kwokwong
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So we will have to download the FPGA codes and our application onto the RAM and then reprogram the entire EPCS flash (thus probably including
the bootloader).[/b]
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May be you can use remote system update feature?
You need to add to your design any kind of communication with external world (uart or ethernet for example).
And than add feature to your programm to write flash at specified address with data recieved via communication interface.
In this way, as I understand, you will need to write your own bootloader if you wish to programm flash with code footprint beginning at address 0x00000000. So firstly you programm your bootloader and then you programm your code.
In other hand may be you will be able to find how much space occupies Altera Flash Programmer bootloader and write your code footprint right after it.
If you discover end address of Altera Flash Programmer bootloader Please post it here - it will be wery usefull to know this.
Info about remote update can be found on Altera web server. This feature is applicable to EPC devices too.