I want to get rid of everyting except bior_pipeline and move it up 1 level.
Note that I have to specify master as the branch to check out.
R5068420:Downloads m026366$ git clone -b master http://mayo-git.mayo.edu/tfsmig/bior_lite.git
Cloning into 'bior_lite'...
remote: Counting objects: 22060, done.
remote: Compressing objects: 100% (9607/9607), done.
remote: Total 22060 (delta 9442), reused 21202 (delta 8861)
Receiving objects: 100% (22060/22060), 78.83 MiB | 38.51 MiB/s, done.
Resolving deltas: 100% (9442/9442), done.
Checking connectivity... done.
R5068420:Downloads m026366$ cd bior_lite/
R5068420:bior_lite m026366$ du -sh .git
 80M	.git
R5068420:bior_lite m026366$ git branch
* master
R5068420:bior_lite m026366$ git rm -r bior_api bior_catalog bior_usage_stats pom.xml 
rm 'bior_api/.idea/.name'
rm 'bior_api/.idea/artifacts/bior_api_war.xml'
rm 'bior_api/.idea/artifacts/bior_api_war_exploded.xml'
rm 'bior_api/.idea/compiler.xml'
rm 'bior_api/.idea/copyright/profiles_settings.xml'
rm 'bior_api/.idea/encodings.xml'
rm 'bior_api/.idea/libraries/Maven__asm_asm_3_1.xml'
rm 'bior_api/.idea/libraries/Maven__com_google_code_findbugs_jsr305_1_3_9.xml'
rm 'bior_api/.idea/libraries/Maven__com_google_code_gson_gson_2_2_2.xml'
rm 'bior_api/.idea/libraries/Maven__com_google_guava_guava_12_0.xml'
rm 'bior_api/.idea/libraries/Maven__com_h2database_h2_1_3_168.xml'
rm 'bior_api/.idea/libraries/Maven__com_jayway_jsonpath_json_path_0_8_1.xml'
rm 'bior_api/.idea/libraries/Maven__com_sun_jersey_contribs_jersey_multipart_1_11.xml'
rm 'bior_api/.idea/libraries/Maven__com_sun_jersey_jersey_client_1_11.xml'
rm 'bior_api/.idea/libraries/Maven__com_sun_jersey_jersey_core_1_11.xml'
rm 'bior_api/.idea/libraries/Maven__com_sun_jersey_jersey_json_1_11.xml'
rm 'bior_api/.idea/libraries/Maven__com_sun_jersey_jersey_server_1_11.xml'
rm 'bior_api/.idea/libraries/Maven__com_sun_jersey_jersey_servlet_1_11.xml'
rm 'bior_api/.idea/libraries/Maven__com_sun_xml_bind_jaxb_impl_2_2_3_1.xml'
rm 'bior_api/.idea/libraries/Maven__com_tinkerpop_pipes_2_0_0.xml'
rm 'bior_api/.idea/libraries/Maven__commons_dbcp_commons_dbcp_1_2_2.xml'
rm 'bior_api/.idea/libraries/Maven__commons_io_commons_io_2_4.xml'
rm 'bior_api/.idea/libraries/Maven__commons_lang_commons_lang_2_2.xml'
rm 'bior_api/.idea/libraries/Maven__commons_pool_commons_pool_1_3.xml'
rm 'bior_api/.idea/libraries/Maven__edu_mayo_mayo_commons_exec_0_0_8_SNAPSHOT.xml'
rm 'bior_api/.idea/libraries/Maven__edu_mayo_pipes_2_2_0_SNAPSHOT.xml'
rm 'bior_api/.idea/libraries/Maven__javax_activation_activation_1_1.xml'
rm 'bior_api/.idea/libraries/Maven__javax_servlet_javax_servlet_api_3_0_1.xml'
rm 'bior_api/.idea/libraries/Maven__javax_xml_bind_jaxb_api_2_2_2.xml'
rm 'bior_api/.idea/libraries/Maven__javax_xml_stream_stax_api_1_0_2.xml'
rm 'bior_api/.idea/libraries/Maven__junit_junit_4_5.xml'
rm 'bior_api/.idea/libraries/Maven__junit_junit_dep_4_4.xml'
rm 'bior_api/.idea/libraries/Maven__log4j_log4j_1_2_14.xml'
rm 'bior_api/.idea/libraries/Maven__net_minidev_json_smart_1_1_1.xml'
rm 'bior_api/.idea/libraries/Maven__net_sourceforge_samtools_1_5_6.xml'
rm 'bior_api/.idea/libraries/Maven__org_apache_commons_commons_compress_1_4_1.xml'
rm 'bior_api/.idea/libraries/Maven__org_biojava_alignment_1_8_2.xml'
rm 'bior_api/.idea/libraries/Maven__org_biojava_bytecode_1_8_2.xml'
rm 'bior_api/.idea/libraries/Maven__org_biojava_core_1_8_2.xml'
rm 'bior_api/.idea/libraries/Maven__org_codehaus_jackson_jackson_core_asl_1_9_2.xml'
rm 'bior_api/.idea/libraries/Maven__org_codehaus_jackson_jackson_jaxrs_1_9_2.xml'
rm 'bior_api/.idea/libraries/Maven__org_codehaus_jackson_jackson_mapper_asl_1_9_2.xml'
rm 'bior_api/.idea/libraries/Maven__org_codehaus_jackson_jackson_xc_1_9_2.xml'
rm 'bior_api/.idea/libraries/Maven__org_codehaus_jettison_jettison_1_1.xml'
rm 'bior_api/.idea/libraries/Maven__org_hamcrest_hamcrest_core_1_1.xml'
rm 'bior_api/.idea/libraries/Maven__org_hamcrest_hamcrest_library_1_1.xml'
rm 'bior_api/.idea/libraries/Maven__org_jmock_jmock_2_5_1.xml'
rm 'bior_api/.idea/libraries/Maven__org_jmock_jmock_junit4_2_5_1.xml'
rm 'bior_api/.idea/libraries/Maven__org_jvnet_mimepull_1_6.xml'
rm 'bior_api/.idea/libraries/Maven__org_objenesis_objenesis_1_2.xml'
rm 'bior_api/.idea/libraries/Maven__org_slf4j_slf4j_api_1_6_4.xml'
rm 'bior_api/.idea/libraries/Maven__org_slf4j_slf4j_log4j12_1_6_4.xml'
rm 'bior_api/.idea/libraries/Maven__org_slf4j_slf4j_simple_1_6_4.xml'
rm 'bior_api/.idea/libraries/Maven__org_tukaani_xz_1_0.xml'
rm 'bior_api/.idea/libraries/Maven__stax_stax_api_1_0_1.xml'
rm 'bior_api/.idea/libraries/Maven__uk_com_robust_it_cloning_1_9_0.xml'
rm 'bior_api/.idea/misc.xml'
rm 'bior_api/.idea/modules.xml'
rm 'bior_api/.idea/scopes/scope_settings.xml'
rm 'bior_api/.idea/uiDesigner.xml'
rm 'bior_api/.idea/vcs.xml'
rm 'bior_api/.idea/workspace.xml'
rm 'bior_catalog/.classpath'
rm 'bior_catalog/.project'
rm 'bior_catalog/.settings/org.eclipse.jdt.core.prefs'
rm 'bior_catalog/.settings/org.eclipse.m2e.core.prefs'
rm 'bior_catalog/License.txt'
rm 'bior_catalog/doc/HUGO.txt'
rm 'bior_catalog/doc/READMEGENES.txt'
rm 'bior_catalog/downloaders/downloadGenes.bash'
rm 'bior_catalog/downloaders/getHGNCData.pl'
rm 'bior_catalog/downloaders/uncompressGenes.bash'
rm 'bior_catalog/license/Apache.txt'
rm 'bior_catalog/license/BSD.txt'
rm 'bior_catalog/license/GPLv3.txt'
rm 'bior_catalog/license/LGPL.txt'
rm 'bior_catalog/license/MIT.txt'
rm 'bior_catalog/license/README.txt'
rm 'bior_catalog/license/XZ.txt'
rm 'bior_catalog/license/deps.txt'
rm 'bior_catalog/license/ensembl.txt'
rm 'bior_catalog/pom.xml'
rm 'bior_catalog/publishers/old_publisher_scripts/Indexer/buildBgzipData.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/Indexer/buildBgzipIndex.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/Indexer/buildH2Db.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/Indexer/buildTabix.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/Indexer/sortFile.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/publish_BGI.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/publish_MirBase.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/publish_NcbiGene.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/publish_cosmic.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/publish_dbsnp.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/publish_esp.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/publish_hapmap.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/publish_hgnc.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/publish_omim.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/publish_ucsc.sh'
rm 'bior_catalog/publishers/old_publisher_scripts/sort_catalog.sh'
rm 'bior_catalog/setupEnv.sh'
