Wrong Bootloader not present warning

[NicoHood]

If I compile a sketch for my custom HoodLoader2 core I now get a warning that the .hex file is missing. However a ISP programming still works. The IDE looks at the internal path, not the hardwarefolder where the HoodLoader2 is installed.
https://github.com/NicoHood/HoodLoader2/tree/dev_205

Also I suggest to somehow access the default bootloaders. For example I added a copy of the Uno/Mega board to add the Serial 1200 baud touch feature. But I still want to use the optiboot bootloader. At the moment I have to put a copy of this hexfile in my repository which I do not prefer since this can be avoided with arduino:optiboothexfilepath.

IDE Warning (when hitting compile):

/Arduino/build/linux/work/arduino-builder -dump-prefs -logger=machine -hardware "/Arduino/build/linux/work/hardware" -hardware "/home/linuxuser/.arduino15/packages" -hardware "/sketchbook/hardware" -tools "/Arduino/build/linux/work/tools-builder" -tools "/Arduino/build/linux/work/hardware/tools/avr" -tools "/home/linuxuser/.arduino15/packages" -libraries "/sketchbook/libraries" -libraries "/Arduino/build/linux/work/libraries" -fqbn=HoodLoader2:avr:HoodLoader2atmega16u2:board=uno -ide-version=10606 -build-path "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp" -warnings=none -prefs=build.warn_data_percentage=75 -verbose "/tmp/untitled1542786869.tmp/sketch_sep26a/sketch_sep26a.ino"
/Arduino/build/linux/work/arduino-builder -compile -logger=machine -hardware "/Arduino/build/linux/work/hardware" -hardware "/home/linuxuser/.arduino15/packages" -hardware "/sketchbook/hardware" -tools "/Arduino/build/linux/work/tools-builder" -tools "/Arduino/build/linux/work/hardware/tools/avr" -tools "/home/linuxuser/.arduino15/packages" -libraries "/sketchbook/libraries" -libraries "/Arduino/build/linux/work/libraries" -fqbn=HoodLoader2:avr:HoodLoader2atmega16u2:board=uno -ide-version=10606 -build-path "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp" -warnings=none -prefs=build.warn_data_percentage=75 -verbose "/tmp/untitled1542786869.tmp/sketch_sep26a/sketch_sep26a.ino"
WARNING: Spurious .git folder in 'AnalogTouch' library
WARNING: Spurious .git folder in 'HID-Project' library
WARNING: Spurious .git folder in 'IRLremote' library
WARNING: Spurious .git folder in 'MSGEQ7' library
WARNING: Spurious .git folder in 'Nintendo' library
WARNING: Spurious .git folder in 'PinChangeInterrupt' library
WARNING: Spurious .git folder in 'RCLSwitch' library
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -w -x c++ -M -MG -MP -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch/sketch_sep26a.ino.cpp"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -w -x c++ -M -MG -MP -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch/sketch_sep26a.ino.cpp"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -w -x c++ -M -MG -MP -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch/sketch_sep26a.ino.cpp"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -w -x c++ -M -MG -MP -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch/sketch_sep26a.ino.cpp"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++"  -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics  -w -x c++ -E -CC -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16       "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch/sketch_sep26a.ino.cpp"
"/Arduino/build/linux/work/tools-builder/ctags/5.8-patched/ctags" -u --language-force=c++ -f - --c++-kinds=svpf --fields=KSTtzns "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/preproc/ctags_target.cpp"
"/Arduino/build/linux/work/tools-builder/ctags/5.8-patched/ctags" -u --language-force=c++ -f - --c++-kinds=svpf --fields=KSTtzns "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/preproc/ctags_target.cpp"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch/sketch_sep26a.ino.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch/sketch_sep26a.ino.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-gcc" -c -g -x assembler-with-cpp -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/wiring_pulse.S" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring_pulse.S.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-gcc" -c -g -Os -w -std=gnu11 -ffunction-sections -fdata-sections -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/WInterrupts.c" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/WInterrupts.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-gcc" -c -g -Os -w -std=gnu11 -ffunction-sections -fdata-sections -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/hooks.c" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/hooks.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-gcc" -c -g -Os -w -std=gnu11 -ffunction-sections -fdata-sections -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/wiring.c" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-gcc" -c -g -Os -w -std=gnu11 -ffunction-sections -fdata-sections -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/wiring_analog.c" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring_analog.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-gcc" -c -g -Os -w -std=gnu11 -ffunction-sections -fdata-sections -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/wiring_digital.c" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring_digital.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-gcc" -c -g -Os -w -std=gnu11 -ffunction-sections -fdata-sections -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/wiring_pulse.c" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring_pulse.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-gcc" -c -g -Os -w -std=gnu11 -ffunction-sections -fdata-sections -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/wiring_shift.c" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring_shift.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/CDC.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/CDC.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/HardwareSerial.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/HardwareSerial.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/HardwareSerial0.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/HardwareSerial0.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/HardwareSerial1.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/HardwareSerial1.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/HardwareSerial2.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/HardwareSerial2.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/HardwareSerial3.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/HardwareSerial3.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/IPAddress.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/IPAddress.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/PluggableUSB.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/PluggableUSB.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/Print.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/Print.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/Stream.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/Stream.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/Tone.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/Tone.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/USBCore.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/USBCore.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/WMath.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/WMath.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/WString.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/WString.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/abi.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/abi.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/main.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/main.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-g++" -c -g -Os -w -std=gnu++11 -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega16u2 -DF_CPU=16000000L -DARDUINO=10606 -DARDUINO_HOODLOADER2 -DARDUINO_ARCH_AVR  -DUSB_VID=0x2341 -DUSB_PID=0x484C '-DUSB_MANUFACTURER="Nico Hood"' '-DUSB_PRODUCT="HoodLoader2 16u2"' -DMAGIC_KEY_POS=(RAMEND-1) -DUSB_EP_SIZE=16 "-I/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino" "-I/sketchbook/hardware/HoodLoader2/avr/variants/HoodLoader2" "/Arduino/build/linux/work/hardware/arduino/avr/cores/arduino/new.cpp" -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/new.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring_pulse.S.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/WInterrupts.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/hooks.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring_analog.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring_digital.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring_pulse.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/wiring_shift.c.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/CDC.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/HardwareSerial.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/HardwareSerial0.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/HardwareSerial1.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/HardwareSerial2.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/HardwareSerial3.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/IPAddress.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/PluggableUSB.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/Print.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/Stream.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/Tone.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/USBCore.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/WMath.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/WString.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/abi.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/main.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-ar" rcs  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/new.cpp.o"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-gcc" -w -Os -Wl,--gc-sections -mmcu=atmega16u2  -o "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch_sep26a.ino.elf" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch/sketch_sep26a.ino.cpp.o" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/core/core.a" "-L/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp" -lm
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-objcopy" -O ihex -j .eeprom --set-section-flags=.eeprom=alloc,load --no-change-warnings --change-section-lma .eeprom=0  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch_sep26a.ino.elf" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch_sep26a.ino.eep"
"/Arduino/build/linux/work/hardware/tools/avr/bin/avr-objcopy" -O ihex -R .eeprom  "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch_sep26a.ino.elf" "/tmp/buildac6989e7f7f14d9950cca6539075540b.tmp/sketch_sep26a.ino.hex"
Bootloader file specified but missing: /Arduino/build/linux/work/hardware/arduino/avr/bootloaders/HexFiles/HoodLoader2_0_5_Uno_atmega16u2.hex

