diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
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rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java
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rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/LocusStatisticsUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java
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rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatisticsUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java
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rename from public/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java
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rename from public/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java
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rename from public/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java
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rename from public/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java
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rename from public/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java
diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java
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rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java
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diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java
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rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java
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diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java
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rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java
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diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java
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diff --git a/public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java b/protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java
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rename from public/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java
rename to protected/java/test/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjects.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffValue.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReader.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
rename to public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java