Compiling the solution I got the following errors in mso.c:
Error 'TC_OVFINTLVL_MED_gc' undeclared (first use in this function) Xprotolab C:\AVR\Studio\Proj\XScopes-Firmware\Source\mso.c 609
Error 'TC_CLKSEL_EVCH5_gc' undeclared (first use in this function) Xprotolab C:\AVR\Studio\Proj\XScopes-Firmware\Source\mso.c 2598
Error 'TC_CLKSEL_EVCH2_gc' undeclared (first use in this function) Xprotolab C:\AVR\Studio\Proj\XScopes-Firmware\Source\mso.c 2607
I see?iox32a4u.h among Dependencies files.
If I change above definitions to their numerical values(e.g.?TC_OVFINTLVL_MED_gc to?(0x02

Now, while debugging using Studio 7 via AVR Dragon I everytime fell into the trap:
00004001 ff.cf ? ? ? ? ? ? ? ?RJMP PC-0x0000 Relative jump
source code was taken from github
?

Also.
Where is bootloader in xprotolab-merged.elf ?
Powering on with Key1 pressed - no reaction.
?
Sorry, OK now

Loading Xprotolab.hex from \XScopes-Firmware-master\Xprotolab\Debug\ via Flip results nothing. /\r\n/Device stays in bootloader mode.

I've been using Atmel Studio 6.2.
Try using the HEX files from the Xprotolab's page.