BGzipLineReader.scala
rename to hail/modules/src/main/scala/is/hail/io/compress/BGzipLineReader.scala
diff --git a/hail/src/main/scala/is/hail/io/compress/LZ4.scala b/hail/modules/src/main/scala/is/hail/io/compress/LZ4.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/compress/LZ4.scala
rename to hail/modules/src/main/scala/is/hail/io/compress/LZ4.scala
diff --git a/hail/src/main/scala/is/hail/io/fs/AzureStorageFS.scala b/hail/modules/src/main/scala/is/hail/io/fs/AzureStorageFS.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/fs/AzureStorageFS.scala
rename to hail/modules/src/main/scala/is/hail/io/fs/AzureStorageFS.scala
diff --git a/hail/src/main/scala/is/hail/io/fs/FS.scala b/hail/modules/src/main/scala/is/hail/io/fs/FS.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/fs/FS.scala
rename to hail/modules/src/main/scala/is/hail/io/fs/FS.scala
diff --git a/hail/src/main/scala/is/hail/io/fs/GoogleStorageFS.scala b/hail/modules/src/main/scala/is/hail/io/fs/GoogleStorageFS.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/fs/GoogleStorageFS.scala
rename to hail/modules/src/main/scala/is/hail/io/fs/GoogleStorageFS.scala
diff --git a/hail/src/main/scala/is/hail/io/fs/HadoopFS.scala b/hail/modules/src/main/scala/is/hail/io/fs/HadoopFS.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/fs/HadoopFS.scala
rename to hail/modules/src/main/scala/is/hail/io/fs/HadoopFS.scala
diff --git a/hail/src/main/scala/is/hail/io/fs/README b/hail/modules/src/main/scala/is/hail/io/fs/README
similarity index 100%
rename from hail/src/main/scala/is/hail/io/fs/README
rename to hail/modules/src/main/scala/is/hail/io/fs/README
diff --git a/hail/src/main/scala/is/hail/io/fs/RouterFS.scala b/hail/modules/src/main/scala/is/hail/io/fs/RouterFS.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/fs/RouterFS.scala
rename to hail/modules/src/main/scala/is/hail/io/fs/RouterFS.scala
diff --git a/hail/src/main/scala/is/hail/io/fs/TerraAzureStorageFS.scala b/hail/modules/src/main/scala/is/hail/io/fs/TerraAzureStorageFS.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/fs/TerraAzureStorageFS.scala
rename to hail/modules/src/main/scala/is/hail/io/fs/TerraAzureStorageFS.scala
diff --git a/hail/src/main/scala/is/hail/io/fs/package.scala b/hail/modules/src/main/scala/is/hail/io/fs/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/fs/package.scala
rename to hail/modules/src/main/scala/is/hail/io/fs/package.scala
diff --git a/hail/src/main/scala/is/hail/io/gen/ExportBGEN.scala b/hail/modules/src/main/scala/is/hail/io/gen/ExportBGEN.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/gen/ExportBGEN.scala
rename to hail/modules/src/main/scala/is/hail/io/gen/ExportBGEN.scala
diff --git a/hail/src/main/scala/is/hail/io/gen/ExportGen.scala b/hail/modules/src/main/scala/is/hail/io/gen/ExportGen.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/gen/ExportGen.scala
rename to hail/modules/src/main/scala/is/hail/io/gen/ExportGen.scala
diff --git a/hail/src/main/scala/is/hail/io/hadoop/ByteArrayOutputFormat.scala b/hail/modules/src/main/scala/is/hail/io/hadoop/ByteArrayOutputFormat.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/hadoop/ByteArrayOutputFormat.scala
rename to hail/modules/src/main/scala/is/hail/io/hadoop/ByteArrayOutputFormat.scala
diff --git a/hail/src/main/scala/is/hail/io/hadoop/BytesOnlyWritable.scala b/hail/modules/src/main/scala/is/hail/io/hadoop/BytesOnlyWritable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/hadoop/BytesOnlyWritable.scala
rename to hail/modules/src/main/scala/is/hail/io/hadoop/BytesOnlyWritable.scala
diff --git a/hail/src/main/scala/is/hail/io/index/IndexReader.scala b/hail/modules/src/main/scala/is/hail/io/index/IndexReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/index/IndexReader.scala
rename to hail/modules/src/main/scala/is/hail/io/index/IndexReader.scala
diff --git a/hail/src/main/scala/is/hail/io/index/IndexWriter.scala b/hail/modules/src/main/scala/is/hail/io/index/IndexWriter.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/index/IndexWriter.scala
rename to hail/modules/src/main/scala/is/hail/io/index/IndexWriter.scala
diff --git a/hail/src/main/scala/is/hail/io/index/InternalNodeBuilder.scala b/hail/modules/src/main/scala/is/hail/io/index/InternalNodeBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/index/InternalNodeBuilder.scala
rename to hail/modules/src/main/scala/is/hail/io/index/InternalNodeBuilder.scala
diff --git a/hail/src/main/scala/is/hail/io/index/LeafNodeBuilder.scala b/hail/modules/src/main/scala/is/hail/io/index/LeafNodeBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/index/LeafNodeBuilder.scala
rename to hail/modules/src/main/scala/is/hail/io/index/LeafNodeBuilder.scala
diff --git a/hail/src/main/scala/is/hail/io/index/StagedIndexReader.scala b/hail/modules/src/main/scala/is/hail/io/index/StagedIndexReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/index/StagedIndexReader.scala
rename to hail/modules/src/main/scala/is/hail/io/index/StagedIndexReader.scala
diff --git a/hail/src/main/scala/is/hail/io/package.scala b/hail/modules/src/main/scala/is/hail/io/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/package.scala
rename to hail/modules/src/main/scala/is/hail/io/package.scala
diff --git a/hail/src/main/scala/is/hail/io/plink/ExportPlink.scala b/hail/modules/src/main/scala/is/hail/io/plink/ExportPlink.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/plink/ExportPlink.scala
rename to hail/modules/src/main/scala/is/hail/io/plink/ExportPlink.scala
diff --git a/hail/src/main/scala/is/hail/io/plink/LoadPlink.scala b/hail/modules/src/main/scala/is/hail/io/plink/LoadPlink.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/plink/LoadPlink.scala
rename to hail/modules/src/main/scala/is/hail/io/plink/LoadPlink.scala
diff --git a/hail/src/main/scala/is/hail/io/reference/FASTAReader.scala b/hail/modules/src/main/scala/is/hail/io/reference/FASTAReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/reference/FASTAReader.scala
rename to hail/modules/src/main/scala/is/hail/io/reference/FASTAReader.scala
diff --git a/hail/src/main/scala/is/hail/io/reference/LiftOver.scala b/hail/modules/src/main/scala/is/hail/io/reference/LiftOver.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/reference/LiftOver.scala
rename to hail/modules/src/main/scala/is/hail/io/reference/LiftOver.scala
diff --git a/hail/src/main/scala/is/hail/io/tabix/TabixReader.scala b/hail/modules/src/main/scala/is/hail/io/tabix/TabixReader.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/tabix/TabixReader.scala
rename to hail/modules/src/main/scala/is/hail/io/tabix/TabixReader.scala
diff --git a/hail/src/main/scala/is/hail/io/vcf/ExportVCF.scala b/hail/modules/src/main/scala/is/hail/io/vcf/ExportVCF.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/vcf/ExportVCF.scala
rename to hail/modules/src/main/scala/is/hail/io/vcf/ExportVCF.scala
diff --git a/hail/src/main/scala/is/hail/io/vcf/LoadVCF.scala b/hail/modules/src/main/scala/is/hail/io/vcf/LoadVCF.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/vcf/LoadVCF.scala
rename to hail/modules/src/main/scala/is/hail/io/vcf/LoadVCF.scala
diff --git a/hail/src/main/scala/is/hail/io/vcf/TabixReadVCFIterator.scala b/hail/modules/src/main/scala/is/hail/io/vcf/TabixReadVCFIterator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/io/vcf/TabixReadVCFIterator.scala
rename to hail/modules/src/main/scala/is/hail/io/vcf/TabixReadVCFIterator.scala
diff --git a/hail/src/main/scala/is/hail/kryo/HailKryoRegistrator.scala b/hail/modules/src/main/scala/is/hail/kryo/HailKryoRegistrator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/kryo/HailKryoRegistrator.scala
rename to hail/modules/src/main/scala/is/hail/kryo/HailKryoRegistrator.scala
diff --git a/hail/src/main/scala/is/hail/linalg/BLAS.scala b/hail/modules/src/main/scala/is/hail/linalg/BLAS.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/linalg/BLAS.scala
rename to hail/modules/src/main/scala/is/hail/linalg/BLAS.scala
diff --git a/hail/src/main/scala/is/hail/linalg/BlockMatrix.scala b/hail/modules/src/main/scala/is/hail/linalg/BlockMatrix.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/linalg/BlockMatrix.scala
rename to hail/modules/src/main/scala/is/hail/linalg/BlockMatrix.scala
diff --git a/hail/src/main/scala/is/hail/linalg/GridPartitioner.scala b/hail/modules/src/main/scala/is/hail/linalg/GridPartitioner.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/linalg/GridPartitioner.scala
rename to hail/modules/src/main/scala/is/hail/linalg/GridPartitioner.scala
diff --git a/hail/src/main/scala/is/hail/linalg/LAPACK.scala b/hail/modules/src/main/scala/is/hail/linalg/LAPACK.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/linalg/LAPACK.scala
rename to hail/modules/src/main/scala/is/hail/linalg/LAPACK.scala
diff --git a/hail/src/main/scala/is/hail/linalg/LinalgCodeUtils.scala b/hail/modules/src/main/scala/is/hail/linalg/LinalgCodeUtils.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/linalg/LinalgCodeUtils.scala
rename to hail/modules/src/main/scala/is/hail/linalg/LinalgCodeUtils.scala
diff --git a/hail/src/main/scala/is/hail/linalg/RowMatrix.scala b/hail/modules/src/main/scala/is/hail/linalg/RowMatrix.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/linalg/RowMatrix.scala
rename to hail/modules/src/main/scala/is/hail/linalg/RowMatrix.scala
diff --git a/hail/src/main/scala/is/hail/linalg/RowPartitioner.scala b/hail/modules/src/main/scala/is/hail/linalg/RowPartitioner.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/linalg/RowPartitioner.scala
rename to hail/modules/src/main/scala/is/hail/linalg/RowPartitioner.scala
diff --git a/hail/src/main/scala/is/hail/lir/Blocks.scala b/hail/modules/src/main/scala/is/hail/lir/Blocks.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/Blocks.scala
rename to hail/modules/src/main/scala/is/hail/lir/Blocks.scala
diff --git a/hail/src/main/scala/is/hail/lir/CFG.scala b/hail/modules/src/main/scala/is/hail/lir/CFG.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/CFG.scala
rename to hail/modules/src/main/scala/is/hail/lir/CFG.scala
diff --git a/hail/src/main/scala/is/hail/lir/Emit.scala b/hail/modules/src/main/scala/is/hail/lir/Emit.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/Emit.scala
rename to hail/modules/src/main/scala/is/hail/lir/Emit.scala
diff --git a/hail/src/main/scala/is/hail/lir/InitializeLocals.scala b/hail/modules/src/main/scala/is/hail/lir/InitializeLocals.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/InitializeLocals.scala
rename to hail/modules/src/main/scala/is/hail/lir/InitializeLocals.scala
diff --git a/hail/src/main/scala/is/hail/lir/Liveness.scala b/hail/modules/src/main/scala/is/hail/lir/Liveness.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/Liveness.scala
rename to hail/modules/src/main/scala/is/hail/lir/Liveness.scala
diff --git a/hail/src/main/scala/is/hail/lir/Locals.scala b/hail/modules/src/main/scala/is/hail/lir/Locals.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/Locals.scala
rename to hail/modules/src/main/scala/is/hail/lir/Locals.scala
diff --git a/hail/src/main/scala/is/hail/lir/PST.scala b/hail/modules/src/main/scala/is/hail/lir/PST.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/PST.scala
rename to hail/modules/src/main/scala/is/hail/lir/PST.scala
diff --git a/hail/src/main/scala/is/hail/lir/Pretty.scala b/hail/modules/src/main/scala/is/hail/lir/Pretty.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/Pretty.scala
rename to hail/modules/src/main/scala/is/hail/lir/Pretty.scala
diff --git a/hail/src/main/scala/is/hail/lir/SimplifyControl.scala b/hail/modules/src/main/scala/is/hail/lir/SimplifyControl.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/SimplifyControl.scala
rename to hail/modules/src/main/scala/is/hail/lir/SimplifyControl.scala
diff --git a/hail/src/main/scala/is/hail/lir/SplitLargeBlocks.scala b/hail/modules/src/main/scala/is/hail/lir/SplitLargeBlocks.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/SplitLargeBlocks.scala
rename to hail/modules/src/main/scala/is/hail/lir/SplitLargeBlocks.scala
diff --git a/hail/src/main/scala/is/hail/lir/SplitMethod.scala b/hail/modules/src/main/scala/is/hail/lir/SplitMethod.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/SplitMethod.scala
rename to hail/modules/src/main/scala/is/hail/lir/SplitMethod.scala
diff --git a/hail/src/main/scala/is/hail/lir/X.scala b/hail/modules/src/main/scala/is/hail/lir/X.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/X.scala
rename to hail/modules/src/main/scala/is/hail/lir/X.scala
diff --git a/hail/src/main/scala/is/hail/lir/package.scala b/hail/modules/src/main/scala/is/hail/lir/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/lir/package.scala
rename to hail/modules/src/main/scala/is/hail/lir/package.scala
diff --git a/hail/src/main/scala/is/hail/methods/FilterPartitions.scala b/hail/modules/src/main/scala/is/hail/methods/FilterPartitions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/FilterPartitions.scala
rename to hail/modules/src/main/scala/is/hail/methods/FilterPartitions.scala
diff --git a/hail/src/main/scala/is/hail/methods/ForceCount.scala b/hail/modules/src/main/scala/is/hail/methods/ForceCount.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/ForceCount.scala
rename to hail/modules/src/main/scala/is/hail/methods/ForceCount.scala
diff --git a/hail/src/main/scala/is/hail/methods/IBD.scala b/hail/modules/src/main/scala/is/hail/methods/IBD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/IBD.scala
rename to hail/modules/src/main/scala/is/hail/methods/IBD.scala
diff --git a/hail/src/main/scala/is/hail/methods/IBSFFI.scala b/hail/modules/src/main/scala/is/hail/methods/IBSFFI.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/IBSFFI.scala
rename to hail/modules/src/main/scala/is/hail/methods/IBSFFI.scala
diff --git a/hail/src/main/scala/is/hail/methods/LinearRegression.scala b/hail/modules/src/main/scala/is/hail/methods/LinearRegression.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/LinearRegression.scala
rename to hail/modules/src/main/scala/is/hail/methods/LinearRegression.scala