rm 'bior_catalog/src/assemble/distribution.xml'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/ColJsonPathPair.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/IndexRow.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/IndexUtils.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/IndexerDatabase.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/IndexerFile.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/IndexerMemory.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/IndexerTabix.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/SortExternal.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/cmd/BuildBgzip.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/cmd/BuildBgzipIndex.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/cmd/BuildH2DbIndex.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/cmd/BuildTabix.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/indexer/cmd/SortFile.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/BGIDanish/BGIPublisher.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/Cosmic/CosmicHeaders.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/Cosmic/CosmicPublisher.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/Cosmic/CosmicTransformPipe.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/Cosmic/KeepLastColPipe.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/ESP/ESPPublisher.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/HGMD/HGMDPublisher.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/HUGO/HUGOPublisher.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/HUGO/NOTE this is the HGNC publisher.txt'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/HapMap/CollapseHapMapVariantsPipe.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/HapMap/HapMap2JSONPipe.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/HapMap/HapMapPublisher.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/HapMap/HapMapPublisherPhase2.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/HapMap/HapMapQueue.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/HapMap/HapMapValidator.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/MIRBase/MirBasePublisher.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/NCBIGene/NCBIGenePublisher.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/OMIM/LoadDisease.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/OMIM/LoadGenes.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/ThousandGenomes/SubPopulationPublisher.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/publishers/UCSC/UCSCPublisher.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/utils/AA_Mapper.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/utils/GetBasesUtil.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/utils/HGVS.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/utils/OneBasedCatalogValidator.java'
rm 'bior_catalog/src/main/java/edu/mayo/bior/utils/SQLParser.java'
rm 'bior_catalog/src/main/resources/catalogName.columns.tsv'
rm 'bior_catalog/src/main/resources/catalogName.datasource.properties'
rm 'bior_catalog/src/main/resources/sys.properties'
rm 'bior_catalog/src/test/java/edu/mayo/bior/indexer/SpeedTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/BGI/BGIPublisherTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/BuildNcbiCatalog.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/Cosmic/CosmicPublisherTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/ESP/ESPPublisherTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/HUGO/HUGOPublisherTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/HapMap/CollapseHapMapVariantsPipeTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/HapMap/HapMapPublisherPhase2Test.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/HapMap/HapMapQueueTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/MIRBase/MirBasePublisherTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/OMIM/OMIMPublisherTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/publishers/UCSC/UCSCPublisherTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/utils/CatalogUtils.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/utils/OneBasedCatalogValidatorTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/utils/SQLParserTest.java'
rm 'bior_catalog/src/test/java/edu/mayo/bior/utils/ValidateColumnsAndDatasourceProperties.java'
rm 'bior_catalog/src/test/resources/catalogData/ncbiGenes.chr17.tar.gz'
rm 'bior_catalog/src/test/resources/testData/bgi/Sanity check - dbSNP to BGI SameVariant.txt'
rm 'bior_catalog/src/test/resources/testData/bgi/bgi.catalog.chr17.bgz'
rm 'bior_catalog/src/test/resources/testData/bgi/bgi.catalog.chr17.bgz.tbi'
rm 'bior_catalog/src/test/resources/testData/bgi/bgi.chr17.catalog.expected.tsv'
rm 'bior_catalog/src/test/resources/testData/bgi/bgi.chr17.catalog.sameVariant.expected.tsv'
rm 'bior_catalog/src/test/resources/testData/bgi/bgi.chr17.input.tsv'
rm 'bior_catalog/src/test/resources/testData/bgi/bgi.chrM.tsv.bgz'
rm 'bior_catalog/src/test/resources/testData/bgi/bgi.chrY.catalog.expected.tsv'
rm 'bior_catalog/src/test/resources/testData/bgi/bgi.chrY.input.tsv'
rm 'bior_catalog/src/test/resources/testData/bgi/dbSNPS_overlap_BRCA1.vcf'
rm 'bior_catalog/src/test/resources/testData/bgi/dbSNPS_overlap_BRCA1.vcf.json.bgz'
rm 'bior_catalog/src/test/resources/testData/bgi/dbSNPS_overlap_BRCA1.vcf.json.bgz.tbi'
rm 'bior_catalog/src/test/resources/testData/bgi/tmpOut/bgi.chr17.catalog.output.tsv'
rm 'bior_catalog/src/test/resources/testData/bgi/tmpOut/bgi.chr17.catalog.sameVariant.output.tsv'
rm 'bior_catalog/src/test/resources/testData/bgi/tmpOut/bgi.chrY.catalog.output.tsv'
rm 'bior_catalog/src/test/resources/testData/cosmic/build37/CosmicCompleteExport_v62_291112First500.tsv.gz'
rm 'bior_catalog/src/test/resources/testData/cosmic/build37/cosmic.expected.tsv'
rm 'bior_catalog/src/test/resources/testData/cosmic/build37/cosmictest.tsv.gz'
rm 'bior_catalog/src/test/resources/testData/cosmic/build37/test_hs_ref_genome.fa.tsv.bgz'
rm 'bior_catalog/src/test/resources/testData/cosmic/build37/test_hs_ref_genome.fa.tsv.bgz.tbi'
rm 'bior_catalog/src/test/resources/testData/cosmic/build38/cosmic.expected.tsv'
rm 'bior_catalog/src/test/resources/testData/cosmic/build38/cosmictest.tsv.gz'
rm 'bior_catalog/src/test/resources/testData/cosmic/build38/test_hs_ref_genome.fa.tsv'
rm 'bior_catalog/src/test/resources/testData/cosmic/build38/test_hs_ref_genome.fa.tsv.bgz'
rm 'bior_catalog/src/test/resources/testData/cosmic/build38/test_hs_ref_genome.fa.tsv.bgz.tbi'
rm 'bior_catalog/src/test/resources/testData/esp/build37/ESP6500SI.chr21.snps_indels.input.vcf'
rm 'bior_catalog/src/test/resources/testData/esp/build37/ESP6500SI_GRCh37.expected.tsv'
rm 'bior_catalog/src/test/resources/testData/esp/build37/ESP6500SI_GRCh37.sample.tsv'
rm 'bior_catalog/src/test/resources/testData/esp/build38/ESP6500SI-V2-SSA137.GRCh38-liftover.chr1.snps_indels.vcf'
rm 'bior_catalog/src/test/resources/testData/esp/build38/ESP6500SI-V2-SSA137.GRCh38-liftover.chr2.snps_indels.vcf'
rm 'bior_catalog/src/test/resources/testData/esp/build38/ESP6500SI_GRCh38.expected.tsv'
rm 'bior_catalog/src/test/resources/testData/hapmap/hapmap.beforePhase2CollapsePopulations.tsv'
