Many thanks for replay.
It looks like 'hardware/arduino/sam/cores/arduino' is an Arduino part with the entry point main.cpp. Then, I think initialization of MCU is done in init() function from 'hardware/arduino/sam/variants/arduino_due_x/variant.cpp'.
The init() uses SystemInit() function, it's probably from 'hardware/arduino/sam/system/CMSIS/Device/ATMEL/sam3xa/source/system_sam3xa.c'.
It seems that this CMSIS folder contains some standard libraries provided by ARM: http://www.arm.com/products/processors/cortex-m/cortex-microcontroller-software-interface-standard.php
'hardware/arduino/sam/system/libsam/' is also interesting, it contains functions to use some pheripherals, like RTC, SPI or Watchdog.