JTag programming

It isn't clear from your posting if you want to program an FPGA on the linux board with the Max 10 FPGA or if you want to program the Max 10 from a linux distro.

I'm not sure if this applies, but remember that the Max 10 is a CPLD. It stores the configuration so it doesn't need to be configured at powerup.

If you want to configure an FPGA on another board from the Max 10 using JTAG, I'd advise against doing that. It's vastly easier to include a configuration flash on your other board and program it from Quartus with a USB blaster. See the Altera documentation (E.g. ch 7 JTAG configuration in the Cyclone V handbook and app note 414 on the Jrunner driver) if you insist on doing it the with JTAG.