rm 'bior_catalog/src/test/resources/testData/hapmap/hapmap.expected.afterPhase2CollapsePopulations.tsv'
rm 'bior_catalog/src/test/resources/testData/hapmap/hapmap.sorted.liftover.first300.tsv'
rm 'bior_catalog/src/test/resources/testData/hapmap/rs10399749_merged.json'
rm 'bior_catalog/src/test/resources/testData/hapmap/rs2691310_merged.json'
rm 'bior_catalog/src/test/resources/testData/hapmap/rs2949420_merged.json'
rm 'bior_catalog/src/test/resources/testData/hapmap/rs2949421_merged.json'
rm 'bior_catalog/src/test/resources/testData/hugo/hgnc.expected.tsv'
rm 'bior_catalog/src/test/resources/testData/hugo/hgnc.expected.tsv.ORIGINAL'
rm 'bior_catalog/src/test/resources/testData/hugo/hgnc_sample_dataset.txt'
rm 'bior_catalog/src/test/resources/testData/hugo/hgnc_sample_dataset.txt.ORIGINAL'
rm 'bior_catalog/src/test/resources/testData/hugo/mike.expected'
rm 'bior_catalog/src/test/resources/testData/mirbase/hsa.gff2'
rm 'bior_catalog/src/test/resources/testData/mirbase/hsa.gff3'
rm 'bior_catalog/src/test/resources/testData/ncbigene/README.txt'
rm 'bior_catalog/src/test/resources/testData/ncbigene/dbSNPchr17.100k.vcf.gz'
rm 'bior_catalog/src/test/resources/testData/ncbigene/hs_ref_GRCh38_chr17.gbs.gz'
rm 'bior_catalog/src/test/resources/testData/omim/genemap'
rm 'bior_catalog/src/test/resources/testData/omim/omim.expected.tsv'
rm 'bior_catalog/src/test/resources/testData/ucsc/coriellDelDup.sql'
rm 'bior_catalog/src/test/resources/testData/ucsc/coriellDelDup.txt.gz'
rm 'bior_catalog/src/test/resources/testData/ucsc/hiSeqDepthTop5Pct.sql'
rm 'bior_catalog/src/test/resources/testData/ucsc/hiSeqDepthTop5Pct.txt.gz'
rm 'bior_catalog/src/test/resources/testData/ucsc/phastConsElements46way.sql'
rm 'bior_catalog/src/test/resources/testData/ucsc/phastConsElements46way.txt.gz'
rm 'bior_catalog/src/test/resources/testData/ucsc/sibTxGraph.sql'
rm 'bior_catalog/src/test/resources/testData/ucsc/switchDbTss.sql'
rm 'bior_catalog/src/test/resources/testData/ucsc/switchDbTss.txt.gz'
rm 'bior_catalog/src/test/resources/testData/ucsc/vistaEnhancers.sql'
rm 'bior_catalog/src/test/resources/testData/ucsc/vistaEnhancers.txt.gz'
rm 'bior_catalog/src/test/resources/testData/ucsc/wgEncodeDacMapabilityConsensusExcludable.sql'
rm 'bior_catalog/src/test/resources/testData/ucsc/wgEncodeDacMapabilityConsensusExcludable.txt.gz'
rm 'bior_catalog/src/test/resources/testData/ucsc/wgEncodeDukeMapabilityRegionsExcludable.sql'
rm 'bior_catalog/src/test/resources/testData/ucsc/wgEncodeDukeMapabilityRegionsExcludable.txt.gz'
rm 'bior_catalog/src/test/resources/testData/util/brca1_gene_range.txt'
rm 'bior_catalog/src/test/resources/testData/util/ncbiRefs.chr17.tsv.bgz'
rm 'bior_catalog/src/test/resources/testData/util/ncbiRefs.chr17.tsv.bgz.tbi'
rm 'bior_usage_stats/.classpath'
rm 'bior_usage_stats/.project'
rm 'bior_usage_stats/.settings/org.eclipse.jdt.core.prefs'
rm 'bior_usage_stats/.settings/org.eclipse.m2e.core.prefs'
rm 'bior_usage_stats/Output/Archive/2013_10_29_BiorUsageStats.zip'
rm 'bior_usage_stats/Output/Archive/2013_10_29a_BiorUsageStats.zip'
rm 'bior_usage_stats/Output/Archive/2013_12_02_BiorUsageStats.zip'
rm 'bior_usage_stats/Output/Archive/2014_03_07_BiorUsageStats.zip'
rm 'bior_usage_stats/Output/Archive/2014_08_28_BiorUsageStats.zip'
rm 'bior_usage_stats/Output/Archive/2014_08_28_BiorUsageStats_small.zip'
rm 'bior_usage_stats/Output/Archive/2014_09_04_BiorUsageStats.zip'
rm 'bior_usage_stats/Output/Archive/2014_09_05_BiorUsageStats.zip'
rm 'bior_usage_stats/Output/Archive/2014_12_19_BiorUsageStats.zip'
rm 'bior_usage_stats/Output/Archive/2015_04_17_BiorUsageStats.zip'
rm 'bior_usage_stats/Output/Archive/2015_04_17_BiorUsageStats_small.zip'
rm 'bior_usage_stats/Output/callsByUserChart.html'
rm 'bior_usage_stats/Output/callsPerCommandChart.html'
rm 'bior_usage_stats/Output/callsPerMonthChart.html'
rm 'bior_usage_stats/Output/demo.css'
rm 'bior_usage_stats/Output/userCallsPerMonth.html'
rm 'bior_usage_stats/README.txt'
rm 'bior_usage_stats/gatherUsageStats.sh'
rm 'bior_usage_stats/pom.xml'
rm 'bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/ChartCmd.java'
rm 'bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/ChartCmdPerMonth.java'
rm 'bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/ChartCmdsPerUserPerMonth.java'
rm 'bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/ChartUser.java'
rm 'bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/Helpers.java'
rm 'bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/UsageStats.java'
rm 'bior_usage_stats/src/main/resources/cmdcalls_template.html'
rm 'bior_usage_stats/src/main/resources/cmdsPerMonth_template.html'
rm 'bior_usage_stats/src/main/resources/userCallsPerMonth_template.html'
rm 'bior_usage_stats/src/main/resources/userNameMappings.properties'
rm 'bior_usage_stats/src/main/resources/usercalls_template.html'
rm 'pom.xml'
R5068420:bior_lite m026366$ git commit -m "Removed folders bior_api bior_catalog bior_usage_stats and pom.xml to just leave bior_pipeline"
[master d94fc35] Removed folders bior_api bior_catalog bior_usage_stats and pom.xml to just leave bior_pipeline
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 delete mode 100644 bior_usage_stats/Output/demo.css
 delete mode 100644 bior_usage_stats/Output/userCallsPerMonth.html
 delete mode 100644 bior_usage_stats/README.txt
 delete mode 100755 bior_usage_stats/gatherUsageStats.sh
 delete mode 100644 bior_usage_stats/pom.xml
 delete mode 100644 bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/ChartCmd.java
 delete mode 100644 bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/ChartCmdPerMonth.java
 delete mode 100644 bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/ChartCmdsPerUserPerMonth.java
 delete mode 100644 bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/ChartUser.java
 delete mode 100644 bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/Helpers.java
 delete mode 100644 bior_usage_stats/src/main/java/edu/mayo/bior/usagestats/UsageStats.java
 delete mode 100644 bior_usage_stats/src/main/resources/cmdcalls_template.html
 delete mode 100644 bior_usage_stats/src/main/resources/cmdsPerMonth_template.html
 delete mode 100644 bior_usage_stats/src/main/resources/userCallsPerMonth_template.html
 delete mode 100644 bior_usage_stats/src/main/resources/userNameMappings.properties
 delete mode 100644 bior_usage_stats/src/main/resources/usercalls_template.html
 delete mode 100644 pom.xml
R5068420:bior_lite m026366$ git mv bior_pipeline/.classpath bior_pipeline/.project bior_pipeline/.settings bior_pipeline/BioR.xml bior_pipeline/License.txt bior_pipeline/README.txt bior_pipeline/RELEASE_NOTES.txt bior_pipeline/bior_annotate_test.sh bior_pipeline/bior_pipeline.iml bior_pipeline/bior_pipeline.jardesc bior_pipeline/bior_variant_to_tjson.xml bior_pipeline/doc bior_pipeline/examples bior_pipeline/license bior_pipeline/pom.xml bior_pipeline/scripts/ bior_pipeline/setupEnv.sh bior_pipeline/setupEnv.sh.external bior_pipeline/snpEff_genes.txt bior_pipeline/snpEff_summary.html bior_pipeline/src .

