PlatformIO file-structure conflicts with forks on github (with Arduino projects)

Does anyone have a verified procedure on how to handle the following workflow:

  1. Fork a Arduino github project (like GitHub - MKFirmware/MK4duo: MK4duo Firmware Printers 3D for Arduino and Arduino due)
  2. Import Arduino IDE Project in Atom
    2.1 That adds the selected folder to a subfolder and creates additional Atom-specific folders
  3. Now the whole github project is out of sync with the upstream project
    3.1 How can I keep syncing with the upstream project? (like here: Syncing a fork - GitHub Docs)
    Submodules? Pointers (if there is such a thing)? Anything?

Maybe the question should go out to the github community…I have limited knowledge of git, so please forgive me my ignorance…

  1. Download
  2. Unzip
  3. Open PlatformIO IDE/Atom and select “Open project”
  4. Choose this folder MK4duo/MK4duo at master · MKFirmware/MK4duo · GitHub
  5. Check “Keep compatible between Arduino IDE”.
  6. Press build button.

1-4 OK, thats what I already tried
5: No such option when opening project. Furthermore, cannot build project:

Can not find PlatformIO project.
Make sure that project you’re trying to buid is a PlatformIO project (e. g., contains platformio.ini).

If I “Import Arduino Project” and check “Keep compatible between Arduino IDE” (guess that is what you meant anyway…), the content of the selected folder is copied to a subfolder with the same name as the parent - along with additional folders. Then the whole thing is messed up in terms of keeping it in SYNC with the upstream project. So your suggestion does not work…

Please sorry, you need yo use Import Arduino Project

Please read my answer, I already tried the Import option.

Import should NOT move selected folder to subfolder but leave it right where it is. Then problem would be solved git-wise.

You can manually configure project structure. See platform-atmelavr/examples/arduino-own-src_dir at develop · platformio/platform-atmelavr · GitHub