The lines in your output that show this are the undefined symbols I was talking about.
startup_sam3xa.c:(.text.Reset_Handler+0x5c): warning: undefined reference to `_erelocate'
startup_sam3xa.c:(.text.Reset_Handler+0x60): warning: undefined reference to `_ezero'
These should be marked as errors but they aren't I'm sure it is related to some of the options in the linking command but as long as my set up works I'm not going to spend much effort to find it.
In any case, you are missing the linker script, for me it is:
${workspace_loc:}/arduinosource/hardware/arduino/sam/variants/arduino_due_x/linker_scripts/gcc/flash.ld
This is in the box at the top of the dialog under Properties->C/C++ Build->Settings->ARM Sourcery Linux GCC C++ Linker->General
Your link process should look like:
Building target: blink.elf
Invoking: ARM Sourcery Linux GCC C++ Linker
arm-none-eabi-g++ -T"workspace/arduinosource/hardware/arduino/sam/variants/arduino_due_x/linker_scripts/gcc/flash.ld" -L"workspace/arduinoDueCore/Release" -L"arduinoDueCore/arduino_due_x" -Wl,-Map,blink.map -lm -lgcc -Wl,--cref -Wl,--check-sections -Wl,--gc-sections -Wl,--entry=Reset_Handler -Wl,--unresolved-symbols=report-all -Wl,--warn-common -Wl,--warn-section-align -Wl,--warn-unresolved-symbols -mcpu=cortex-m3 -mthumb -o "blink.elf" -Wl,--start-group ./src/Blink.o workspace/arduinoDueCore/Release/syscalls_sam3.o -larduinoDueCore -lsam_sam3x8e_gcc_rel -Wl,--end-group
Finished building target: blink.elf
make --no-print-directory post-build
workspace/arduinosource/hardware/tools/g++_arm_none_eabi/bin/arm-none-eabi-objcopy -O binary blink.elf blink.bin
Invoking: ARM Sourcery Linux GNU Create Flash Image
arm-none-eabi-objcopy -O ihex blink.elf "blink.hex"
Finished building: blink.hex
Invoking: ARM Sourcery Linux GNU Create Listing
arm-none-eabi-objdump -h -S blink.elf > "blink.lst"
Finished building: blink.lst
Of course your paths will be different, but the only thing I see missing is the -T ...linker_scripts/gcc/flash.ld
If you still don't get a blinking led, do a make clean before you make debug. You have the default debug and release make targets, I use only release which is also changing the paths a bit, shouldn't make any difference though.