Interestingly, as far as git is concerned, now that bior_pipeline doesn't have any more files in it, it doesn't exist anymore because it doesn't track dirs:
http://stackoverflow.com/questions/10074582/git-how-to-remove-empty-folder-and-push-that-change
R5068420:bior_lite m026366$ git commit
[master acb5796] Moving files from bior_pipeline to top level.
 797 files changed, 0 insertions(+), 0 deletions(-)
 rename bior_pipeline/.classpath => .classpath (100%)
 rename bior_pipeline/.project => .project (100%)
 rename {bior_pipeline/.settings => .settings}/org.eclipse.jdt.core.prefs (100%)
 rename {bior_pipeline/.settings => .settings}/org.eclipse.m2e.core.prefs (100%)
 rename bior_pipeline/BioR.xml => BioR.xml (100%)
 rename bior_pipeline/License.txt => License.txt (100%)
 rename bior_pipeline/README.txt => README.txt (100%)
 rename bior_pipeline/RELEASE_NOTES.txt => RELEASE_NOTES.txt (100%)
 rename bior_pipeline/bior_annotate_test.sh => bior_annotate_test.sh (100%)
 rename bior_pipeline/bior_pipeline.iml => bior_pipeline.iml (100%)
 rename bior_pipeline/bior_pipeline.jardesc => bior_pipeline.jardesc (100%)
 rename bior_pipeline/bior_variant_to_tjson.xml => bior_variant_to_tjson.xml (100%)
 rename {bior_pipeline/doc => doc}/BioRQuickstart.docx (100%)
 rename {bior_pipeline/doc => doc}/BioRQuickstart.pdf (100%)
 rename {bior_pipeline/doc => doc}/BioR_Bioinformatics20130927.docx (100%)
 rename {bior_pipeline/doc => doc}/BioR_Supplementary_Material.docx (100%)
 rename {bior_pipeline/doc => doc}/BioR_UserGuide_v2.1.x.pdf (100%)
 rename {bior_pipeline/doc => doc}/BioR_UserGuide_v2.2.x.pdf (100%)
 rename {bior_pipeline/doc => doc}/The Biological Repository.docx (100%)
 rename {bior_pipeline/examples => examples}/README.txt (100%)
 rename {bior_pipeline/examples => examples}/example.vcf (100%)
 rename {bior_pipeline/examples => examples}/example1.sh (100%)
 rename {bior_pipeline/examples => examples}/example2.sh (100%)
 rename {bior_pipeline/examples => examples}/example3.sh (100%)
 rename {bior_pipeline/examples => examples}/example4.sh (100%)
 rename {bior_pipeline/examples => examples}/example4_bad.sh (100%)
 rename {bior_pipeline/examples => examples}/example5.sh (100%)
 rename {bior_pipeline/examples => examples}/example6.sh (100%)
 rename {bior_pipeline/examples => examples}/examplePos.tsv (100%)
 rename {bior_pipeline/examples => examples}/exampleRsID.tsv (100%)
 rename {bior_pipeline/examples/quickstart2 => examples}/example_chr17.vcf (100%)
 rename {bior_pipeline/examples => examples}/out1.tsv (100%)
 rename {bior_pipeline/examples => examples}/out2.tsv (100%)
 rename {bior_pipeline/examples => examples}/out3.tsv (100%)
 rename {bior_pipeline/examples => examples}/out4.tsv (100%)
 rename {bior_pipeline/examples => examples}/out5.tsv (100%)
 rename {bior_pipeline/examples => examples}/out6.tsv (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/STEP1.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/STEP2.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/STEP3.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/STEP4.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/data/NCBIGene/GRCh37_p10/genes.columns.tsv (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/data/NCBIGene/GRCh37_p10/genes.datasource.properties (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/data/NCBIGene/GRCh37_p10/genes.tsv.bgz (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/data/NCBIGene/GRCh37_p10/genes.tsv.bgz.tbi (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/data/NCBIGene/GRCh37_p10/index/genes.HGNC.idx.h2.db (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/data/NCBIGene/GRCh37_p10/index/genes.gene.idx.h2.db (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/data/NCBIGene/GRCh37_p10/index/genes.note.idx.h2.db (100%)
 rename {bior_pipeline/examples => examples}/quickstart1/geneList.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/STEP1.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/STEP2.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/STEP3.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/STEP4.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/STEP5.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/STEP6.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/STEP7.txt (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/data/dbSNP/137/00Part.tsv.tsv (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/data/dbSNP/137/00Part.tsv.tsv.bgz (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/data/dbSNP/137/00Part.tsv.tsv.bgz.tbi (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/data/dbSNP/137/clinvarPart.columns.tsv (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/data/dbSNP/137/clinvarPart.datasource.properties (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/data/dbSNP/137/clinvarPart.tsv (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/data/dbSNP/137/clinvarPart.tsv.bgz (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/data/dbSNP/137/clinvarPart.tsv.bgz.tbi (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/data/dbSNP/137/index/clinvarPart.ID.idx.h2.db (100%)
 rename {bior_pipeline/examples => examples}/quickstart2/example.vcf (100%)
 rename {bior_pipeline/examples => examples/quickstart2}/example_chr17.vcf (100%)
 rename {bior_pipeline/examples => examples}/status6.out (100%)
 rename {bior_pipeline/license => license}/Apache.txt (100%)
 rename {bior_pipeline/license => license}/BSD.txt (100%)
 rename {bior_pipeline/license => license}/GPLv3.txt (100%)
 rename {bior_pipeline/license => license}/LGPL.txt (100%)
 rename {bior_pipeline/license => license}/MIT.txt (100%)
 rename {bior_pipeline/license => license}/README.txt (100%)
 rename {bior_pipeline/license => license}/XZ.txt (100%)
 rename {bior_pipeline/license => license}/deps.txt (100%)
 rename {bior_pipeline/license => license}/ensembl.txt (100%)
 rename bior_pipeline/pom.xml => pom.xml (100%)
 rename {bior_pipeline/scripts => scripts}/TestVcf/ReadAny.jar (100%)
 rename {bior_pipeline/scripts => scripts}/TestVcf/testVcf.sh (100%)
 rename {bior_pipeline/scripts => scripts}/UserExamples/GWAS_to_catalog/PCR_imputed/chr17.her2neg.pvalues.txt.gz (100%)
 rename {bior_pipeline/scripts => scripts}/UserExamples/GWAS_to_catalog/PCR_imputed/chr17.int.her2neg.pvalues.txt.gz (100%)
 rename {bior_pipeline/scripts => scripts}/UserExamples/GWAS_to_catalog/PCR_imputed/chr17.int.pvalues.txt.gz (100%)
 rename {bior_pipeline/scripts => scripts}/UserExamples/GWAS_to_catalog/PCR_imputed/chr17.pvalues.txt.gz (100%)
 rename {bior_pipeline/scripts => scripts}/UserExamples/GWAS_to_catalog/PCR_inv_imputed/chr17.her2neg.pvalues.txt.gz (100%)
 rename {bior_pipeline/scripts => scripts}/UserExamples/GWAS_to_catalog/PCR_inv_imputed/chr17.int.her2neg.pvalues.txt.gz (100%)
 rename {bior_pipeline/scripts => scripts}/UserExamples/GWAS_to_catalog/PCR_inv_imputed/chr17.int.pvalues.txt.gz (100%)
 rename {bior_pipeline/scripts => scripts}/UserExamples/GWAS_to_catalog/PCR_inv_imputed/chr17.pvalues.txt.gz (100%)
 rename {bior_pipeline/scripts => scripts}/UserExamples/GWAS_to_catalog/Project approach.txt (100%)
 rename {bior_pipeline/scripts => scripts}/buildExternalDeployment.sh (100%)
 rename {bior_pipeline/scripts => scripts}/downloadFullCatalogs.sh (100%)
 rename {bior_pipeline/scripts => scripts}/downloadSmallCatalogs.sh (100%)
 rename {bior_pipeline/scripts => scripts}/testTabixIndexes.sh (100%)
 rename bior_pipeline/setupEnv.sh => setupEnv.sh (100%)
 rename bior_pipeline/setupEnv.sh.external => setupEnv.sh.external (100%)
 rename bior_pipeline/snpEff_genes.txt => snpEff_genes.txt (100%)
 rename bior_pipeline/snpEff_summary.html => snpEff_summary.html (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/BuildCatalog.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/BuildCatalogStepExecuteException.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/BuildCatalogStepInputException.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/BuildCatalogStepInterface.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/BuildInfo.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/BuildInfoKey.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/BuildStepKey.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/CreatePropFilesStep.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/CreateStep.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/HelpDocStep.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/IndexesStep.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/MakeJsonStep.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/MergeColumnsTsv.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/MergeDataSourceProperties.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/MergeMetadataStep.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/StepLogger.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/SummaryStep.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/VerifyStep.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/buildcatalog/note - this is the huge overall catalog building command.txt (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/Catalog.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/CatalogColumn.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/CatalogColumnInfo.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/CatalogFileUtils.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/CatalogFiles.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/CatalogFormatException.