diff --git a/hail/src/main/scala/is/hail/methods/LocalLDPrune.scala b/hail/modules/src/main/scala/is/hail/methods/LocalLDPrune.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/LocalLDPrune.scala
rename to hail/modules/src/main/scala/is/hail/methods/LocalLDPrune.scala
diff --git a/hail/src/main/scala/is/hail/methods/LocalWhitening.scala b/hail/modules/src/main/scala/is/hail/methods/LocalWhitening.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/LocalWhitening.scala
rename to hail/modules/src/main/scala/is/hail/methods/LocalWhitening.scala
diff --git a/hail/src/main/scala/is/hail/methods/LogisticRegression.scala b/hail/modules/src/main/scala/is/hail/methods/LogisticRegression.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/LogisticRegression.scala
rename to hail/modules/src/main/scala/is/hail/methods/LogisticRegression.scala
diff --git a/hail/src/main/scala/is/hail/methods/MatrixExportEntriesByCol.scala b/hail/modules/src/main/scala/is/hail/methods/MatrixExportEntriesByCol.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/MatrixExportEntriesByCol.scala
rename to hail/modules/src/main/scala/is/hail/methods/MatrixExportEntriesByCol.scala
diff --git a/hail/src/main/scala/is/hail/methods/NPartitions.scala b/hail/modules/src/main/scala/is/hail/methods/NPartitions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/NPartitions.scala
rename to hail/modules/src/main/scala/is/hail/methods/NPartitions.scala
diff --git a/hail/src/main/scala/is/hail/methods/Nirvana.scala b/hail/modules/src/main/scala/is/hail/methods/Nirvana.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/Nirvana.scala
rename to hail/modules/src/main/scala/is/hail/methods/Nirvana.scala
diff --git a/hail/src/main/scala/is/hail/methods/PCA.scala b/hail/modules/src/main/scala/is/hail/methods/PCA.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/PCA.scala
rename to hail/modules/src/main/scala/is/hail/methods/PCA.scala
diff --git a/hail/src/main/scala/is/hail/methods/PCRelate.scala b/hail/modules/src/main/scala/is/hail/methods/PCRelate.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/PCRelate.scala
rename to hail/modules/src/main/scala/is/hail/methods/PCRelate.scala
diff --git a/hail/src/main/scala/is/hail/methods/PoissonRegression.scala b/hail/modules/src/main/scala/is/hail/methods/PoissonRegression.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/PoissonRegression.scala
rename to hail/modules/src/main/scala/is/hail/methods/PoissonRegression.scala
diff --git a/hail/src/main/scala/is/hail/methods/Skat.scala b/hail/modules/src/main/scala/is/hail/methods/Skat.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/Skat.scala
rename to hail/modules/src/main/scala/is/hail/methods/Skat.scala
diff --git a/hail/src/main/scala/is/hail/methods/VEP.scala b/hail/modules/src/main/scala/is/hail/methods/VEP.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/methods/VEP.scala
rename to hail/modules/src/main/scala/is/hail/methods/VEP.scala
diff --git a/hail/src/main/scala/is/hail/misc/BGZipBlocks.scala b/hail/modules/src/main/scala/is/hail/misc/BGZipBlocks.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/misc/BGZipBlocks.scala
rename to hail/modules/src/main/scala/is/hail/misc/BGZipBlocks.scala
diff --git a/hail/src/main/scala/is/hail/package.scala b/hail/modules/src/main/scala/is/hail/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/package.scala
rename to hail/modules/src/main/scala/is/hail/package.scala
diff --git a/hail/src/main/scala/is/hail/rvd/AbstractRVDSpec.scala b/hail/modules/src/main/scala/is/hail/rvd/AbstractRVDSpec.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/rvd/AbstractRVDSpec.scala
rename to hail/modules/src/main/scala/is/hail/rvd/AbstractRVDSpec.scala
diff --git a/hail/src/main/scala/is/hail/rvd/KeyedRVD.scala b/hail/modules/src/main/scala/is/hail/rvd/KeyedRVD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/rvd/KeyedRVD.scala
rename to hail/modules/src/main/scala/is/hail/rvd/KeyedRVD.scala
diff --git a/hail/src/main/scala/is/hail/rvd/PartitionBoundOrdering.scala b/hail/modules/src/main/scala/is/hail/rvd/PartitionBoundOrdering.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/rvd/PartitionBoundOrdering.scala
rename to hail/modules/src/main/scala/is/hail/rvd/PartitionBoundOrdering.scala
diff --git a/hail/src/main/scala/is/hail/rvd/RVD.scala b/hail/modules/src/main/scala/is/hail/rvd/RVD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/rvd/RVD.scala
rename to hail/modules/src/main/scala/is/hail/rvd/RVD.scala
diff --git a/hail/src/main/scala/is/hail/rvd/RVDContext.scala b/hail/modules/src/main/scala/is/hail/rvd/RVDContext.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/rvd/RVDContext.scala
rename to hail/modules/src/main/scala/is/hail/rvd/RVDContext.scala
diff --git a/hail/src/main/scala/is/hail/rvd/RVDPartitionInfo.scala b/hail/modules/src/main/scala/is/hail/rvd/RVDPartitionInfo.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/rvd/RVDPartitionInfo.scala
rename to hail/modules/src/main/scala/is/hail/rvd/RVDPartitionInfo.scala
diff --git a/hail/src/main/scala/is/hail/rvd/RVDPartitioner.scala b/hail/modules/src/main/scala/is/hail/rvd/RVDPartitioner.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/rvd/RVDPartitioner.scala
rename to hail/modules/src/main/scala/is/hail/rvd/RVDPartitioner.scala
diff --git a/hail/src/main/scala/is/hail/rvd/RVDType.scala b/hail/modules/src/main/scala/is/hail/rvd/RVDType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/rvd/RVDType.scala
rename to hail/modules/src/main/scala/is/hail/rvd/RVDType.scala
diff --git a/hail/src/main/scala/is/hail/services/BatchClient.scala b/hail/modules/src/main/scala/is/hail/services/BatchClient.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/services/BatchClient.scala
rename to hail/modules/src/main/scala/is/hail/services/BatchClient.scala
diff --git a/hail/src/main/scala/is/hail/services/BatchConfig.scala b/hail/modules/src/main/scala/is/hail/services/BatchConfig.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/services/BatchConfig.scala
rename to hail/modules/src/main/scala/is/hail/services/BatchConfig.scala
diff --git a/hail/src/main/scala/is/hail/services/DeployConfig.scala b/hail/modules/src/main/scala/is/hail/services/DeployConfig.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/services/DeployConfig.scala
rename to hail/modules/src/main/scala/is/hail/services/DeployConfig.scala
diff --git a/hail/src/main/scala/is/hail/services/JSONLogLayout.scala b/hail/modules/src/main/scala/is/hail/services/JSONLogLayout.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/services/JSONLogLayout.scala
rename to hail/modules/src/main/scala/is/hail/services/JSONLogLayout.scala
diff --git a/hail/src/main/scala/is/hail/services/NettyProxy.scala b/hail/modules/src/main/scala/is/hail/services/NettyProxy.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/services/NettyProxy.scala
rename to hail/modules/src/main/scala/is/hail/services/NettyProxy.scala
diff --git a/hail/src/main/scala/is/hail/services/README b/hail/modules/src/main/scala/is/hail/services/README
similarity index 100%
rename from hail/src/main/scala/is/hail/services/README
rename to hail/modules/src/main/scala/is/hail/services/README
diff --git a/hail/src/main/scala/is/hail/services/oauth2.scala b/hail/modules/src/main/scala/is/hail/services/oauth2.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/services/oauth2.scala
rename to hail/modules/src/main/scala/is/hail/services/oauth2.scala
diff --git a/hail/src/main/scala/is/hail/services/package.scala b/hail/modules/src/main/scala/is/hail/services/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/services/package.scala
rename to hail/modules/src/main/scala/is/hail/services/package.scala
diff --git a/hail/src/main/scala/is/hail/services/requests.scala b/hail/modules/src/main/scala/is/hail/services/requests.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/services/requests.scala
rename to hail/modules/src/main/scala/is/hail/services/requests.scala
diff --git a/hail/src/main/scala/is/hail/services/tls/package.scala b/hail/modules/src/main/scala/is/hail/services/tls/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/services/tls/package.scala
rename to hail/modules/src/main/scala/is/hail/services/tls/package.scala
diff --git a/hail/src/main/scala/is/hail/sparkextras/BlockedRDD.scala b/hail/modules/src/main/scala/is/hail/sparkextras/BlockedRDD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/sparkextras/BlockedRDD.scala
rename to hail/modules/src/main/scala/is/hail/sparkextras/BlockedRDD.scala
diff --git a/hail/src/main/scala/is/hail/sparkextras/ContextPairRDDFunctions.scala b/hail/modules/src/main/scala/is/hail/sparkextras/ContextPairRDDFunctions.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/sparkextras/ContextPairRDDFunctions.scala
rename to hail/modules/src/main/scala/is/hail/sparkextras/ContextPairRDDFunctions.scala
diff --git a/hail/src/main/scala/is/hail/sparkextras/ContextRDD.scala b/hail/modules/src/main/scala/is/hail/sparkextras/ContextRDD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/sparkextras/ContextRDD.scala
rename to hail/modules/src/main/scala/is/hail/sparkextras/ContextRDD.scala
diff --git a/hail/src/main/scala/is/hail/sparkextras/IndexReadRDD.scala b/hail/modules/src/main/scala/is/hail/sparkextras/IndexReadRDD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/sparkextras/IndexReadRDD.scala
rename to hail/modules/src/main/scala/is/hail/sparkextras/IndexReadRDD.scala
diff --git a/hail/src/main/scala/is/hail/sparkextras/MapPartitionsWithValueRDD.scala b/hail/modules/src/main/scala/is/hail/sparkextras/MapPartitionsWithValueRDD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/sparkextras/MapPartitionsWithValueRDD.scala
rename to hail/modules/src/main/scala/is/hail/sparkextras/MapPartitionsWithValueRDD.scala
diff --git a/hail/src/main/scala/is/hail/sparkextras/MultiWayZipPartitionsRDD.scala b/hail/modules/src/main/scala/is/hail/sparkextras/MultiWayZipPartitionsRDD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/sparkextras/MultiWayZipPartitionsRDD.scala
rename to hail/modules/src/main/scala/is/hail/sparkextras/MultiWayZipPartitionsRDD.scala
diff --git a/hail/src/main/scala/is/hail/sparkextras/OriginUnionRDD.scala b/hail/modules/src/main/scala/is/hail/sparkextras/OriginUnionRDD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/sparkextras/OriginUnionRDD.scala
rename to hail/modules/src/main/scala/is/hail/sparkextras/OriginUnionRDD.scala
diff --git a/hail/src/main/scala/is/hail/sparkextras/ReorderedPartitionsRDD.scala b/hail/modules/src/main/scala/is/hail/sparkextras/ReorderedPartitionsRDD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/sparkextras/ReorderedPartitionsRDD.scala
rename to hail/modules/src/main/scala/is/hail/sparkextras/ReorderedPartitionsRDD.scala
diff --git a/hail/src/main/scala/is/hail/sparkextras/RepartitionedOrderedRDD2.scala b/hail/modules/src/main/scala/is/hail/sparkextras/RepartitionedOrderedRDD2.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/sparkextras/RepartitionedOrderedRDD2.scala
rename to hail/modules/src/main/scala/is/hail/sparkextras/RepartitionedOrderedRDD2.scala
diff --git a/hail/src/main/scala/is/hail/stats/GeneralizedChiSquaredDistribution.scala b/hail/modules/src/main/scala/is/hail/stats/GeneralizedChiSquaredDistribution.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/stats/GeneralizedChiSquaredDistribution.scala
rename to hail/modules/src/main/scala/is/hail/stats/GeneralizedChiSquaredDistribution.scala
diff --git a/hail/src/main/scala/is/hail/stats/LeveneHaldane.scala b/hail/modules/src/main/scala/is/hail/stats/LeveneHaldane.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/stats/LeveneHaldane.scala
rename to hail/modules/src/main/scala/is/hail/stats/LeveneHaldane.scala
diff --git a/hail/src/main/scala/is/hail/stats/LinearMixedModel.scala b/hail/modules/src/main/scala/is/hail/stats/LinearMixedModel.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/stats/LinearMixedModel.scala
rename to hail/modules/src/main/scala/is/hail/stats/LinearMixedModel.scala
diff --git a/hail/src/main/scala/is/hail/stats/LinearRegressionModel.scala b/hail/modules/src/main/scala/is/hail/stats/LinearRegressionModel.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/stats/LinearRegressionModel.scala
rename to hail/modules/src/main/scala/is/hail/stats/LinearRegressionModel.scala
diff --git a/hail/src/main/scala/is/hail/stats/LogisticRegressionModel.scala b/hail/modules/src/main/scala/is/hail/stats/LogisticRegressionModel.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/stats/LogisticRegressionModel.scala
rename to hail/modules/src/main/scala/is/hail/stats/LogisticRegressionModel.scala
diff --git a/hail/src/main/scala/is/hail/stats/PoissonRegressionModel.scala b/hail/modules/src/main/scala/is/hail/stats/PoissonRegressionModel.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/stats/PoissonRegressionModel.scala
rename to hail/modules/src/main/scala/is/hail/stats/PoissonRegressionModel.scala
diff --git a/hail/src/main/scala/is/hail/stats/RegressionUtils.scala b/hail/modules/src/main/scala/is/hail/stats/RegressionUtils.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/stats/RegressionUtils.scala
rename to hail/modules/src/main/scala/is/hail/stats/RegressionUtils.scala
diff --git a/hail/src/main/scala/is/hail/stats/eigSymD.scala b/hail/modules/src/main/scala/is/hail/stats/eigSymD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/stats/eigSymD.scala
rename to hail/modules/src/main/scala/is/hail/stats/eigSymD.scala
diff --git a/hail/src/main/scala/is/hail/stats/package.scala b/hail/modules/src/main/scala/is/hail/stats/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/stats/package.scala
rename to hail/modules/src/main/scala/is/hail/stats/package.scala
diff --git a/hail/src/main/scala/is/hail/types/BaseType.scala b/hail/modules/src/main/scala/is/hail/types/BaseType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/BaseType.scala
rename to hail/modules/src/main/scala/is/hail/types/BaseType.scala