Sketch uses 3,548 bytes (28%) of program storage space. Maximum is 12,288 bytes.
Global variables use 91 bytes (17%) of dynamic memory, leaving 421 bytes for local variables. Maximum is 512 bytes.

Successful avdude ISP programming:

/Arduino/build/linux/work/hardware/tools/avr/bin/avrdude -C/Arduino/build/linux/work/hardware/tools/avr/etc/avrdude.conf -v -patmega16u2 -carduino -P/dev/ttyACM2 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xFC:m -Uhfuse:w:0xD8:m -Ulfuse:w:0xEF:m 

avrdude: Version 6.0.1, compiled on Apr 14 2015 at 19:04:16
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "/Arduino/build/linux/work/hardware/tools/avr/etc/avrdude.conf"
         User configuration file is "/home/linuxuser/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : /dev/ttyACM2
         Using Programmer              : arduino
         Overriding Baud Rate          : 19200
         AVR Part                      : ATmega16U2
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PC6
         RESET disposition             : possible i/o
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    20     4    0 no        512    4    128  9000  9000 0x00 0x00
           flash         65     6   128    0 yes     16384  128    128  4500  4500 0x00 0x00
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : Arduino
         Description     : Arduino
         Hardware Version: 2
         Firmware Version: 1.18
         Topcard         : Unknown
         Vtarget         : 0.0 V
         Varef           : 0.0 V
         Oscillator      : Off
         SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

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

avrdude: Device signature = 0x1e9489
avrdude: erasing chip
avrdude: reading input file "0x3F"
avrdude: writing lock (1 bytes):

Writing | ################################################## | 100% 0.02s

avrdude: 1 bytes of lock written
avrdude: verifying lock memory against 0x3F:
avrdude: load data lock data from input file 0x3F:
avrdude: input file 0x3F contains 1 bytes
avrdude: reading on-chip lock data:

Reading | ################################################## | 100% 0.02s

avrdude: verifying ...
avrdude: 1 bytes of lock verified
avrdude: reading input file "0xFC"
avrdude: writing efuse (1 bytes):

