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Here is a the source code for compiling and uploading Arduino programs from the command line without the use of the Arduino environment or Java. You will still need a number of other programs. On the Mac or Windows, it's probably easiest just to download and install the Arduino software. On Linux, you will need to install avr-gcc (whose package is usually called gcc-avr), avr-libc and avrdude.
Download: arduino-0011-core.zip
Instructions for writing, compiling/verifying, and uploading your programs are in the Makefile.