diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCallerAccuracyTest.java b/archive/java/src/org/broadinstitute/sting/multisamplecaller/MultiSampleCallerAccuracyTest.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/ConsensusSequence.java b/archive/java/src/org/broadinstitute/sting/oldindels/ConsensusSequence.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/DiscardingPileReceiver.java b/archive/java/src/org/broadinstitute/sting/oldindels/DiscardingPileReceiver.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/DiscardingReceiver.java b/archive/java/src/org/broadinstitute/sting/oldindels/DiscardingReceiver.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/Indel.java b/archive/java/src/org/broadinstitute/sting/oldindels/Indel.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java b/archive/java/src/org/broadinstitute/sting/oldindels/IndelInspectorMain.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndelRecordPileCollector.java b/archive/java/src/org/broadinstitute/sting/oldindels/IndelRecordPileCollector.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndexedSequence.java b/archive/java/src/org/broadinstitute/sting/oldindels/IndexedSequence.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/IntervalComparator.java b/archive/java/src/org/broadinstitute/sting/oldindels/IntervalComparator.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/KmerCodeIterator.java b/archive/java/src/org/broadinstitute/sting/oldindels/KmerCodeIterator.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/MSAColumn.java b/archive/java/src/org/broadinstitute/sting/oldindels/MSAColumn.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/Matrix.java b/archive/java/src/org/broadinstitute/sting/oldindels/Matrix.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/MultipleAlignment.java b/archive/java/src/org/broadinstitute/sting/oldindels/MultipleAlignment.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/PairwiseAlignment.java b/archive/java/src/org/broadinstitute/sting/oldindels/PairwiseAlignment.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/PassThroughWriter.java b/archive/java/src/org/broadinstitute/sting/oldindels/PassThroughWriter.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java b/archive/java/src/org/broadinstitute/sting/oldindels/PileBuilder.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/RecordPileReceiver.java b/archive/java/src/org/broadinstitute/sting/oldindels/RecordPileReceiver.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/RecordReceiver.java b/archive/java/src/org/broadinstitute/sting/oldindels/RecordReceiver.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/SequencePile.java b/archive/java/src/org/broadinstitute/sting/oldindels/SequencePile.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java b/archive/java/src/org/broadinstitute/sting/oldindels/ShowMSA.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/StrictlyUpperTriangularMatrix.java b/archive/java/src/org/broadinstitute/sting/oldindels/StrictlyUpperTriangularMatrix.java
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diff --git a/java/src/org/broadinstitute/sting/playground/indels/SymmetricMatrix.java b/archive/java/src/org/broadinstitute/sting/oldindels/SymmetricMatrix.java
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