Add output file type, collect all files

Core/Remote/piscal_launcher.sh

@@ -89,8 +89,7 @@ pushd $run_directory >> /dev/null
 if [ -z "$test_output_directory" ]; then
     eval $piscal_executable
 else
-    cp "$test_output_directory"/* "$output_directory_touser"/
-    cp "$test_output_directory"/* "$output_directory_nottouser"/
+    cp -r "$test_output_directory"/* "$output_directory_base"/
 fi
 
 popd >> /dev/null
@@ -99,6 +98,7 @@ popd >> /dev/null
 if [ -z "$suppress_storage_copy" ]; then
     cp "$output_directory_touser"/* "$storage_directory"/
     cp "$output_directory_nottouser"/* "$storage_directory"/
+    cp "$cleaned_input_directory"/* "$storage_directory"/
 fi
 
 # notify given url of completion