diff --git a/hail/src/main/scala/is/hail/types/Box.scala b/hail/modules/src/main/scala/is/hail/types/Box.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/Box.scala
rename to hail/modules/src/main/scala/is/hail/types/Box.scala
diff --git a/hail/src/main/scala/is/hail/types/MapTypes.scala b/hail/modules/src/main/scala/is/hail/types/MapTypes.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/MapTypes.scala
rename to hail/modules/src/main/scala/is/hail/types/MapTypes.scala
diff --git a/hail/src/main/scala/is/hail/types/TypeWithRequiredness.scala b/hail/modules/src/main/scala/is/hail/types/TypeWithRequiredness.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/TypeWithRequiredness.scala
rename to hail/modules/src/main/scala/is/hail/types/TypeWithRequiredness.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EArray.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EArray.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EArray.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EBaseStruct.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EBaseStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EBaseStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EBaseStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EBinary.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EBinary.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EBinary.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EBinary.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EBlockMatrixNDArray.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EBlockMatrixNDArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EBlockMatrixNDArray.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EBlockMatrixNDArray.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EBoolean.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EBoolean.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EBoolean.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EBoolean.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EContainer.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EContainer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EContainer.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EContainer.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EFloat32.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EFloat32.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EFloat32.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EFloat32.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EFloat64.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EFloat64.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EFloat64.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EFloat64.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EInt32.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EInt32.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EInt32.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EInt32.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EInt64.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EInt64.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EInt64.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EInt64.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/ENDArrayColumnMajor.scala b/hail/modules/src/main/scala/is/hail/types/encoded/ENDArrayColumnMajor.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/ENDArrayColumnMajor.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/ENDArrayColumnMajor.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/ENumpyBinaryNDArray.scala b/hail/modules/src/main/scala/is/hail/types/encoded/ENumpyBinaryNDArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/ENumpyBinaryNDArray.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/ENumpyBinaryNDArray.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/ERNGState.scala b/hail/modules/src/main/scala/is/hail/types/encoded/ERNGState.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/ERNGState.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/ERNGState.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EStructOfArrays.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EStructOfArrays.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EStructOfArrays.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EStructOfArrays.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EType.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EType.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EType.scala
diff --git a/hail/src/main/scala/is/hail/types/encoded/EUnsortedSet.scala b/hail/modules/src/main/scala/is/hail/types/encoded/EUnsortedSet.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/encoded/EUnsortedSet.scala
rename to hail/modules/src/main/scala/is/hail/types/encoded/EUnsortedSet.scala
diff --git a/hail/src/main/scala/is/hail/types/package.scala b/hail/modules/src/main/scala/is/hail/types/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/package.scala
rename to hail/modules/src/main/scala/is/hail/types/package.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PArray.scala b/hail/modules/src/main/scala/is/hail/types/physical/PArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PArray.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PArray.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PArrayBackedContainer.scala b/hail/modules/src/main/scala/is/hail/types/physical/PArrayBackedContainer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PArrayBackedContainer.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PArrayBackedContainer.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PBaseStruct.scala b/hail/modules/src/main/scala/is/hail/types/physical/PBaseStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PBaseStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PBaseStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PBinary.scala b/hail/modules/src/main/scala/is/hail/types/physical/PBinary.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PBinary.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PBinary.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PBoolean.scala b/hail/modules/src/main/scala/is/hail/types/physical/PBoolean.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PBoolean.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PBoolean.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCall.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCall.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCall.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCall.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalArray.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalArray.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalArray.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalBaseStruct.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalBaseStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalBaseStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalBaseStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalBinary.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalBinary.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalBinary.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalBinary.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalCall.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalCall.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalCall.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalCall.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalDict.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalDict.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalDict.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalDict.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalInterval.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalInterval.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalInterval.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalInterval.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalLocus.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalLocus.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalLocus.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalLocus.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalNDArray.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalNDArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalNDArray.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalNDArray.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalSet.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalSet.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalSet.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalSet.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalString.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalString.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalString.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalString.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalStruct.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PCanonicalTuple.scala b/hail/modules/src/main/scala/is/hail/types/physical/PCanonicalTuple.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PCanonicalTuple.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PCanonicalTuple.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PContainer.scala b/hail/modules/src/main/scala/is/hail/types/physical/PContainer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PContainer.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PContainer.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PDict.scala b/hail/modules/src/main/scala/is/hail/types/physical/PDict.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PDict.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PDict.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PField.scala b/hail/modules/src/main/scala/is/hail/types/physical/PField.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PField.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PField.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PFloat32.scala b/hail/modules/src/main/scala/is/hail/types/physical/PFloat32.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PFloat32.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PFloat32.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PFloat64.scala b/hail/modules/src/main/scala/is/hail/types/physical/PFloat64.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PFloat64.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PFloat64.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PInt32.scala b/hail/modules/src/main/scala/is/hail/types/physical/PInt32.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PInt32.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PInt32.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PInt64.scala b/hail/modules/src/main/scala/is/hail/types/physical/PInt64.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PInt64.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PInt64.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PInterval.scala b/hail/modules/src/main/scala/is/hail/types/physical/PInterval.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PInterval.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PInterval.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PIterable.scala b/hail/modules/src/main/scala/is/hail/types/physical/PIterable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PIterable.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PIterable.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PLocus.scala b/hail/modules/src/main/scala/is/hail/types/physical/PLocus.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PLocus.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PLocus.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PNDArray.scala b/hail/modules/src/main/scala/is/hail/types/physical/PNDArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PNDArray.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PNDArray.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PNumeric.scala b/hail/modules/src/main/scala/is/hail/types/physical/PNumeric.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PNumeric.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PNumeric.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PPrimitive.scala b/hail/modules/src/main/scala/is/hail/types/physical/PPrimitive.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PPrimitive.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PPrimitive.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PSet.scala b/hail/modules/src/main/scala/is/hail/types/physical/PSet.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PSet.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PSet.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PString.scala b/hail/modules/src/main/scala/is/hail/types/physical/PString.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PString.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PString.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PStruct.scala b/hail/modules/src/main/scala/is/hail/types/physical/PStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PSubsetStruct.scala b/hail/modules/src/main/scala/is/hail/types/physical/PSubsetStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PSubsetStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PSubsetStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PTuple.scala b/hail/modules/src/main/scala/is/hail/types/physical/PTuple.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PTuple.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PTuple.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PType.scala b/hail/modules/src/main/scala/is/hail/types/physical/PType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PType.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PType.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PUnrealizable.scala b/hail/modules/src/main/scala/is/hail/types/physical/PUnrealizable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PUnrealizable.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PUnrealizable.