So I omitted that part, and when i tried to bootload it did not work properly. I then remembered I commented out your naked main function and so I UNCOMMENTED it and then recompiled and bootloaded and it bootloaded successfully and was able to boot. However, the same error blink occured when i tried to program. Not sure what the problem could be anymore. I even tried to change everything to the internal 8mhz clock and again it successfully boots but cannot actually be reprogrammed.
I was thinking it might help to run the bootloader in the arduino definition and when i changed the chAudioboot.c file to change the definition and then tried to build the project again this is the error I got.
~/Desktop/AudioBoot $ ./build.sh
chAudioBoot.c: In function 'setup':
chAudioBoot.c:98:4: warning: implicit declaration of function 'pinMode' [-Wimplicit-function-declaration]
chAudioBoot.c:98:20: error: 'OUTPUT' undeclared (first use in this function)
chAudioBoot.c:98:20: note: each undeclared identifier is reported only once for each function it appears in
chAudioBoot.c:99:4: error: 'Serial' undeclared (first use in this function)
chAudioBoot.c: In function 'loop':
chAudioBoot.c:104:4: warning: implicit declaration of function 'a_main' [-Wimplicit-function-declaration]
chAudioBoot.c: At top level:
chAudioBoot.c:127:6: warning: conflicting types for 'a_main' [enabled by default]
chAudioBoot.c:104:4: note: previous implicit declaration of 'a_main' was here
chAudioBoot.c:299:1: error: unknown type name 'uint8_t'
chAudioBoot.c:312:1: error: unknown type name 'uint8_t'
chAudioBoot.c: In function 'receiveFrame':
chAudioBoot.c:314:3: error: unknown type name 'uint16_t'
chAudioBoot.c:316:3: error: unknown type name 'uint16_t'
chAudioBoot.c:317:3: error: unknown type name 'uint16_t'
chAudioBoot.c:318:3: error: unknown type name 'uint16_t'
chAudioBoot.c:319:3: error: unknown type name 'uint8_t'
chAudioBoot.c:320:3: error: unknown type name 'uint8_t'
chAudioBoot.c:321:3: error: unknown type name 'uint8_t'
chAudioBoot.c:322:3: error: unknown type name 'uint16_t'
chAudioBoot.c:327:5: error: 'PINB' undeclared (first use in this function)
chAudioBoot.c:327:5: error: 'PB4' undeclared (first use in this function)
chAudioBoot.c:332:3: error: 'TCNT2' undeclared (first use in this function)
chAudioBoot.c:390:5: error: unknown type name 'uint16_t'
chAudioBoot.c:390:19: error: 'uint16_t' undeclared (first use in this function)
chAudioBoot.c:390:28: error: expected ',' or ';' before 'FrameData'
chAudioBoot.c:396:5: error: 'Serial' undeclared (first use in this function)
chAudioBoot.c:407:31: error: 'HEX' undeclared (first use in this function)
chAudioBoot.c:425:26: error: 'true' undeclared (first use in this function)
chAudioBoot.c:426:15: error: 'false' undeclared (first use in this function)
chAudioBoot.c: At top level:
chAudioBoot.c:437:25: error: unknown type name 'uint32_t'
chAudioBoot.c:437:40: error: unknown type name 'uint8_t'
chAudioBoot.c: In function 'runProgramm':
chAudioBoot.c:477:2: error: 'DDRB' undeclared (first use in this function)
chAudioBoot.c:478:2: error: 'DDRC' undeclared (first use in this function)
chAudioBoot.c:479:2: error: 'DDRD' undeclared (first use in this function)
chAudioBoot.c:480:2: warning: implicit declaration of function 'cli' [-Wimplicit-function-declaration]
chAudioBoot.c: In function 'a_main':
chAudioBoot.c:505:3: error: 'Serial' undeclared (first use in this function)
chAudioBoot.c:508:3: error: unknown type name 'uint8_t'
chAudioBoot.c:510:3: error: unknown type name 'uint16_t'
chAudioBoot.c:511:3: error: unknown type name 'uint8_t'
chAudioBoot.c:514:3: error: unknown type name 'uint8_t'
chAudioBoot.c:518:8: error: 'TCNT2' undeclared (first use in this function)
chAudioBoot.c:524:10: warning: implicit declaration of function 'digitalWrite' [-Wimplicit-function-declaration]
chAudioBoot.c:524:10: warning: implicit declaration of function 'digitalRead' [-Wimplicit-function-declaration]
chAudioBoot.c:535:12: error: 'LOW' undeclared (first use in this function)
chAudioBoot.c:541:11: error: 'PINB' undeclared (first use in this function)
chAudioBoot.c:541:11: error: 'PB4' undeclared (first use in this function)
chAudioBoot.c:550:3: error: 'HIGH' undeclared (first use in this function)
rm: audioboot.hex: No such file or directory
avr-objcopy: 'audioboot.elf': No such file
avr-objdump: 'audioboot.hex': No such file
avr-objdump: section '.sec1' mentioned in a -j option, but not found in any input file