Eliminate double-database close log messages

* BdbModule.java
   split openDatabase() to openManagedDatabase() (auto-closed) and plain openDatabase() (caller-closes)
   set TempStoredSortedMap to use unmanaged openDatabase
* (others)
   use openManagedDatabase()

commons/src/main/java/org/archive/util/ObjectIdentityBdbCache.java

@@ -549,7 +549,7 @@ implements ObjectIdentityCache<String, V>, Closeable, Serializable {
         final void clearPhantom() {
             if (this.phantom != null) {
                 this.phantom.clear();
-                this.phantom = null;
+//                this.phantom = null;
             }
             super.clear();
         }