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/PVoid.scala b/hail/modules/src/main/scala/is/hail/types/physical/PVoid.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/PVoid.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/PVoid.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/StoredSTypePType.scala b/hail/modules/src/main/scala/is/hail/types/physical/StoredSTypePType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/StoredSTypePType.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/StoredSTypePType.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/package.scala b/hail/modules/src/main/scala/is/hail/types/physical/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/package.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/package.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/SCode.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/SCode.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/SCode.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/SCode.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/SType.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/SType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/SType.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/SType.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/SingleCodeSCode.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/SingleCodeSCode.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/SingleCodeSCode.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/SingleCodeSCode.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SInsertFieldsStruct.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SInsertFieldsStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SInsertFieldsStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SInsertFieldsStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaArray.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaArray.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaArray.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaBytes.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaBytes.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaBytes.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaBytes.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaString.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaString.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaString.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SJavaString.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SRNGState.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SRNGState.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SRNGState.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SRNGState.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStackInterval.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SStackInterval.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStackInterval.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SStackInterval.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStackStruct.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SStackStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStackStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SStackStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStringPointer.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SStringPointer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStringPointer.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SStringPointer.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStructView.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SStructView.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SStructView.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SStructView.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/concrete/SUnreachable.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SUnreachable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/concrete/SUnreachable.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/concrete/SUnreachable.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SBinary.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SBinary.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SBinary.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SBinary.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SCall.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SCall.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SCall.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SCall.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SContainer.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SContainer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SContainer.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SContainer.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SInterval.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SInterval.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SInterval.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SInterval.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SLocus.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SLocus.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SLocus.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SLocus.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SNDArray.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SNDArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SNDArray.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SNDArray.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SStream.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SStream.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SStream.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SString.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SString.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SString.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SString.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SVoid.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SVoid.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/SVoid.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/SVoid.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/interfaces/package.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/interfaces/package.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/interfaces/package.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SBoolean.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SBoolean.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SBoolean.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SBoolean.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat32.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat32.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat32.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat32.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat64.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat64.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat64.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SFloat64.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SInt32.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SInt32.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SInt32.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SInt32.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SInt64.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SInt64.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SInt64.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SInt64.scala
diff --git a/hail/src/main/scala/is/hail/types/physical/stypes/primitives/SPrimitive.scala b/hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SPrimitive.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/physical/stypes/primitives/SPrimitive.scala
rename to hail/modules/src/main/scala/is/hail/types/physical/stypes/primitives/SPrimitive.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/BlockMatrixType.scala b/hail/modules/src/main/scala/is/hail/types/virtual/BlockMatrixType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/BlockMatrixType.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/BlockMatrixType.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/Field.scala b/hail/modules/src/main/scala/is/hail/types/virtual/Field.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/Field.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/Field.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/MatrixType.scala b/hail/modules/src/main/scala/is/hail/types/virtual/MatrixType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/MatrixType.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/MatrixType.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TArray.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TArray.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TArray.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TBaseStruct.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TBaseStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TBaseStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TBaseStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TBinary.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TBinary.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TBinary.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TBinary.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TBoolean.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TBoolean.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TBoolean.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TBoolean.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TCall.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TCall.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TCall.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TCall.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TContainer.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TContainer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TContainer.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TContainer.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TDict.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TDict.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TDict.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TDict.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TFloat32.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TFloat32.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TFloat32.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TFloat32.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TFloat64.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TFloat64.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TFloat64.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TFloat64.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TInt32.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TInt32.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TInt32.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TInt32.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TInt64.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TInt64.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TInt64.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TInt64.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TIntegral.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TIntegral.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TIntegral.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TIntegral.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TInterval.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TInterval.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TInterval.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TInterval.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TIterable.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TIterable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TIterable.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TIterable.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TLocus.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TLocus.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TLocus.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TLocus.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TNDArray.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TNDArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TNDArray.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TNDArray.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TNumeric.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TNumeric.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TNumeric.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TNumeric.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TRNGState.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TRNGState.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TRNGState.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TRNGState.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TSet.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TSet.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TSet.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TSet.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TStream.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TStream.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TStream.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TString.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TString.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TString.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TString.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TStruct.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TStruct.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TStruct.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TStruct.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TTuple.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TTuple.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TTuple.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TTuple.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TUnion.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TUnion.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TUnion.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TUnion.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TVariable.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TVariable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TVariable.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TVariable.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TVoid.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TVoid.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TVoid.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TVoid.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/TableType.scala b/hail/modules/src/main/scala/is/hail/types/virtual/TableType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/TableType.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/TableType.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/Type.scala b/hail/modules/src/main/scala/is/hail/types/virtual/Type.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/Type.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/Type.scala
