Build on Ubuntu

AVR

Install toolchain

sudo aptitude install binutils-avr gcc-avr avr-libc gdb-avr

Configure and compile

cd fc-controller / sb-controller (choose one of them)
./configure --with-toolchaindir=/usr/lib/gcc
make

Now you should have an sb-ctrl.hex/rc-ctrl.hex in your directory. The Makefiles have several methods to flash. I use an STK500 to flash (serial port is /dev/ttyS0, you have to alter Makefile.am to change that):

make sb-flash-stk500

You can also use AVR Dragon to flash the Atmels

make sb-flash-dragon

ARM

Extract toolchain to /opt/ (for example Axel Burri's)

sudo apt-get install automake1.10
./configure --enable-ctrl-amir --enable-ctrl-bh --enable-ctrl-pt1 --enable-usb-bootloader --enable-usb-bootloader-switch --with-toolchaindir=/opt/arm-4.1.2 --with-isp-port=/dev/ttyUSB0
make

While developing, its a good idea to choose a fast flash method. This is the USB flash method, which takes about 3 seconds. But you need to flash the bootloader first.

make bl-flash-serial

Then you just can type to flash your FC again:

make fc-flash-usb