Remove uses of log4j in picard, it's still a required transitively

* replace the dependency with a version constraint so we don't import a buggy version

build.gradle

@@ -67,8 +67,8 @@ dependencies {
     api 'org.broadinstitute:barclay:5.0.0'
 
     //log4j api and core used in logging
-    api 'org.apache.logging.log4j:log4j-api:' +log4jVersion
-    implementation 'org.apache.logging.log4j:log4j-core:' + log4jVersion
+    implementation 'org.apache.logging.log4j:log4j-api:' +log4jVersion
+    runtimeOnly 'org.apache.logging.log4j:log4j-core:' + log4jVersion
 
     //gkl and associated native bindings
     implementation('com.intel.gkl:gkl:0.8.11'){

src/main/java/picard/nio/DeleteRecursive.java

@@ -1,7 +1,7 @@
 package picard.nio;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+import htsjdk.samtools.util.Log;
+
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -15,10 +15,10 @@
  *
  * <p>This class is a modification of {@link htsjdk.samtools.util.nio.DeleteOnExitPathHook}
  *
- * This class should be considered an implementation detail of {@link IOUtils#deleteOnExit(Path)} and not used directly.
+ * This class should be considered an implementation detail of {@link GATKIOUtils#deleteOnExit(Path)} and not used directly.
  */
 class DeleteRecursivelyOnExitPathHook {
-    private static final Logger LOG = LogManager.getLogger(DeleteRecursivelyOnExitPathHook.class);
+    private static final Log LOG = Log.getInstance(DeleteRecursivelyOnExitPathHook.class);
     private static LinkedHashSet<Path> paths = new LinkedHashSet<>();
     static {
         Runtime.getRuntime().addShutdownHook(new Thread(DeleteRecursivelyOnExitPathHook::runHooks));
@@ -60,8 +60,8 @@ static void runHooks() {
             try {
                 GATKIOUtils.deleteRecursively(path);
             } catch (final Exception e) {
-                // do nothing if cannot be deleted, because it is a shutdown hook
-                LOG.debug(() -> "Could not recursively delete " + path.toString() + " during JVM shutdown because we encountered the following exception:", e);
+                // do nothing if itcannot be deleted, because it is a shutdown hook
+                LOG.debug(e, "Could not recursively delete ", path.toString(), " during JVM shutdown because we encountered the following exception:");
             }
         }
     }