Enable C99, with gnu extensions

The default for GCC is gnu90 (C90 with gnu extensions), which does not
allow things like declaring variables in for loops, or // comments. This
switches to gnu99, which allows compiling more code.
Explicitely specify std=gnu++98 for C++ compilation

This is the default for GCC, but specifying it explicitely makes it more
clear what C standard is being used.
Remove atmega16u2 code and toolchain bits

This repository should contain just the Pinoccio core for use with the
Arduino IDE, so these bits will be moved to another place.
Move the hardware/pinoccio/avr directory to top level

This allows cloning this repository into the the `hardware` directory in
the Arduino sketchbook to make it work, instead of having to clone it
separately and copy or symlink it into the `hardware` directory.