And here's console output for the published Blink.cpp:
00:39:07 **** Incremental Build of configuration Debug for project ArduinoTemplate ****
make all
Building target: ArduinoTemplate.elf
Invoking: ARM Sourcery Mac OS X GCC C++ Linker
arm-none-eabi-g++ -L"/Users/victor/Documents/arduino-workspace/ArduinoDueLib/Debug" -L"/Users/victor/Documents/arduino-workspace/ArduinoDueLib/variants/arduino_due_x" -Wl,-Map,ArduinoTemplate.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 "ArduinoTemplate.elf" -Wl,--start-group ./Blink.o ./main.o /Users/victor/Documents/arduino-workspace/ArduinoDueLib/Debug/syscalls_sam3.o -lArduinoDueLib -lsam_sam3x8e_gcc_rel -Wl,--end-group
/Applications/Arduino-due.app/Contents/Resources/Java/hardware/tools/g++_arm_none_eabi/bin/../lib/gcc/arm-none-eabi/4.4.1/../../../../arm-none-eabi/bin/ld: warning: changing start of section .fini by 2 bytes
/Applications/Arduino-due.app/Contents/Resources/Java/hardware/tools/g++_arm_none_eabi/bin/../lib/gcc/arm-none-eabi/4.4.1/../../../../arm-none-eabi/bin/ld: warning: changing start of section .fini by 2 bytes
Finished building target: ArduinoTemplate.elf
/Applications/Arduino-due.app/Contents/Resources/Java/hardware/tools/g++_arm_none_eabi/bin/../lib/gcc/arm-none-eabi/4.4.1/../../../../arm-none-eabi/bin/ld: warning: changing start of section .fini by 2 bytes
/Users/victor/Documents/arduino-workspace/ArduinoDueLib/variants/arduino_due_x/libsam_sam3x8e_gcc_rel.a(startup_sam3xa.o): In function `Reset_Handler':
startup_sam3xa.c:(.text.Reset_Handler+0x54): warning: undefined reference to `_srelocate'
startup_sam3xa.c:(.text.Reset_Handler+0x58): warning: undefined reference to `_szero'
/Applications/Xcode.app/Contents/Developer/usr/bin/make --no-print-directory post-build
/Applications/Arduino-due.app/Contents/Resources/Java/hardware/tools/g++_arm_none_eabi/bin/arm-none-eabi-objcopy -O binary ArduinoTemplate.elf ArduinoTemplate.bin
Invoking: ARM Sourcery Mac OS X GNU Create Flash Image
arm-none-eabi-objcopy -O ihex ArduinoTemplate.elf "ArduinoTemplate.hex"
Finished building: ArduinoTemplate.hex
Invoking: ARM Sourcery Mac OS X GNU Create Listing
arm-none-eabi-objdump -h -S ArduinoTemplate.elf > "ArduinoTemplate.lst"
Finished building: ArduinoTemplate.lst
startup_sam3xa.c:(.text.Reset_Handler+0x5c): warning: undefined reference to `_erelocate'
startup_sam3xa.c:(.text.Reset_Handler+0x60): warning: undefined reference to `_ezero'
Invoking: ARM Sourcery Mac OS X GNU Print Size
arm-none-eabi-size --format=berkeley ArduinoTemplate.elf
text data bss dec hex filename
4078 16 424 4518 11a6 ArduinoTemplate.elf
Finished building: ArduinoTemplate.siz
startup_sam3xa.c:(.text.Reset_Handler+0x64): warning: undefined reference to `_sfixed'
00:39:08 Build Finished (took 942ms)
Aand it's not working. I don't see anything weird except for some Warnings and the fact that something inside Eclipse is using XCode's make, but I don't know if this is usual or not