Using serial communication in .c-files

I would consider using HoodLoader2 instead of that LUFA project. If you can't do that, you can compile parts of the Arduino Core together with the LUFA project.

The main steps:

• Add the necessary Arduino source files to the SRC variable in the Makefile.
• Add the Arduino core folder to the include path by appending to the CC_FLAGS and CXX_FLAGS variables.
• Move the main function to a new main.cpp file and add it to the Makefile SRC as well.
• Include the Joystick.h file in your main file in an extern "C" block.
• Include the HardwareSerial.h file in your main file as well.

My files after these changes:

Makefile

# Set the MCU accordingly to your device (e.g. at90usb1286 for a Teensy 2.0++, or atmega16u2 for an Arduino UNO R3)
MCU          = atmega16u2
ARCH         = AVR8
F_CPU        = 16000000
F_USB        = $(F_CPU)
OPTIMIZATION = s
TARGET       = Joystick
SRC          = $(TARGET).c Descriptors.c main.cpp $(LUFA_SRC_USB)
LUFA_PATH    = ./lufa/LUFA
CC_FLAGS     = -DUSE_LUFA_CONFIG_HEADER -IConfig/
LD_FLAGS     =


ARDUINO_PATH = ${HOME}/.arduino15/packages/arduino/hardware/avr/1.8.1/cores/arduino
SRC         += $(ARDUINO_PATH)/HardwareSerial.cpp
SRC         += $(ARDUINO_PATH)/HardwareSerial1.cpp
SRC         += $(ARDUINO_PATH)/Print.cpp
CXX_FLAGS   += -I$(ARDUINO_PATH) -I./HoodLoader2/avr/variants/HoodLoader2
CC_FLAGS    += -I$(ARDUINO_PATH) -I./HoodLoader2/avr/variants/HoodLoader2

...

main.cpp

extern "C" {
#include "Joystick.h"
}

#include <HardwareSerial.h>

// Main entry point.
int main(void) {
    // We'll start by performing hardware and peripheral setup.
    SetupHardware();
    // We'll then enable global interrupts for our use.
    GlobalInterruptEnable();
    // Initialize the UART
    Serial1.begin(115200);
    Serial1.println(F("Hello, world"));
    // Once that's done, we'll enter an infinite loop.
    for (;;)
    {
        // We need to run our task to process and deliver data for our IN and OUT endpoints.
        HID_Task();
        // We also need to run the main USB management task.
        USB_USBTask();
    }
}

Joystick.c
Deleted the main function.

To get it to compile after these changes:

# (inside of the snowball-thrower folder)
git submodule add https://github.com/NicoHood/HoodLoader2.git HoodLoader2
make

This compiles without problems for me, but I have no idea if it actually works.

Edit:

You'll notice that the program uses more RAM than the ATmeg16U2 has available. You could solve this by moving the step array to PROGMEM, or by shrinking the Serial buffers.

avr-size --mcu=atmega16u2 --format=avr Joystick.elf
AVR Memory Usage
----------------
Device: atmega16u2

Program:    5076 bytes (31.0% Full)
(.text + .data + .bootloader)

Data:        527 bytes (102.9% Full)
(.data + .bss + .noinit)

 [INFO]    : Finished building project "Joystick".