You can use the Just In Time Code feature. It involves writing a windows executable to generate a hex file. Whenever you program the device with your firmware, then immediately after programming the firmware, your window executable will be called, and the generated hex file will be programmed.

So you could write a simple executable that reads in your binary java file and converts it to an intel hex file, then select your exectuable in Flash Magic.

Free Windows Compilers are available from various places, including http://www.idiom.com/free-compilers/

Let me know if you have any questions or problems.

Andy
Embedded Systems Academy
aayre@esacademy.com