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/CatalogMetadataConstant.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/CatalogTabixEntry.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/GoldenAttribute.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/HumanBuildAssembly.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/index/IndexDatabaseCreator.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/index/IndexStats.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/list/CatalogInfo.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalog/list/CatalogListGenerator.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogremoveduplicates/CatalogRemoveDuplicatesPipe.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/CatalogDataSource.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/CatalogEntryGoldenJson.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/CatalogOrderVerifier.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/CatalogOrderVerifierThread.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/CatalogRowVerifier.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/CatalogVerifier.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/HumanReferenceInfo.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/MessageLogger.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/SeqLookup.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/VerifierExecutionException.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/VerifierInputException.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/VerifyCatalogUtils.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/catalogvalidator/VerifyHumanVariantCatalog.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/AnnotateCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/BED2JSONCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/BuildCatalogCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/CatalogRemoveDuplicatesCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/ChunkCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/Cmds.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/CompressCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/ConcatCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/CreateCatalogCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/CreateCatalogPropsCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/CreateTab2JSONConfig.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/DrillCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/GBKs2JSONCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/GFF2JSONCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/GenericScriptCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/IndexCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/LookupCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/MergeCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/OverlapPipelineCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/PrettyPrintCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/RefAlleleCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/SNPEffCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/SameVariantCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/Tab2JSONCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/TjsonToVcfCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/TrimSpacesCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/VCF2VariantCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/VEPCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/Variant2JSONCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/cli/cmd/VerifyCatalogCommand.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/InfoMetaObject.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/SNPEff/SNPEFFEXE.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/SNPEff/SNPEFFPipeline.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/SNPEff/SNPEffHelper.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/SNPEff/SNPEffPostProcessPipeline.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/SNPEff/SNPEffectHolder.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/TjsonToVcfPipe.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/AlleleFreq.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/AlleleFrequenciesPipeline.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/AnnotateEXE.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/Cleaner.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/EndLineGeneratorPipe.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/JsonColumn.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/OverlapingFeaturesPipeline.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/SplitFile.java (100%)
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 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/TreatPipe.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/TreatPipeline.properties (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/TreatPipelineMultiCmd.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/TreatPipelineSingleThread.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/TreatUtils.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/VariantInfo.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/BgiFormatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/CosmicFormatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/DbsnpClinvarFormatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/DbsnpFormatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/EspFormatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/FormatUtils.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/Formatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/FormatterPipeFunction.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/HapmapFormatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/HgncFormatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/MirBaseFormatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/NcbiGeneFormatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/OmimFormatter.java (100%)
 rename {bior_pipeline/src => src}/main/java/edu/mayo/bior/pipeline/Treat/format/SNPEffFormatter.java (100%)
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 rename {bior_pipeline/src => src}/test/resources/metadata/createCatalogProps/testJsonDepth.tsv (100%)
 rename {bior_pipeline/src => src}/test/resources/metadata/createCatalogProps/testJsonDepth.tsv.bgz (100%)
 rename {bior_pipeline/src/test/resources/metadata/createCatalogProps => src/test/resources/metadata/createCatalogProps/testTargetFolder}/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites_GRCh37.columns.tsv.blacklist.biorweb.expected (100%)
 rename {bior_pipeline/src/test/resources/metadata/createCatalogProps => src/test/resources/metadata/createCatalogProps/testTargetFolder}/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites_GRCh37.columns.tsv.blacklist.expected (100%)
 rename {bior_pipeline/src => src}/test/resources/metadata/createCatalogProps/testTargetFolder/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites_GRCh37.columns.tsv.expected (100%)
 rename {bior_pipeline/src => src}/test/resources/metadata/createCatalogProps/testTargetFolder/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites_GRCh37.datasource.properties.expected (100%)
 rename {bior_pipeline/src => src}/test/resources/metadata/createCatalogProps/testTargetFolder/NOTE - these files are the result of using vcf input files to fill in the columns.tsv description and so will be different from the ones in the parent folder.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/metadata/qualityControlOnCatalogs.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/metadata/tsvsample.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/metadata/valid4_1.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/metadata/validvcf.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/miniCatalog/dbSNP_01.README.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/miniCatalog/dbSNP_01.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/miniCatalog/espsample.tsv.bgz (100%)
 rename {bior_pipeline/src => src}/test/resources/miniCatalog/espsample.tsv.bgz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/miniCatalog/expectedOutput.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/miniCatalog/geneTestCatalog.tsv.bgz (100%)
 rename {bior_pipeline/src => src}/test/resources/miniCatalog/geneTestCatalog.tsv.bgz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/overlapCatalog.tsv.bgz (100%)
 rename {bior_pipeline/src => src}/test/resources/overlapCatalog.tsv.bgz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/refAllele.fasta.tsv.bgz (100%)
 rename {bior_pipeline/src => src}/test/resources/refAllele.fasta.tsv.bgz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/ref_assembly/GRCh37/genome_GRCh37.tsv (100%)
 rename {bior_pipeline/src => src}/test/resources/ref_assembly/GRCh37/genome_GRCh37.tsv.bgz (100%)
 rename {bior_pipeline/src => src}/test/resources/ref_assembly/GRCh37/genome_GRCh37.tsv.bgz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/remoteexec/bior.devserver.properties (100%)
 rename {bior_pipeline/src => src}/test/resources/sameVariant.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/sameVariantCatalog.tsv.bgz (100%)
