Thanks for both suggestions. I've tried uPyCraft on Linux and it works.
But then I've remembered Thonny. Tried it and it also works on Linux and has many features for MicroPython @ Atom Lite : View->File, edit file on microcontroller flash memory, etc.
I also recommend mpfshell, it works 100% on Linux to copy files with Atom Lite/Matrix & UIFlow 1.4.5(.1).