Remove scratch directory completely, not just its files. See !95.

src/main/java/nl/wur/bif/pantools/pangenome/GenomeLayer.java

@@ -2148,6 +2148,9 @@ public class GenomeLayer {
             System.err.println("Error occurred during localization: " + e);
             e.printStackTrace(System.err);
             System.exit(1);
+        } finally {
+            if (!keepIntermediateFiles)
+                deleteDirectoryRecursively(scratchDirectory);
         }
 
         try (Transaction tx = GRAPH_DB.beginTx()) {
@@ -2215,7 +2218,8 @@ public class GenomeLayer {
         add_sequence_properties(scratchDirectory);
         localize_nodes();
         genome_overview();
-        
+
+        deleteDirectoryRecursively(scratchDirectory);
         System.out.println("\rNumber of kmers:   " + indexSc.length());
         System.out.println("Number of nodes:   " + num_nodes);
         System.out.println("Number of edges:   " + num_edges);
@@ -3457,4 +3461,18 @@ public class GenomeLayer {
         }
         return directory;
     }
+
+    /**
+     * Delete a directory and its contents.
+     * @param directory path to directory.
+     */
+    public void deleteDirectoryRecursively(Path directory) throws IOException {
+        try (Stream<Path> paths = Files.walk(directory)) {
+            //noinspection ResultOfMethodCallIgnored
+            paths
+                .sorted(Comparator.reverseOrder())
+                .map(Path::toFile)
+                .forEach(File::delete);
+        }
+    }
 }