RECON stands for Reconfigurable which is a collection of different flavours of NIOS-based embedded system. With RECON repository, new user can quickly turn their Altera low-cost FPGA dev board into a more a familiar microcontroller system such as AVR and start making custom logic based off this initial infrastructure.
hw : FPGA hardare/hdl/qsys files + cmn : common HDL reused across different architecres + recon_xxx : NIOS-based architectures
sw : Drivers/applications/demo + cmn : drivers for peripherals in hw/cmn + examples: demonstration applications + recon_xxx/bsp: preconfigured bsp for a recon_xxx architecture. For further information, go to the directory and type >make help