That’s exactly the reason.
The fact that jupyter runs as root will inevitably cause folders created within this context to be root-owned.
However, what you describe at the beginning (regarding the jupyter_notebook dir) should not happen. If you look at this PYNQ/qemu.sh at master · Xilinx/PYNQ · GitHub
(bottom) you will see that permissions are set to xilinx:xilinx
That of course is not the case for user-created folders while using jupyter, since the process owner for the server, as you mention, is root.
My best advice is that you set the permissions yourself opening a terminal in Jupyter (right click on “New” at top right and then “Terminal”) with chown xilinx:xilinx your-folder. I know this is a workaround, but this “dichotomy” as you describe it is currently sort of a limitation that we don’t really have plans to address at the moment.
Another (possible) solution might be that you SSH as root (password is xilinx as well for root). To enable it you’ll have to uncomment the “#PermitRootLogin” line of /etc/ssh/sshd_config and set it to yes
vim /etc/ssh/sshd_config
uncomment “#PermitRootLogin …”
PermitRootLogin yes
save the file and restart ssh service (or the board)
/etc/init.d/ssh restart
That should do.