improve log output when closing the graph (#165)

example output:
```
2020-10-05 14:04:17.291 DEBUG uninstalled GC monitors.
2020-10-05 14:04:17.961 INFO progress of clearing references: 18.96%
2020-10-05 14:04:18.591 INFO progress of clearing references: 37.92%
2020-10-05 14:04:19.119 INFO progress of clearing references: 56.88%
2020-10-05 14:04:19.716 INFO progress of clearing references: 75.84%
2020-10-05 14:04:20.255 INFO progress of clearing references: 94.80%
2020-10-05 14:04:20.346 INFO progress of clearing references: 100.00%
2020-10-05 14:04:20.346 INFO cleared all clearable references
2020-10-05 14:04:20.346 DEBUG closing OdbStorage
```

Author: mpollmeier

core/src/main/java/overflowdb/ReferenceManager.java

@@ -1,9 +1,9 @@
 package overflowdb;
 
-import overflowdb.storage.OdbStorage;
-import overflowdb.util.NamedThreadFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import overflowdb.storage.OdbStorage;
+import overflowdb.util.NamedThreadFactory;
 
 import java.util.ArrayList;
 import java.util.Collections;
@@ -83,8 +83,8 @@ private void syncClearReferences(final int releaseCount) {
     if (!refsToClear.isEmpty()) {
       safelyClearReferences(refsToClear);
       if (logger.isInfoEnabled()) logger.info("completed clearing of " + refsToClear.size() + " references");
-      if (logger.isDebugEnabled()) logger.debug("current clearable queue size: " + clearableRefs.size());
-      if (logger.isDebugEnabled()) logger.debug("references cleared in total: " + totalReleaseCount);
+      if (logger.isDebugEnabled()) logger.debug("remaining clearable references: " + clearableRefs.size());
+      if (logger.isTraceEnabled()) logger.trace("references cleared in total: " + totalReleaseCount);
     }
   }
 
@@ -161,17 +161,26 @@ private static SerializedNode serializeReference(NodeRef ref) {
       return null;
   }
 
-
   /**
    * writes all references to disk overflow, blocks until complete.
    * useful when saving the graph
    */
   public void clearAllReferences() {
+    int initialRefCount = clearableRefs.size();
+    int clearedCount = 0;
     while (!clearableRefs.isEmpty()) {
-      int clearableRefsSize = clearableRefs.size();
-      logger.info("clearing all (" + clearableRefsSize + ") references - this may take some time");
       try {
-        syncClearReferences(clearableRefsSize);
+        final List<NodeRef> refsToClear = collectRefsToClear(releaseCount);
+        if (!refsToClear.isEmpty()) {
+          int clearCountCurr = refsToClear.size();
+          safelyClearReferences(refsToClear);
+          clearedCount += clearCountCurr;
+        }
+
+        if (logger.isInfoEnabled()) {
+          float progressPercent = 100f * clearedCount / initialRefCount;
+          logger.info(String.format("progress of clearing references: %.2f%s", Float.min(100f, progressPercent), "%"));
+        }
       } catch (Exception e) {
         throw new RuntimeException("error while clearing references to disk", e);
       }

core/src/main/java/overflowdb/storage/OdbStorage.java

@@ -96,7 +96,7 @@ public <A extends Node> A readNode(final long id) throws IOException {
   /** flush any remaining changes in underlying storage to disk */
   public void flush() {
     if (mvstore != null) {
-      logger.debug("flushing to disk");
+      logger.trace("flushing to disk");
       mvstore.commit();
     }
   }