/targets/wiring/ in the source repository only contains the object files. Wheres the source for these object files?
ex. Encoder.o or any other file in that directory
Also, is there any way to write for arduino in low level... maybe something like assembly? Anyone got an assembler, opcode list?
Arduino hardware is based on the atmega8 or atmega168, which is an AVR microcontroller. You can program it in assembler or plain C using AVR Studio. The Arduino language makes AVR programming much easier, and the hardware platform is some sort of de facto standard. Arduino IDE generates plain AVR C. You can start here: http://www.atmel.com or here as well: http://www.avrfreaks.net
You can probably get the source for those files from Wiring.
You can write low level code.
Check the datasheet for the assembler and opcode information.
One thing I like doing is compiling the C code with -S. That makes gcc spit out the assembly code.
The Wiring target isn't even really used, it was more of an experiment to see if it made sense to support the Wiring board from the Arduino environment, but it's probably easier just to use the Wiring environment directly. The source code for those files is available from the Wiring repository: http://wiring.uniandes.edu.co/source/trunk/wiring/core/