eclipse photon with cdt-arduino plugin can't upload sketches
It sounds to me like Eclipse doesn't know how to reboot the board into the bootloader.

Traditional Arduinos automatically boot into the bootloader when the board is reset, and the board resets every time you open the serial port thanks to the USB chip having DTR connected (through a capacitor) to the reset pin of the man MCU.

Chips with a direct USB connection can't do that (boards like the M0 Feather, the Leonardo, etc).  Instead they have to be rebooted by opening the serial port at 1200 baud and then closing it again.

With the "traditional" boards the IDE neither knows, nor cares, about rebooting the board - it just happens. However with direct USB boards the IDE has to have specific code to perform the reboot at the right time. The Arduino IDE has that code. However I would guess that the Eclipse plugin either doesn't implement that, or doesn't have the ability to implement it.

So you will have to manually reset the board for programming.