 rename {bior_pipeline/src => src}/test/resources/sameVariantCatalog.tsv.bgz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/test.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/Catalogs.tsv (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/ChrPos.test (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/ChrPos.test.results (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/Fields.tsv (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/bb.test.bim (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/bimAnnotatedResults.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/bimAnnotatedResults.txt.MIKE (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/bimAnnotatedResults.txt.MIKE.README (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/bimDrilledResults.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/bimNewAnnotatedResults.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/bimOldAnnotatedResults.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/bimOldDrilledResults.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/bimResults.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/fromPos.expected.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/id.test (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/VariantToJson/id.test.results (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/catalogvalidator/00-All.vcf.columns.tsv (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/catalogvalidator/hgncCatalogEntries.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/catalogvalidator/json-UNKNOWN (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/catalogvalidator/json378197 (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/catalogvalidator/jsonOnlyCatalogEntries.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/catalogvalidator/mini_catalog.json (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/tabix/00-First1K_GRCh37.tsv.bgz (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/tabix/00-First1K_GRCh37.tsv.bgz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/testData/tabix/index/00-First1K_GRCh37.ID.idx.h2.db (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/manycmds/manycmds.input.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/manycmds/manycmds.out.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/manycmds/treatInputData (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/manycmds/treatOutputWithMetadata1 (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/manycmds/treatVcfiserOutput (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/badVariants.expected.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/badVariants.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/example.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/exeOnly_noMultiIndels.expected.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/exeOnly_noMultiIndels.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/file.eff.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/significantEffects.input.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/significantEffects_cmdJar.expected.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/snpEff.preProcess.expected.1.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/snpEff.preProcess.input.1.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/snpEffExeOnly.expected.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/snpEffOutput205.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/snpEffOutput205RAW.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/test.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/treat.expected.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/variantsNoMultiIndels.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/variantsSingleAndMultiChange.expected.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/variantsSingleAndMultiChange.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/variantsWithMultipleInsertionsDeletions.expected.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/snpeff/variantsWithMultipleInsertionsDeletions.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/treat/snpEffOutput.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/treat/treatExample.xls (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/treat/treatInput.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/bypass.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/cancer.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/cancer.vcf.vep (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/dbSNPS_overlap_BRCA1.vcf.vep (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/dbSNPS_overlap_BRCA1.vcf.vep.old (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/example.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/example.vcf.vep (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/example.vcf.vep.correct (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/example.vcf.vep.drill (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/vep.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/vepsample.expected.fanout.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/vepsample.expected.fanout2.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/vepsample.expected.mid.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/vepsample.expected.worstonly.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/tools/vep/vepsample.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/10000.1tomany.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.1000_genomes.tsv.gz (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.1000_genomes.tsv.gz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.ESP.tsv.gz (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.ESP.tsv.gz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.bgi.tsv (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.bgi.tsv.gz (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.bgi.tsv.gz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.dbsnp.tsv.gz (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.dbsnp.tsv.gz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.genes.tsv.gz (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.genes.tsv.gz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.hapmap.tsv.gz (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/brca1.hapmap.tsv.gz.tbi (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/all.config (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/all_invalid.config (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/dbsnpOnly.config (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/empty.config (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/smallSubset.config (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/smallSubset_output.tsv (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/some_invalid.config (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/subset.config (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/subset_datasource.config (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/subset_datasource_output.tsv (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/configtest/subset_output.tsv (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/expected/expected.10000.1tomany.out (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/BgiFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/BgiFormatter.test2.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/CosmicFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/CosmicFormatter.test2.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/DbsnpClinvarFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/DbsnpFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/DbsnpFormatter.test2.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/EntrezGeneFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/EntrezGeneFormatter.test2.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/HapmapFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/HgncFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/HgncFormatter.test2.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/MirBaseFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/SNPEffFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/SNPEffFormatter.test2.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/ThousandGenomesFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/ThousandGenomesFormatter.test2.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/UcscBlacklistedFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/UcscConservationFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/UcscEnhancerFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/UcscRegulationFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/UcscRepeatFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/UcscTfbsFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/UcscTssFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/UcscUniqueFormatter.test1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/VEPFormatter.brca1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/formatters/VEPHgncFormatter.brca1.json (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/gold.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/gold_output.tsv (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/interesting.txt (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/tmp.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/treat/treat.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/vcfizer/annotate.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/vcfizer/annotateVcfized.vcf (100%)
 rename {bior_pipeline/src => src}/test/resources/vcfizer/annotateVcfized.vcf.old (100%)

