[_iiu1]

Leaving aside the fact that open source toolchains exist for various Lattice FPGA's (the ice-40 and ecp5 etc)

About the simplest environment for doing what you just described is http://papilio.cc/

While using the existing Xilinx Webpack tools for actual synthesis, place and routing, etc. the Papilio Design-IDE will LITERALLY let you add peripherals to virtual Arduino like appendages! It takes advantage of a number of community projects like the Wishbone bus, and achieves a nearly drag-n-drop level of visual design tool.

Once you have loaded your custom arduino chip onto the papilio boards FPGA you can program it with a modified version of the Arduino IDE!!!!

One of their virtual chips you can start with IS the arduino atmega 328! Another is the ZPU-ino, an implementation of the Zylin ZPU (a 32bit mcu) done by Alvie Boy that allows you to program this much more powerful device ALSO by the Arduino IDE!