diff --git a/hail/src/main/scala/is/hail/types/virtual/VType.scala b/hail/modules/src/main/scala/is/hail/types/virtual/VType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/types/virtual/VType.scala
rename to hail/modules/src/main/scala/is/hail/types/virtual/VType.scala
diff --git a/hail/src/main/scala/is/hail/utils/AbsoluteFuzzyComparable.scala b/hail/modules/src/main/scala/is/hail/utils/AbsoluteFuzzyComparable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/AbsoluteFuzzyComparable.scala
rename to hail/modules/src/main/scala/is/hail/utils/AbsoluteFuzzyComparable.scala
diff --git a/hail/src/main/scala/is/hail/utils/ArrayOfByteArrayOutputStream.scala b/hail/modules/src/main/scala/is/hail/utils/ArrayOfByteArrayOutputStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/ArrayOfByteArrayOutputStream.scala
rename to hail/modules/src/main/scala/is/hail/utils/ArrayOfByteArrayOutputStream.scala
diff --git a/hail/src/main/scala/is/hail/utils/ArrayStack.scala b/hail/modules/src/main/scala/is/hail/utils/ArrayStack.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/ArrayStack.scala
rename to hail/modules/src/main/scala/is/hail/utils/ArrayStack.scala
diff --git a/hail/src/main/scala/is/hail/utils/BinaryHeap.scala b/hail/modules/src/main/scala/is/hail/utils/BinaryHeap.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/BinaryHeap.scala
rename to hail/modules/src/main/scala/is/hail/utils/BinaryHeap.scala
diff --git a/hail/src/main/scala/is/hail/utils/BitVector.scala b/hail/modules/src/main/scala/is/hail/utils/BitVector.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/BitVector.scala
rename to hail/modules/src/main/scala/is/hail/utils/BitVector.scala
diff --git a/hail/src/main/scala/is/hail/utils/Bitstring.scala b/hail/modules/src/main/scala/is/hail/utils/Bitstring.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/Bitstring.scala
rename to hail/modules/src/main/scala/is/hail/utils/Bitstring.scala
diff --git a/hail/src/main/scala/is/hail/utils/BoxedArrayBuilder.scala b/hail/modules/src/main/scala/is/hail/utils/BoxedArrayBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/BoxedArrayBuilder.scala
rename to hail/modules/src/main/scala/is/hail/utils/BoxedArrayBuilder.scala
diff --git a/hail/src/main/scala/is/hail/utils/BufferedAggregatorIterator.scala b/hail/modules/src/main/scala/is/hail/utils/BufferedAggregatorIterator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/BufferedAggregatorIterator.scala
rename to hail/modules/src/main/scala/is/hail/utils/BufferedAggregatorIterator.scala
diff --git a/hail/src/main/scala/is/hail/utils/BytePacker.scala b/hail/modules/src/main/scala/is/hail/utils/BytePacker.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/BytePacker.scala
rename to hail/modules/src/main/scala/is/hail/utils/BytePacker.scala
diff --git a/hail/src/main/scala/is/hail/utils/ByteTrackingInputStream.scala b/hail/modules/src/main/scala/is/hail/utils/ByteTrackingInputStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/ByteTrackingInputStream.scala
rename to hail/modules/src/main/scala/is/hail/utils/ByteTrackingInputStream.scala
diff --git a/hail/src/main/scala/is/hail/utils/Cache.scala b/hail/modules/src/main/scala/is/hail/utils/Cache.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/Cache.scala
rename to hail/modules/src/main/scala/is/hail/utils/Cache.scala
diff --git a/hail/src/main/scala/is/hail/utils/CompressionUtils.scala b/hail/modules/src/main/scala/is/hail/utils/CompressionUtils.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/CompressionUtils.scala
rename to hail/modules/src/main/scala/is/hail/utils/CompressionUtils.scala
diff --git a/hail/src/main/scala/is/hail/utils/Context.scala b/hail/modules/src/main/scala/is/hail/utils/Context.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/Context.scala
rename to hail/modules/src/main/scala/is/hail/utils/Context.scala
diff --git a/hail/src/main/scala/is/hail/utils/DateFormatUtils.scala b/hail/modules/src/main/scala/is/hail/utils/DateFormatUtils.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/DateFormatUtils.scala
rename to hail/modules/src/main/scala/is/hail/utils/DateFormatUtils.scala
diff --git a/hail/src/main/scala/is/hail/utils/DoubleNumericConversion.scala b/hail/modules/src/main/scala/is/hail/utils/DoubleNumericConversion.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/DoubleNumericConversion.scala
rename to hail/modules/src/main/scala/is/hail/utils/DoubleNumericConversion.scala
diff --git a/hail/src/main/scala/is/hail/utils/EitherIsAMonad.scala b/hail/modules/src/main/scala/is/hail/utils/EitherIsAMonad.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/EitherIsAMonad.scala
rename to hail/modules/src/main/scala/is/hail/utils/EitherIsAMonad.scala
diff --git a/hail/src/main/scala/is/hail/utils/ErrorHandling.scala b/hail/modules/src/main/scala/is/hail/utils/ErrorHandling.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/ErrorHandling.scala
rename to hail/modules/src/main/scala/is/hail/utils/ErrorHandling.scala
diff --git a/hail/src/main/scala/is/hail/utils/ExecutionTimer.scala b/hail/modules/src/main/scala/is/hail/utils/ExecutionTimer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/ExecutionTimer.scala
rename to hail/modules/src/main/scala/is/hail/utils/ExecutionTimer.scala
diff --git a/hail/src/main/scala/is/hail/utils/ExportType.scala b/hail/modules/src/main/scala/is/hail/utils/ExportType.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/ExportType.scala
rename to hail/modules/src/main/scala/is/hail/utils/ExportType.scala
diff --git a/hail/src/main/scala/is/hail/utils/FastSeq.scala b/hail/modules/src/main/scala/is/hail/utils/FastSeq.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/FastSeq.scala
rename to hail/modules/src/main/scala/is/hail/utils/FastSeq.scala
diff --git a/hail/src/main/scala/is/hail/utils/FlipbookIterator.scala b/hail/modules/src/main/scala/is/hail/utils/FlipbookIterator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/FlipbookIterator.scala
rename to hail/modules/src/main/scala/is/hail/utils/FlipbookIterator.scala
diff --git a/hail/src/main/scala/is/hail/utils/Graph.scala b/hail/modules/src/main/scala/is/hail/utils/Graph.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/Graph.scala
rename to hail/modules/src/main/scala/is/hail/utils/Graph.scala
diff --git a/hail/src/main/scala/is/hail/utils/HTTPClient.scala b/hail/modules/src/main/scala/is/hail/utils/HTTPClient.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/HTTPClient.scala
rename to hail/modules/src/main/scala/is/hail/utils/HTTPClient.scala
diff --git a/hail/src/main/scala/is/hail/utils/HailIterator.scala b/hail/modules/src/main/scala/is/hail/utils/HailIterator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/HailIterator.scala
rename to hail/modules/src/main/scala/is/hail/utils/HailIterator.scala
diff --git a/hail/src/main/scala/is/hail/utils/HashMethods.scala b/hail/modules/src/main/scala/is/hail/utils/HashMethods.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/HashMethods.scala
rename to hail/modules/src/main/scala/is/hail/utils/HashMethods.scala
diff --git a/hail/src/main/scala/is/hail/utils/Interval.scala b/hail/modules/src/main/scala/is/hail/utils/Interval.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/Interval.scala
rename to hail/modules/src/main/scala/is/hail/utils/Interval.scala
diff --git a/hail/src/main/scala/is/hail/utils/JSON.scala b/hail/modules/src/main/scala/is/hail/utils/JSON.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/JSON.scala
rename to hail/modules/src/main/scala/is/hail/utils/JSON.scala
diff --git a/hail/src/main/scala/is/hail/utils/LoggerOutputStream.scala b/hail/modules/src/main/scala/is/hail/utils/LoggerOutputStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/LoggerOutputStream.scala
rename to hail/modules/src/main/scala/is/hail/utils/LoggerOutputStream.scala
diff --git a/hail/src/main/scala/is/hail/utils/Logging.scala b/hail/modules/src/main/scala/is/hail/utils/Logging.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/Logging.scala
rename to hail/modules/src/main/scala/is/hail/utils/Logging.scala
diff --git a/hail/src/main/scala/is/hail/utils/MemoryBufferWrapper.scala b/hail/modules/src/main/scala/is/hail/utils/MemoryBufferWrapper.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/MemoryBufferWrapper.scala
rename to hail/modules/src/main/scala/is/hail/utils/MemoryBufferWrapper.scala
diff --git a/hail/src/main/scala/is/hail/utils/MissingArrayBuilder.scala b/hail/modules/src/main/scala/is/hail/utils/MissingArrayBuilder.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/MissingArrayBuilder.scala
rename to hail/modules/src/main/scala/is/hail/utils/MissingArrayBuilder.scala
diff --git a/hail/src/main/scala/is/hail/utils/MultiArray2.scala b/hail/modules/src/main/scala/is/hail/utils/MultiArray2.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/MultiArray2.scala
rename to hail/modules/src/main/scala/is/hail/utils/MultiArray2.scala
diff --git a/hail/src/main/scala/is/hail/utils/Muple.scala b/hail/modules/src/main/scala/is/hail/utils/Muple.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/Muple.scala
rename to hail/modules/src/main/scala/is/hail/utils/Muple.scala
diff --git a/hail/src/main/scala/is/hail/utils/NumericImplicits.scala b/hail/modules/src/main/scala/is/hail/utils/NumericImplicits.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/NumericImplicits.scala
rename to hail/modules/src/main/scala/is/hail/utils/NumericImplicits.scala
diff --git a/hail/src/main/scala/is/hail/utils/NumericPair.scala b/hail/modules/src/main/scala/is/hail/utils/NumericPair.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/NumericPair.scala
rename to hail/modules/src/main/scala/is/hail/utils/NumericPair.scala
diff --git a/hail/src/main/scala/is/hail/utils/OrderingView.scala b/hail/modules/src/main/scala/is/hail/utils/OrderingView.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/OrderingView.scala
rename to hail/modules/src/main/scala/is/hail/utils/OrderingView.scala
diff --git a/hail/src/main/scala/is/hail/utils/ParseTrieNode.scala b/hail/modules/src/main/scala/is/hail/utils/ParseTrieNode.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/ParseTrieNode.scala
rename to hail/modules/src/main/scala/is/hail/utils/ParseTrieNode.scala
diff --git a/hail/src/main/scala/is/hail/utils/PartitionCounts.scala b/hail/modules/src/main/scala/is/hail/utils/PartitionCounts.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/PartitionCounts.scala
rename to hail/modules/src/main/scala/is/hail/utils/PartitionCounts.scala
diff --git a/hail/src/main/scala/is/hail/utils/Py4jUtils.scala b/hail/modules/src/main/scala/is/hail/utils/Py4jUtils.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/Py4jUtils.scala
rename to hail/modules/src/main/scala/is/hail/utils/Py4jUtils.scala
diff --git a/hail/src/main/scala/is/hail/utils/RelativeFuzzyComparable.scala b/hail/modules/src/main/scala/is/hail/utils/RelativeFuzzyComparable.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/RelativeFuzzyComparable.scala
rename to hail/modules/src/main/scala/is/hail/utils/RelativeFuzzyComparable.scala
diff --git a/hail/src/main/scala/is/hail/utils/RestartableByteArrayInputStream.scala b/hail/modules/src/main/scala/is/hail/utils/RestartableByteArrayInputStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/RestartableByteArrayInputStream.scala
rename to hail/modules/src/main/scala/is/hail/utils/RestartableByteArrayInputStream.scala
diff --git a/hail/src/main/scala/is/hail/utils/SemanticVersion.scala b/hail/modules/src/main/scala/is/hail/utils/SemanticVersion.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/SemanticVersion.scala
rename to hail/modules/src/main/scala/is/hail/utils/SemanticVersion.scala
diff --git a/hail/src/main/scala/is/hail/utils/SerializableHadoopConfiguration.scala b/hail/modules/src/main/scala/is/hail/utils/SerializableHadoopConfiguration.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/SerializableHadoopConfiguration.scala
rename to hail/modules/src/main/scala/is/hail/utils/SerializableHadoopConfiguration.scala
diff --git a/hail/src/main/scala/is/hail/utils/SpillingCollectIterator.scala b/hail/modules/src/main/scala/is/hail/utils/SpillingCollectIterator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/SpillingCollectIterator.scala
rename to hail/modules/src/main/scala/is/hail/utils/SpillingCollectIterator.scala
diff --git a/hail/src/main/scala/is/hail/utils/StackSafe.scala b/hail/modules/src/main/scala/is/hail/utils/StackSafe.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/StackSafe.scala
rename to hail/modules/src/main/scala/is/hail/utils/StackSafe.scala
diff --git a/hail/src/main/scala/is/hail/utils/StringEscapeUtils.scala b/hail/modules/src/main/scala/is/hail/utils/StringEscapeUtils.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/StringEscapeUtils.scala