Download BFG Repo-Cleaner from https://rtyley.github.io/bfg-repo-cleaner/. I got a jar file to run with java
R5068420:bior_lite m026366$ alias bfg='java -jar ../bfg-1.12.13.jar'
R5068420:bior_lite m026366$ du -sh .git
 80M	.git
R5068420:bior_lite m026366$ for d in bior_api bior_catalog bior_usage_stats; do echo $d; bfg --delete-folders $d; done
bior_api

Using repo : /Users/m026366/Downloads/bior_lite/.git

Found 746 objects to protect
Found 14 tag-pointing refs : refs/tags/2.0-beta-2013-07-15-bior_catalog, refs/tags/2.0-beta-2013-07-15-bior_pipeline, refs/tags/2.0-beta-APR12, ...
Found 6 commit-pointing refs : HEAD, refs/heads/master, refs/remotes/origin/BIOR2.1.1, ...

Protected commits
-----------------

These are your protected commits, and so their contents will NOT be altered:

 * commit acb5796a (protected by 'HEAD')

Cleaning
--------

Found 3000 commits
Cleaning commits:       100% (3000/3000)
Cleaning commits completed in 807 ms.

Updating 2 Refs
---------------

	Ref                          Before     After   
	------------------------------------------------
	refs/heads/master          | acb5796a | a09bb078
	refs/remotes/origin/master | ec9ef463 | 94eb858c

Updating references:    100% (2/2)
...Ref update completed in 12 ms.

Commit Tree-Dirt History
------------------------

	Earliest                                              Latest
	|                                                          |
	................................................DDDDDDDDDDDD

	D = dirty commits (file tree fixed)
	m = modified commits (commit message or parents changed)
	. = clean commits (no changes to file tree)

	                        Before     After   
	-------------------------------------------
	First modified commit | 9c0fc5fe | 2b1f02cf
	Last dirty commit     | ec9ef463 | 94eb858c


In total, 845 object ids were changed. Full details are logged here:

	/Users/m026366/Downloads/bior_lite.bfg-report/2016-08-31/22-28-35

BFG run is complete! When ready, run: git reflog expire --expire=now --all && git gc --prune=now --aggressive


Has the BFG saved you time?  Support the BFG on BountySource:  https://j.mp/fund-bfg


bior_catalog

Using repo : /Users/m026366/Downloads/bior_lite/.git

Found 746 objects to protect
Found 14 tag-pointing refs : refs/tags/2.0-beta-2013-07-15-bior_catalog, refs/tags/2.0-beta-2013-07-15-bior_pipeline, refs/tags/2.0-beta-APR12, ...
Found 6 commit-pointing refs : HEAD, refs/heads/master, refs/remotes/origin/BIOR2.1.1, ...

Protected commits
-----------------

These are your protected commits, and so their contents will NOT be altered:

 * commit a09bb078 (protected by 'HEAD')

Cleaning
--------

Found 3000 commits
Cleaning commits:       100% (3000/3000)
Cleaning commits completed in 1,569 ms.

Updating 3 Refs
---------------

	Ref                                          Before     After   
	----------------------------------------------------------------
	refs/heads/master                          | a09bb078 | 1e5fc6eb
	refs/remotes/origin/master                 | 94eb858c | 94c6977c
	refs/tags/2.0-beta-2013-07-15-bior_catalog | daab7c01 | 2fbd07dc

Updating references:    100% (3/3)
...Ref update completed in 13 ms.

Commit Tree-Dirt History
------------------------

	Earliest                                              Latest
	|                                                          |
	DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD

	D = dirty commits (file tree fixed)
	m = modified commits (commit message or parents changed)
	. = clean commits (no changes to file tree)

	                        Before     After   
	-------------------------------------------
	First modified commit | 9b3f73b8 | 8a56cdab
	Last dirty commit     | 94eb858c | 94c6977c


In total, 3233 object ids were changed. Full details are logged here:

	/Users/m026366/Downloads/bior_lite.bfg-report/2016-08-31/22-28-37

BFG run is complete! When ready, run: git reflog expire --expire=now --all && git gc --prune=now --aggressive


Has the BFG saved you time?  Support the BFG on BountySource:  https://j.mp/fund-bfg


bior_usage_stats

Using repo : /Users/m026366/Downloads/bior_lite/.git

Found 746 objects to protect
Found 14 tag-pointing refs : refs/tags/2.0-beta-2013-07-15-bior_catalog, refs/tags/2.0-beta-2013-07-15-bior_pipeline, refs/tags/2.0-beta-APR12, ...
Found 6 commit-pointing refs : HEAD, refs/heads/master, refs/remotes/origin/BIOR2.1.1, ...

