pyside6-deploy automatically adds qml files under project. The list of qml files are saved to qml_files option under  [qt] in pysidedeploy.spec file, and passed to Nuitka as following. 

#PySide6/scripts/deploy/nuitka_helper.py:

qml_args = []
if qml_files:
     qml_args.append("--include-qt-plugins=all")
     qml_args.extend([
           f"--include-data-files={qml_file}=./{qml_file.name}"
           for qml_file in qml_files
      ])

However, qml_file variable here is absolute path, and qml_file.name has no information about the directory structure.

This comes problem to me, because the qml files are structured in my project. Unless all qml files are stored project root, it seems strange to lose all directory structures.