rename to hail/modules/src/main/scala/is/hail/utils/StringEscapeUtils.scala
diff --git a/hail/src/main/scala/is/hail/utils/StringSocketAppender.scala b/hail/modules/src/main/scala/is/hail/utils/StringSocketAppender.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/StringSocketAppender.scala
rename to hail/modules/src/main/scala/is/hail/utils/StringSocketAppender.scala
diff --git a/hail/src/main/scala/is/hail/utils/TextInputFilterAndReplace.scala b/hail/modules/src/main/scala/is/hail/utils/TextInputFilterAndReplace.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/TextInputFilterAndReplace.scala
rename to hail/modules/src/main/scala/is/hail/utils/TextInputFilterAndReplace.scala
diff --git a/hail/src/main/scala/is/hail/utils/Traceback.scala b/hail/modules/src/main/scala/is/hail/utils/Traceback.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/Traceback.scala
rename to hail/modules/src/main/scala/is/hail/utils/Traceback.scala
diff --git a/hail/src/main/scala/is/hail/utils/TracingInputStream.scala b/hail/modules/src/main/scala/is/hail/utils/TracingInputStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/TracingInputStream.scala
rename to hail/modules/src/main/scala/is/hail/utils/TracingInputStream.scala
diff --git a/hail/src/main/scala/is/hail/utils/TracingOutputStream.scala b/hail/modules/src/main/scala/is/hail/utils/TracingOutputStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/TracingOutputStream.scala
rename to hail/modules/src/main/scala/is/hail/utils/TracingOutputStream.scala
diff --git a/hail/src/main/scala/is/hail/utils/TreeTraversal.scala b/hail/modules/src/main/scala/is/hail/utils/TreeTraversal.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/TreeTraversal.scala
rename to hail/modules/src/main/scala/is/hail/utils/TreeTraversal.scala
diff --git a/hail/src/main/scala/is/hail/utils/TruncatedArrayIndexedSeq.scala b/hail/modules/src/main/scala/is/hail/utils/TruncatedArrayIndexedSeq.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/TruncatedArrayIndexedSeq.scala
rename to hail/modules/src/main/scala/is/hail/utils/TruncatedArrayIndexedSeq.scala
diff --git a/hail/src/main/scala/is/hail/utils/TryAll.scala b/hail/modules/src/main/scala/is/hail/utils/TryAll.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/TryAll.scala
rename to hail/modules/src/main/scala/is/hail/utils/TryAll.scala
diff --git a/hail/src/main/scala/is/hail/utils/UnionFind.scala b/hail/modules/src/main/scala/is/hail/utils/UnionFind.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/UnionFind.scala
rename to hail/modules/src/main/scala/is/hail/utils/UnionFind.scala
diff --git a/hail/src/main/scala/is/hail/utils/package.scala b/hail/modules/src/main/scala/is/hail/utils/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/package.scala
rename to hail/modules/src/main/scala/is/hail/utils/package.scala
diff --git a/hail/src/main/scala/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala b/hail/modules/src/main/scala/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala
rename to hail/modules/src/main/scala/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala
diff --git a/hail/src/main/scala/is/hail/utils/prettyPrint/PrettyPrintWriter.scala b/hail/modules/src/main/scala/is/hail/utils/prettyPrint/PrettyPrintWriter.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/prettyPrint/PrettyPrintWriter.scala
rename to hail/modules/src/main/scala/is/hail/utils/prettyPrint/PrettyPrintWriter.scala
diff --git a/hail/src/main/scala/is/hail/utils/prettyPrint/package.scala b/hail/modules/src/main/scala/is/hail/utils/prettyPrint/package.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/prettyPrint/package.scala
rename to hail/modules/src/main/scala/is/hail/utils/prettyPrint/package.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/ByteTrackingOutputStream.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/ByteTrackingOutputStream.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/ByteTrackingOutputStream.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/ByteTrackingOutputStream.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/Implicits.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/Implicits.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/Implicits.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/Implicits.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichArray.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichArray.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichArray.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichArray.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichBoolean.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichBoolean.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichBoolean.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichBoolean.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichCodeInputBuffer.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichCodeInputBuffer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichCodeInputBuffer.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichCodeInputBuffer.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichCodeIterator.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichCodeIterator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichCodeIterator.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichCodeIterator.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichCodeOutputBuffer.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichCodeOutputBuffer.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichCodeOutputBuffer.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichCodeOutputBuffer.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichCodeRegion.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichCodeRegion.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichCodeRegion.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichCodeRegion.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichContextIterator.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichContextIterator.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichContextIterator.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichContextIterator.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichContextRDD.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichContextRDD.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichContextRDD.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichContextRDD.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichContextRDDRow.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichContextRDDRow.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichContextRDDRow.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichContextRDDRow.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichDenseMatrixDouble.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichDenseMatrixDouble.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichDenseMatrixDouble.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichDenseMatrixDouble.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichEnumeration.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichEnumeration.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichEnumeration.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichEnumeration.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichIndexedRowMatrix.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichIndexedRowMatrix.scala
similarity index 100%
rename from hail/src/main/scala/is/hail/utils/richUtils/RichIndexedRowMatrix.scala
rename to hail/modules/src/main/scala/is/hail/utils/richUtils/RichIndexedRowMatrix.scala
diff --git a/hail/src/main/scala/is/hail/utils/richUtils/RichIndexedSeq.scala b/hail/modules/src/main/scala/is/hail/utils/richUtils/RichIndexedSeq.scala
similarity index 100%
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diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG01378.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01378.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG01378.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01378.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG01378.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01378.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG01378.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01378.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG01383.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01383.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG01383.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01383.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG01383.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01383.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG01383.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01383.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG01384.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01384.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG01384.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01384.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG01384.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01384.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG01384.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG01384.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG02188.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02188.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG02188.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02188.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG02188.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02188.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG02188.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02188.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG02223.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02223.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG02223.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02223.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG02223.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02223.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG02223.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02223.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG02224.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02224.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG02224.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02224.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG02224.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02224.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG02224.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02224.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG02230.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02230.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG02230.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02230.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG02230.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02230.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG02230.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG02230.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG03088.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03088.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG03088.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03088.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG03088.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03088.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG03088.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03088.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG03363.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03363.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG03363.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03363.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG03363.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03363.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG03363.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03363.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG03578.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03578.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG03578.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03578.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG03578.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03578.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG03578.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03578.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG03805.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03805.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG03805.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03805.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG03805.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03805.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG03805.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03805.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG03833.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03833.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG03833.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03833.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG03833.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03833.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG03833.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG03833.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG04001.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG04001.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG04001.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG04001.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG04001.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG04001.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG04001.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG04001.