Protected commits
-----------------

These are your protected commits, and so their contents will NOT be altered:

 * commit 1e5fc6eb (protected by 'HEAD')

Cleaning
--------

Found 3000 commits
Cleaning commits:       100% (3000/3000)
Cleaning commits completed in 1,221 ms.

Updating 2 Refs
---------------

	Ref                          Before     After   
	------------------------------------------------
	refs/heads/master          | 1e5fc6eb | 62598dee
	refs/remotes/origin/master | 94c6977c | 8efe5b38

Updating references:    100% (2/2)
...Ref update completed in 12 ms.

Commit Tree-Dirt History
------------------------

	Earliest                                              Latest
	|                                                          |
	....................................................DDDDDDDD

	D = dirty commits (file tree fixed)
	m = modified commits (commit message or parents changed)
	. = clean commits (no changes to file tree)

	                        Before     After   
	-------------------------------------------
	First modified commit | ea4a74b6 | 2fb50cf0
	Last dirty commit     | 94c6977c | 8efe5b38


In total, 625 object ids were changed. Full details are logged here:

	/Users/m026366/Downloads/bior_lite.bfg-report/2016-08-31/22-28-39

BFG run is complete! When ready, run: git reflog expire --expire=now --all && git gc --prune=now --aggressive


Has the BFG saved you time?  Support the BFG on BountySource:  https://j.mp/fund-bfg

R5068420:bior_lite m026366$ du -sh .git
 97M	.git

R5068420:bior_lite m026366$ git reflog expire --expire=now --all && git gc --prune=now --aggressive
Counting objects: 21513, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (17686/17686), done.
Writing objects: 100% (21513/21513), done.
Total 21513 (delta 9510), reused 9999 (delta 0)
R5068420:bior_lite m026366$ du -sh .git
 67M	.git

Then I removed tags not related to bior_pipeline
R5068420:bior_lite m026366$ for t in 2.0-beta-2013-07-15-bior_catalog 2.0-beta-2013-07-15-bior_pipeline 2.0-beta-APR12 2.1.0-2013-09-11-bior_pipeline bior_catalog_2.2.1_2014-02-13 bior_catalog_2.2.2_2015-06-30 bior_catalog_2.2.3_2015-07-13 bior_catalog_2.2.4_2015-07-14 bior_pipeline; do git tag -d $t; done
Deleted tag '2.0-beta-2013-07-15-bior_catalog' (was 2fbd07d)
Deleted tag '2.0-beta-2013-07-15-bior_pipeline' (was 5556b0c)
Deleted tag '2.0-beta-APR12' (was d1c974a)
Deleted tag '2.1.0-2013-09-11-bior_pipeline' (was f27a685)
Deleted tag 'bior_catalog_2.2.1_2014-02-13' (was ef1b090)
Deleted tag 'bior_catalog_2.2.2_2015-06-30' (was 578fdd0)
Deleted tag 'bior_catalog_2.2.3_2015-07-13' (was dbe42c2)
Deleted tag 'bior_catalog_2.2.4_2015-07-14' (was 3cbf784)
Deleted tag 'bior_pipeline' (was 76e5697)
R5068420:bior_lite m026366$ git tag
bior_pipeline_2.1.0_2013-09-11
bior_pipeline_2.2.0_2013-11-27
bior_pipeline_2.2.1_2014-02-13
bior_pipeline_2.3.0_2014-04-22
bior_pipeline_2.4.1_2015-04-12

Check out how the repo looks on mayo-git before putting on TFS
R5068420:bior_lite m026366$ git push --mirror git@mayo-git.mayo.edu:rider.david/tfs-bior-toolkit.git
Counting objects: 18088, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (6924/6924), done.
Writing objects: 100% (18088/18088), 29.02 MiB | 32.08 MiB/s, done.
Total 18088 (delta 8136), reused 17990 (delta 8130)
To git@mayo-git.mayo.edu:rider.david/tfs-bior-toolkit.git
 * [new branch]      master -> master
 * [new branch]      origin/BIOR2.1.1 -> origin/BIOR2.1.1
 * [new branch]      origin/HEAD -> origin/HEAD
 * [new branch]      origin/bior_pipeline_2.4.1 -> origin/bior_pipeline_2.4.1
 * [new branch]      origin/master -> origin/master
 * [new tag]         bior_pipeline_2.1.0_2013-09-11 -> bior_pipeline_2.1.0_2013-09-11
 * [new tag]         bior_pipeline_2.2.0_2013-11-27 -> bior_pipeline_2.2.0_2013-11-27
 * [new tag]         bior_pipeline_2.2.1_2014-02-13 -> bior_pipeline_2.2.1_2014-02-13
 * [new tag]         bior_pipeline_2.3.0_2014-04-22 -> bior_pipeline_2.3.0_2014-04-22
 * [new tag]         bior_pipeline_2.4.1_2015-04-12 -> bior_pipeline_2.4.1_2015-04-12

Putting it up on TFS
R5068420:bior_lite m026366$ git push --mirror http://tfs.mayo.edu:8080/tfs/MayoClinic/IMA/_git/bior-toolkit
Username for 'http://tfs.mayo.edu:8080': m026366
Password for 'http://m026366@tfs.mayo.edu:8080': 
Counting objects: 18088, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (6924/6924), done.
Writing objects: 100% (18088/18088), 29.16 MiB | 18.12 MiB/s, done.
Total 18088 (delta 8136), reused 17990 (delta 8130)
remote: Analyzing objects... (18088/18088) (4089 ms)
remote: Storing packfile... done (5814 ms)
remote: Storing index... done (286 ms)
To http://tfs.mayo.edu:8080/tfs/MayoClinic/IMA/_git/bior-toolkit
 * [new branch]      master -> master
 * [new branch]      origin/BIOR2.1.1 -> origin/BIOR2.1.1
 * [new branch]      origin/HEAD -> origin/HEAD
 * [new branch]      origin/bior_pipeline_2.4.1 -> origin/bior_pipeline_2.4.1
 * [new branch]      origin/master -> origin/master
 * [new tag]         bior_pipeline_2.1.0_2013-09-11 -> bior_pipeline_2.1.0_2013-09-11
 * [new tag]         bior_pipeline_2.2.0_2013-11-27 -> bior_pipeline_2.2.0_2013-11-27
 * [new tag]         bior_pipeline_2.2.1_2014-02-13 -> bior_pipeline_2.2.1_2014-02-13
 * [new tag]         bior_pipeline_2.3.0_2014-04-22 -> bior_pipeline_2.3.0_2014-04-22
 * [new tag]         bior_pipeline_2.4.1_2015-04-12 -> bior_pipeline_2.4.1_2015-04-12
