Include the .qortal folder in the merge output, since it will be needed for validation. We may choose to exclude it from the final output path, but for now it is left there to make debugging easier.

src/main/java/org/qortal/arbitrary/ArbitraryDataMerge.java

@@ -33,6 +33,7 @@ public class ArbitraryDataMerge {
             this.copyPreviousStateToMergePath();
             this.loadMetadata();
             this.applyDifferences();
+            this.copyMetadata();
 
         } finally {
             this.postExecute();
@@ -79,14 +80,14 @@ public class ArbitraryDataMerge {
         for (Path path : addedPaths) {
             LOGGER.info("File was added: {}", path.toString());
             Path filePath = Paths.get(this.pathAfter.toString(), path.toString());
-            ArbitraryDataMerge.copyFilePathToBaseDir(filePath, this.mergePath, path);
+            ArbitraryDataMerge.copyPathToBaseDir(filePath, this.mergePath, path);
         }
 
         List<Path> modifiedPaths = this.metadata.getModifiedPaths();
         for (Path path : modifiedPaths) {
             LOGGER.info("File was modified: {}", path.toString());
             Path filePath = Paths.get(this.pathAfter.toString(), path.toString());
-            ArbitraryDataMerge.copyFilePathToBaseDir(filePath, this.mergePath, path);
+            ArbitraryDataMerge.copyPathToBaseDir(filePath, this.mergePath, path);
         }
 
         List<Path> removedPaths = this.metadata.getRemovedPaths();
@@ -96,15 +97,30 @@ public class ArbitraryDataMerge {
         }
     }
 
+    private void copyMetadata() throws IOException {
+        Path filePath = Paths.get(this.pathAfter.toString(), ".qortal");
+        ArbitraryDataMerge.copyPathToBaseDir(filePath, this.mergePath, Paths.get(".qortal"));
+    }
+
 
-    private static void copyFilePathToBaseDir(Path source, Path base, Path relativePath) throws IOException {
+    private static void copyPathToBaseDir(Path source, Path base, Path relativePath) throws IOException {
         if (!Files.exists(source)) {
             throw new IOException(String.format("File not found: %s", source.toString()));
         }
 
+        File sourceFile = source.toFile();
         Path dest = Paths.get(base.toString(), relativePath.toString());
         LOGGER.trace("Copying {} to {}", source, dest);
-        Files.copy(source, dest, StandardCopyOption.REPLACE_EXISTING);
+
+        if (sourceFile.isFile()) {
+            Files.copy(source, dest, StandardCopyOption.REPLACE_EXISTING);
+        }
+        else if (sourceFile.isDirectory()) {
+            FilesystemUtils.copyAndReplaceDirectory(source.toString(), dest.toString());
+        }
+        else {
+            throw new IOException(String.format("Invalid file: %s", source.toString()));
+        }
     }
 
     private static void copyDirPathToBaseDir(Path source, Path base, Path relativePath) throws IOException {