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG04158.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG04158.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG04158.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG04158.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/HG04158.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/HG04158.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/HG04158.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/HG04158.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA11830.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA11830.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA11830.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA11830.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA11830.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA11830.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA11830.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA11830.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA12249.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA12249.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA12249.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA12249.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA12249.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA12249.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA12249.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA12249.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18507.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18507.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18507.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18507.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18507.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18507.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18507.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18507.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18530.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18530.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18530.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18530.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18530.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18530.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18530.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18530.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18534.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18534.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18534.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18534.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18534.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18534.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18534.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18534.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18609.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18609.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18609.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18609.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18609.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18609.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18609.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18609.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18613.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18613.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18613.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18613.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18613.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18613.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18613.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18613.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18618.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18618.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18618.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18618.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18618.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18618.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18618.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18618.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18969.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18969.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18969.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18969.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA18969.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18969.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA18969.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA18969.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA19456.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA19456.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA19456.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA19456.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA19456.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA19456.hg38.g.vcf.gz.tbi
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA19456.hg38.g.vcf.gz.tbi
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA19456.hg38.g.vcf.gz.tbi
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA19747.hg38.g.vcf.gz b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA19747.hg38.g.vcf.gz
similarity index 100%
rename from hail/src/test/resources/gvcfs/1kg_chr22/NA19747.hg38.g.vcf.gz
rename to hail/modules/src/test/resources/gvcfs/1kg_chr22/NA19747.hg38.g.vcf.gz
diff --git a/hail/src/test/resources/gvcfs/1kg_chr22/NA19747.hg38.g.vcf.gz.tbi b/hail/modules/src/test/resources/gvcfs/1kg_chr22/NA19747.hg38.g.vcf.gz.tbi
similarity index 100%
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diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/metadata.json.gz b/hail/modules/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/metadata.json.gz
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diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/metadata.json.gz b/hail/modules/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/metadata.json.gz
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diff --git a/hail/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825 b/hail/modules/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825
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rename to hail/modules/src/test/resources/vds/1kg_chr22_5_samples.vds/variant_data/rows/rows/parts/part-0-17-0-0-d938f6be-dda9-85ad-2638-838d588ae825
diff --git a/hail/src/test/resources/vep_grch38_input_req_indexed_cache.tsv b/hail/modules/src/test/resources/vep_grch38_input_req_indexed_cache.tsv
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diff --git a/hail/src/test/scala/is/hail/expr/ir/TakeByAggregatorSuite.scala b/hail/modules/src/test/scala/is/hail/expr/ir/TakeByAggregatorSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/expr/ir/TakeByAggregatorSuite.scala
rename to hail/modules/src/test/scala/is/hail/expr/ir/TakeByAggregatorSuite.scala
diff --git a/hail/src/test/scala/is/hail/expr/ir/TestUtils.scala b/hail/modules/src/test/scala/is/hail/expr/ir/TestUtils.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/expr/ir/TestUtils.scala
rename to hail/modules/src/test/scala/is/hail/expr/ir/TestUtils.scala
diff --git a/hail/src/test/scala/is/hail/expr/ir/TrapNodeSuite.scala b/hail/modules/src/test/scala/is/hail/expr/ir/TrapNodeSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/expr/ir/TrapNodeSuite.scala
rename to hail/modules/src/test/scala/is/hail/expr/ir/TrapNodeSuite.scala
diff --git a/hail/src/test/scala/is/hail/expr/ir/UtilFunctionsSuite.scala b/hail/modules/src/test/scala/is/hail/expr/ir/UtilFunctionsSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/expr/ir/UtilFunctionsSuite.scala
rename to hail/modules/src/test/scala/is/hail/expr/ir/UtilFunctionsSuite.scala
diff --git a/hail/src/test/scala/is/hail/expr/ir/agg/DownsampleSuite.scala b/hail/modules/src/test/scala/is/hail/expr/ir/agg/DownsampleSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/expr/ir/agg/DownsampleSuite.scala
rename to hail/modules/src/test/scala/is/hail/expr/ir/agg/DownsampleSuite.scala
diff --git a/hail/src/test/scala/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala b/hail/modules/src/test/scala/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala
similarity index 100%
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rename to hail/modules/src/test/scala/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala
diff --git a/hail/src/test/scala/is/hail/expr/ir/analyses/SemanticHashSuite.scala b/hail/modules/src/test/scala/is/hail/expr/ir/analyses/SemanticHashSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/expr/ir/analyses/SemanticHashSuite.scala
rename to hail/modules/src/test/scala/is/hail/expr/ir/analyses/SemanticHashSuite.scala
diff --git a/hail/src/test/scala/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala b/hail/modules/src/test/scala/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala
rename to hail/modules/src/test/scala/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala
diff --git a/hail/src/test/scala/is/hail/expr/ir/table/TableGenSuite.scala b/hail/modules/src/test/scala/is/hail/expr/ir/table/TableGenSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/expr/ir/table/TableGenSuite.scala
rename to hail/modules/src/test/scala/is/hail/expr/ir/table/TableGenSuite.scala
diff --git a/hail/src/test/scala/is/hail/io/AvroReaderSuite.scala b/hail/modules/src/test/scala/is/hail/io/AvroReaderSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/io/AvroReaderSuite.scala
rename to hail/modules/src/test/scala/is/hail/io/AvroReaderSuite.scala
diff --git a/hail/src/test/scala/is/hail/io/ByteArrayReaderSuite.scala b/hail/modules/src/test/scala/is/hail/io/ByteArrayReaderSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/io/ByteArrayReaderSuite.scala
rename to hail/modules/src/test/scala/is/hail/io/ByteArrayReaderSuite.scala
diff --git a/hail/src/test/scala/is/hail/io/IndexBTreeSuite.scala b/hail/modules/src/test/scala/is/hail/io/IndexBTreeSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/io/IndexBTreeSuite.scala
rename to hail/modules/src/test/scala/is/hail/io/IndexBTreeSuite.scala
diff --git a/hail/src/test/scala/is/hail/io/IndexSuite.scala b/hail/modules/src/test/scala/is/hail/io/IndexSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/io/IndexSuite.scala
rename to hail/modules/src/test/scala/is/hail/io/IndexSuite.scala
diff --git a/hail/src/test/scala/is/hail/io/TabixSuite.scala b/hail/modules/src/test/scala/is/hail/io/TabixSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/io/TabixSuite.scala
rename to hail/modules/src/test/scala/is/hail/io/TabixSuite.scala
diff --git a/hail/src/test/scala/is/hail/io/compress/BGzipCodecSuite.scala b/hail/modules/src/test/scala/is/hail/io/compress/BGzipCodecSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/io/compress/BGzipCodecSuite.scala
rename to hail/modules/src/test/scala/is/hail/io/compress/BGzipCodecSuite.scala
diff --git a/hail/src/test/scala/is/hail/io/fs/AzureStorageFSSuite.scala b/hail/modules/src/test/scala/is/hail/io/fs/AzureStorageFSSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/io/fs/AzureStorageFSSuite.scala
rename to hail/modules/src/test/scala/is/hail/io/fs/AzureStorageFSSuite.scala
diff --git a/hail/src/test/scala/is/hail/io/fs/FSSuite.scala b/hail/modules/src/test/scala/is/hail/io/fs/FSSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/io/fs/FSSuite.scala
rename to hail/modules/src/test/scala/is/hail/io/fs/FSSuite.scala
diff --git a/hail/src/test/scala/is/hail/io/fs/FakeFS.scala b/hail/modules/src/test/scala/is/hail/io/fs/FakeFS.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/io/fs/FakeFS.scala
rename to hail/modules/src/test/scala/is/hail/io/fs/FakeFS.scala
diff --git a/hail/src/test/scala/is/hail/io/fs/GoogleStorageFSSuite.scala b/hail/modules/src/test/scala/is/hail/io/fs/GoogleStorageFSSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/io/fs/GoogleStorageFSSuite.scala
rename to hail/modules/src/test/scala/is/hail/io/fs/GoogleStorageFSSuite.scala
diff --git a/hail/src/test/scala/is/hail/linalg/BlockMatrixSuite.scala b/hail/modules/src/test/scala/is/hail/linalg/BlockMatrixSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/linalg/BlockMatrixSuite.scala
rename to hail/modules/src/test/scala/is/hail/linalg/BlockMatrixSuite.scala
diff --git a/hail/src/test/scala/is/hail/linalg/GridPartitionerSuite.scala b/hail/modules/src/test/scala/is/hail/linalg/GridPartitionerSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/linalg/GridPartitionerSuite.scala
rename to hail/modules/src/test/scala/is/hail/linalg/GridPartitionerSuite.scala
diff --git a/hail/src/test/scala/is/hail/linalg/RowMatrixSuite.scala b/hail/modules/src/test/scala/is/hail/linalg/RowMatrixSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/linalg/RowMatrixSuite.scala
rename to hail/modules/src/test/scala/is/hail/linalg/RowMatrixSuite.scala
diff --git a/hail/src/test/scala/is/hail/linalg/RowPartitionerSuite.scala b/hail/modules/src/test/scala/is/hail/linalg/RowPartitionerSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/linalg/RowPartitionerSuite.scala
rename to hail/modules/src/test/scala/is/hail/linalg/RowPartitionerSuite.scala
diff --git a/hail/src/test/scala/is/hail/lir/CompileTimeRequirednessSuite.scala b/hail/modules/src/test/scala/is/hail/lir/CompileTimeRequirednessSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/lir/CompileTimeRequirednessSuite.scala
rename to hail/modules/src/test/scala/is/hail/lir/CompileTimeRequirednessSuite.scala
diff --git a/hail/src/test/scala/is/hail/lir/LIRSplitSuite.scala b/hail/modules/src/test/scala/is/hail/lir/LIRSplitSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/lir/LIRSplitSuite.scala
rename to hail/modules/src/test/scala/is/hail/lir/LIRSplitSuite.scala
diff --git a/hail/src/test/scala/is/hail/methods/ExprSuite.scala b/hail/modules/src/test/scala/is/hail/methods/ExprSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/methods/ExprSuite.scala
