Revert "Wrap cache in JBrowseLuceneSearch to allow closing of readers"

This reverts commit a434a5b.

Author: bbimber

mGAP/src/org/labkey/mgap/columnTransforms/LuceneIndexTransform.java

@@ -1,11 +1,14 @@
 package org.labkey.mgap.columnTransforms;
 
+import org.apache.commons.io.FileUtils;
 import org.jetbrains.annotations.Nullable;
-import org.labkey.api.jbrowse.JBrowseService;
 import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
 import org.labkey.mgap.etl.EtlQueueManager;
 
 import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
 
 public class LuceneIndexTransform extends OutputFileTransform
 {
@@ -24,7 +27,6 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip
         // NOTE: lucene is a special case since the DB tracks one file, but we need this whole folder:
         File sourceDir = f.getParentFile();
         File targetDir = new File(subdir, "LuceneIndex");
-        JBrowseService.get().clearLuceneCacheEntry(targetDir);
         EtlQueueManager.get().queueRsyncCopy(getContainerUser().getContainer(), sourceDir, targetDir);
 
         return new File(targetDir, sourceDir.getName() + "/" + f.getName());