TIMER1 CTC Interrupts not working with avr-gcc

Question

I am attempting to program my arduino in plain C, and I've come across some very strange behavior. If I load the following code from the Arduino IDE, it works as expected and toggles Pin 6 every 100ms. However, if I compile it with avr-gcc and then load it with avrdude, no interrupts are run. Here is the C code:

#include <avr/io.h>
#include <avr/interrupt.h>

int main();
void timer1_init();

int main()
{
    // connect led to pin PD6
    DDRD |= (1 << 6);
    PORTD |= (1 << 6);

    // initialize timer
    timer1_init();

    // loop forever
    while(1)
    {
        // do nothing
        // whenever a match occurs, ISR is fired
        // toggle the led in the ISR itself
        // no need to keep track of any flag bits here
        // done!
    }
}

// initialize timer, interrupt and variable
void timer1_init()
{
    /*cli();*/
    /*TCCR1A = 0;*/
    /*TCCR1B = 0;*/
    /*TCNT1 = 0;*/
    OCR1A = 24999;
    TCCR1B |= _BV(WGM12) | _BV(CS11) | _BV(CS10);
    TIMSK1 |= _BV(OCIE1A);
    sei();
}

ISR (TIMER1_COMPA_vect)
{
    // toggle led here
    PORTD ^= (1 << 6);
}

And here is the Makefile I'm using to load it onto the arduino:

CC = avr-gcc
CFLAGS = -g -O0 -Wall -fno-exceptions -ffunction-sections -fdata-sections -mmcu=atmega328p -DF_CPU=16000000L -MMD -DUSB_VID=null -DUSB_PID=null -DARDUINO=106

SOURCE = test

all: load

$(SOURCE): $(SOURCE).o
    $(CC) $(SOURCE).o -o $(SOURCE)

hex: $(SOURCE)
    avr-objcopy -O ihex -R .eeprom $(SOURCE) $(SOURCE).hex

load: hex
    avrdude -F -V -c arduino -p ATMEGA328P -P /dev/tty.usbmodem1411 -b 115200 -U flash:w:$(SOURCE).hex

clean:
    rm -f *.o *.hex
    rm -f `find . -perm 755 | perl -pe 's/\.\n//g' | perl -pe 's/\.\/(\w+)\n/\1 /g'`

Is there something that the arduino ide automatically adds to it that makes it work? What am I missing?

Edit: Here is the make output:

avr-gcc -g -O0 -Wall -fno-exceptions -ffunction-sections -fdata-sections -mmcu=atmega328p -DF_CPU=16000000L -MMD -DUSB_VID=null -DUSB_PID=null -DARDUINO=106   -c -o test.o test.c
avr-gcc test.o -o test
avr-objcopy -O ihex -R .eeprom test test.hex
avrdude -F -V -c arduino -p ATMEGA328P -P /dev/tty.usbmodem1411 -b 115200 -U flash:w:test.hex

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.01s

avrdude: Device signature = 0x1e950f
avrdude: NOTE: "flash" memory has been specified, an erase cycle will be performed
         To disable this feature, specify the -D option.
         avrdude: erasing chip
         avrdude: reading input file "test.hex"
         avrdude: input file test.hex auto detected as Intel Hex
         avrdude: writing flash (196 bytes):

         Writing | ################################################## | 100% 0.04s

         avrdude: 196 bytes of flash written

         avrdude: safemode: Fuses OK (E:00, H:00, L:00)

         avrdude done.  Thank you.

Answer 1

I just tried using arduino-mk https://github.com/sudar/Arduino-Makefile, and it worked, so I guess I'm just going to stick with that.