rename to hail/modules/src/test/scala/is/hail/methods/ExprSuite.scala
diff --git a/hail/src/test/scala/is/hail/methods/LocalLDPruneSuite.scala b/hail/modules/src/test/scala/is/hail/methods/LocalLDPruneSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/methods/LocalLDPruneSuite.scala
rename to hail/modules/src/test/scala/is/hail/methods/LocalLDPruneSuite.scala
diff --git a/hail/src/test/scala/is/hail/methods/MultiArray2Suite.scala b/hail/modules/src/test/scala/is/hail/methods/MultiArray2Suite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/methods/MultiArray2Suite.scala
rename to hail/modules/src/test/scala/is/hail/methods/MultiArray2Suite.scala
diff --git a/hail/src/test/scala/is/hail/methods/SkatSuite.scala b/hail/modules/src/test/scala/is/hail/methods/SkatSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/methods/SkatSuite.scala
rename to hail/modules/src/test/scala/is/hail/methods/SkatSuite.scala
diff --git a/hail/src/test/scala/is/hail/rvd/RVDPartitionerSuite.scala b/hail/modules/src/test/scala/is/hail/rvd/RVDPartitionerSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/rvd/RVDPartitionerSuite.scala
rename to hail/modules/src/test/scala/is/hail/rvd/RVDPartitionerSuite.scala
diff --git a/hail/src/test/scala/is/hail/services/BatchClientSuite.scala b/hail/modules/src/test/scala/is/hail/services/BatchClientSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/services/BatchClientSuite.scala
rename to hail/modules/src/test/scala/is/hail/services/BatchClientSuite.scala
diff --git a/hail/src/test/scala/is/hail/stats/FisherExactTestSuite.scala b/hail/modules/src/test/scala/is/hail/stats/FisherExactTestSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/stats/FisherExactTestSuite.scala
rename to hail/modules/src/test/scala/is/hail/stats/FisherExactTestSuite.scala
diff --git a/hail/src/test/scala/is/hail/stats/GeneralizedChiSquaredDistributionSuite.scala b/hail/modules/src/test/scala/is/hail/stats/GeneralizedChiSquaredDistributionSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/stats/GeneralizedChiSquaredDistributionSuite.scala
rename to hail/modules/src/test/scala/is/hail/stats/GeneralizedChiSquaredDistributionSuite.scala
diff --git a/hail/src/test/scala/is/hail/stats/LeveneHaldaneSuite.scala b/hail/modules/src/test/scala/is/hail/stats/LeveneHaldaneSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/stats/LeveneHaldaneSuite.scala
rename to hail/modules/src/test/scala/is/hail/stats/LeveneHaldaneSuite.scala
diff --git a/hail/src/test/scala/is/hail/stats/LogisticRegressionModelSuite.scala b/hail/modules/src/test/scala/is/hail/stats/LogisticRegressionModelSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/stats/LogisticRegressionModelSuite.scala
rename to hail/modules/src/test/scala/is/hail/stats/LogisticRegressionModelSuite.scala
diff --git a/hail/src/test/scala/is/hail/stats/StatsSuite.scala b/hail/modules/src/test/scala/is/hail/stats/StatsSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/stats/StatsSuite.scala
rename to hail/modules/src/test/scala/is/hail/stats/StatsSuite.scala
diff --git a/hail/src/test/scala/is/hail/stats/eigSymDSuite.scala b/hail/modules/src/test/scala/is/hail/stats/eigSymDSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/stats/eigSymDSuite.scala
rename to hail/modules/src/test/scala/is/hail/stats/eigSymDSuite.scala
diff --git a/hail/src/test/scala/is/hail/testUtils/AltAllele.scala b/hail/modules/src/test/scala/is/hail/testUtils/AltAllele.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/testUtils/AltAllele.scala
rename to hail/modules/src/test/scala/is/hail/testUtils/AltAllele.scala
diff --git a/hail/src/test/scala/is/hail/testUtils/Variant.scala b/hail/modules/src/test/scala/is/hail/testUtils/Variant.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/testUtils/Variant.scala
rename to hail/modules/src/test/scala/is/hail/testUtils/Variant.scala
diff --git a/hail/src/test/scala/is/hail/types/encoded/ETypeSuite.scala b/hail/modules/src/test/scala/is/hail/types/encoded/ETypeSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/encoded/ETypeSuite.scala
rename to hail/modules/src/test/scala/is/hail/types/encoded/ETypeSuite.scala
diff --git a/hail/src/test/scala/is/hail/types/physical/PBaseStructSuite.scala b/hail/modules/src/test/scala/is/hail/types/physical/PBaseStructSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/physical/PBaseStructSuite.scala
rename to hail/modules/src/test/scala/is/hail/types/physical/PBaseStructSuite.scala
diff --git a/hail/src/test/scala/is/hail/types/physical/PBinarySuite.scala b/hail/modules/src/test/scala/is/hail/types/physical/PBinarySuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/physical/PBinarySuite.scala
rename to hail/modules/src/test/scala/is/hail/types/physical/PBinarySuite.scala
diff --git a/hail/src/test/scala/is/hail/types/physical/PCallSuite.scala b/hail/modules/src/test/scala/is/hail/types/physical/PCallSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/physical/PCallSuite.scala
rename to hail/modules/src/test/scala/is/hail/types/physical/PCallSuite.scala
diff --git a/hail/src/test/scala/is/hail/types/physical/PContainerTest.scala b/hail/modules/src/test/scala/is/hail/types/physical/PContainerTest.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/physical/PContainerTest.scala
rename to hail/modules/src/test/scala/is/hail/types/physical/PContainerTest.scala
diff --git a/hail/src/test/scala/is/hail/types/physical/PIntervalSuite.scala b/hail/modules/src/test/scala/is/hail/types/physical/PIntervalSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/physical/PIntervalSuite.scala
rename to hail/modules/src/test/scala/is/hail/types/physical/PIntervalSuite.scala
diff --git a/hail/src/test/scala/is/hail/types/physical/PNDArraySuite.scala b/hail/modules/src/test/scala/is/hail/types/physical/PNDArraySuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/physical/PNDArraySuite.scala
rename to hail/modules/src/test/scala/is/hail/types/physical/PNDArraySuite.scala
diff --git a/hail/src/test/scala/is/hail/types/physical/PTypeSuite.scala b/hail/modules/src/test/scala/is/hail/types/physical/PTypeSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/physical/PTypeSuite.scala
rename to hail/modules/src/test/scala/is/hail/types/physical/PTypeSuite.scala
diff --git a/hail/src/test/scala/is/hail/types/physical/PhysicalTestUtils.scala b/hail/modules/src/test/scala/is/hail/types/physical/PhysicalTestUtils.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/physical/PhysicalTestUtils.scala
rename to hail/modules/src/test/scala/is/hail/types/physical/PhysicalTestUtils.scala
diff --git a/hail/src/test/scala/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala b/hail/modules/src/test/scala/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala
rename to hail/modules/src/test/scala/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala
diff --git a/hail/src/test/scala/is/hail/types/virtual/TStructSuite.scala b/hail/modules/src/test/scala/is/hail/types/virtual/TStructSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/types/virtual/TStructSuite.scala
rename to hail/modules/src/test/scala/is/hail/types/virtual/TStructSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/ArrayBuilderSuite.scala b/hail/modules/src/test/scala/is/hail/utils/ArrayBuilderSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/ArrayBuilderSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/ArrayBuilderSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/ArrayStackSuite.scala b/hail/modules/src/test/scala/is/hail/utils/ArrayStackSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/ArrayStackSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/ArrayStackSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/BinaryHeapSuite.scala b/hail/modules/src/test/scala/is/hail/utils/BinaryHeapSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/BinaryHeapSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/BinaryHeapSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/BitVectorSuite.scala b/hail/modules/src/test/scala/is/hail/utils/BitVectorSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/BitVectorSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/BitVectorSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/BufferedAggregatorIteratorSuite.scala b/hail/modules/src/test/scala/is/hail/utils/BufferedAggregatorIteratorSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/BufferedAggregatorIteratorSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/BufferedAggregatorIteratorSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/FlipbookIteratorSuite.scala b/hail/modules/src/test/scala/is/hail/utils/FlipbookIteratorSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/FlipbookIteratorSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/FlipbookIteratorSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/GraphSuite.scala b/hail/modules/src/test/scala/is/hail/utils/GraphSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/GraphSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/GraphSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/HashMethodsSuite.scala b/hail/modules/src/test/scala/is/hail/utils/HashMethodsSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/HashMethodsSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/HashMethodsSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/IntervalSuite.scala b/hail/modules/src/test/scala/is/hail/utils/IntervalSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/IntervalSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/IntervalSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/PartitionCountsSuite.scala b/hail/modules/src/test/scala/is/hail/utils/PartitionCountsSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/PartitionCountsSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/PartitionCountsSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/RichArraySuite.scala b/hail/modules/src/test/scala/is/hail/utils/RichArraySuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/RichArraySuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/RichArraySuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/RichDenseMatrixDoubleSuite.scala b/hail/modules/src/test/scala/is/hail/utils/RichDenseMatrixDoubleSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/RichDenseMatrixDoubleSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/RichDenseMatrixDoubleSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/RichIndexedRowMatrixSuite.scala b/hail/modules/src/test/scala/is/hail/utils/RichIndexedRowMatrixSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/RichIndexedRowMatrixSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/RichIndexedRowMatrixSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/RichRDDSuite.scala b/hail/modules/src/test/scala/is/hail/utils/RichRDDSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/RichRDDSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/RichRDDSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/RowIntervalSuite.scala b/hail/modules/src/test/scala/is/hail/utils/RowIntervalSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/RowIntervalSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/RowIntervalSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/SemanticVersionSuite.scala b/hail/modules/src/test/scala/is/hail/utils/SemanticVersionSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/SemanticVersionSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/SemanticVersionSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/SpillingCollectIteratorSuite.scala b/hail/modules/src/test/scala/is/hail/utils/SpillingCollectIteratorSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/SpillingCollectIteratorSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/SpillingCollectIteratorSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/TreeTraversalSuite.scala b/hail/modules/src/test/scala/is/hail/utils/TreeTraversalSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/TreeTraversalSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/TreeTraversalSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/UnionFindSuite.scala b/hail/modules/src/test/scala/is/hail/utils/UnionFindSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/UnionFindSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/UnionFindSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/UtilsSuite.scala b/hail/modules/src/test/scala/is/hail/utils/UtilsSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/UtilsSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/UtilsSuite.scala
diff --git a/hail/src/test/scala/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala b/hail/modules/src/test/scala/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala
rename to hail/modules/src/test/scala/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala
diff --git a/hail/src/test/scala/is/hail/variant/GenotypeSuite.scala b/hail/modules/src/test/scala/is/hail/variant/GenotypeSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/variant/GenotypeSuite.scala
rename to hail/modules/src/test/scala/is/hail/variant/GenotypeSuite.scala
diff --git a/hail/src/test/scala/is/hail/variant/LocusIntervalSuite.scala b/hail/modules/src/test/scala/is/hail/variant/LocusIntervalSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/variant/LocusIntervalSuite.scala
rename to hail/modules/src/test/scala/is/hail/variant/LocusIntervalSuite.scala
diff --git a/hail/src/test/scala/is/hail/variant/ReferenceGenomeSuite.scala b/hail/modules/src/test/scala/is/hail/variant/ReferenceGenomeSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/variant/ReferenceGenomeSuite.scala
rename to hail/modules/src/test/scala/is/hail/variant/ReferenceGenomeSuite.scala
diff --git a/hail/src/test/scala/is/hail/variant/vsm/PartitioningSuite.scala b/hail/modules/src/test/scala/is/hail/variant/vsm/PartitioningSuite.scala
similarity index 100%
rename from hail/src/test/scala/is/hail/variant/vsm/PartitioningSuite.scala
rename to hail/modules/src/test/scala/is/hail/variant/vsm/PartitioningSuite.scala