Writing | ################################################## | 100% 0.02s

avrdude: 1 bytes of efuse written
avrdude: verifying efuse memory against 0xFC:
avrdude: load data efuse data from input file 0xFC:
avrdude: input file 0xFC contains 1 bytes
avrdude: reading on-chip efuse data:

Reading | ################################################## | 100% 0.02s

avrdude: verifying ...
avrdude: 1 bytes of efuse verified
avrdude: reading input file "0xD8"
avrdude: writing hfuse (1 bytes):

Writing | ################################################## | 100% 0.02s

avrdude: 1 bytes of hfuse written
avrdude: verifying hfuse memory against 0xD8:
avrdude: load data hfuse data from input file 0xD8:
avrdude: input file 0xD8 contains 1 bytes
avrdude: reading on-chip hfuse data:

Reading | ################################################## | 100% 0.02s

avrdude: verifying ...
avrdude: 1 bytes of hfuse verified
avrdude: reading input file "0xEF"
avrdude: writing lfuse (1 bytes):

Writing | ################################################## | 100% 0.02s

avrdude: 1 bytes of lfuse written
avrdude: verifying lfuse memory against 0xEF:
avrdude: load data lfuse data from input file 0xEF:
avrdude: input file 0xEF contains 1 bytes
avrdude: reading on-chip lfuse data:

Reading | ################################################## | 100% 0.02s

avrdude: verifying ...
avrdude: 1 bytes of lfuse verified

avrdude done.  Thank you.

/Arduino/build/linux/work/hardware/tools/avr/bin/avrdude -C/Arduino/build/linux/work/hardware/tools/avr/etc/avrdude.conf -v -patmega16u2 -carduino -P/dev/ttyACM2 -b19200 -Uflash:w:/sketchbook/hardware/HoodLoader2/avr/bootloaders/HexFiles/HoodLoader2_0_5_Uno_atmega16u2.hex:i -Ulock:w:0x0F:m 

avrdude: Version 6.0.1, compiled on Apr 14 2015 at 19:04:16
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "/Arduino/build/linux/work/hardware/tools/avr/etc/avrdude.conf"
         User configuration file is "/home/linuxuser/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : /dev/ttyACM2
         Using Programmer              : arduino
         Overriding Baud Rate          : 19200
         AVR Part                      : ATmega16U2
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PC6
         RESET disposition             : possible i/o
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    20     4    0 no        512    4    128  9000  9000 0x00 0x00
           flash         65     6   128    0 yes     16384  128    128  4500  4500 0x00 0x00
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : Arduino
         Description     : Arduino
         Hardware Version: 2
         Firmware Version: 1.18
         Topcard         : Unknown
         Vtarget         : 0.0 V
         Varef           : 0.0 V
         Oscillator      : Off
         SCK period      : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

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

avrdude: Device signature = 0x1e9489
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 "/sketchbook/hardware/HoodLoader2/avr/bootloaders/HexFiles/HoodLoader2_0_5_Uno_atmega16u2.hex"
avrdude: writing flash (16384 bytes):

Writing | ################################################## | 100% 0.00s

avrdude: 16384 bytes of flash written
avrdude: verifying flash memory against /sketchbook/hardware/HoodLoader2/avr/bootloaders/HexFiles/HoodLoader2_0_5_Uno_atmega16u2.hex:
avrdude: load data flash data from input file /sketchbook/hardware/HoodLoader2/avr/bootloaders/HexFiles/HoodLoader2_0_5_Uno_atmega16u2.hex:
avrdude: input file /sketchbook/hardware/HoodLoader2/avr/bootloaders/HexFiles/HoodLoader2_0_5_Uno_atmega16u2.hex contains 16384 bytes
avrdude: reading on-chip flash data:

Reading | ################################################## | 100% 0.00s

avrdude: verifying ...
avrdude: 16384 bytes of flash verified
avrdude: reading input file "0x0F"
avrdude: writing lock (1 bytes):

Writing | ################################################## | 100% 0.06s

avrdude: 1 bytes of lock written
avrdude: verifying lock memory against 0x0F:
avrdude: load data lock data from input file 0x0F:
avrdude: input file 0x0F contains 1 bytes
avrdude: reading on-chip lock data:

Reading | ################################################## | 100% 0.02s

avrdude: verifying ...
avrdude: 1 bytes of lock verified

avrdude done.  Thank you.

[per1234]

I now get a warning that the .hex file is missing.

See #3831

I suggest to somehow access the default bootloaders.

#2656 (and I agree, this is a very necessary feature)

[ffissore]

This issue was moved to arduino/arduino-builder#20

[NicoHood]

I'd like to reopen this in a similar context.
I think the check should look if a bootloader file is present. However if you use an ISP it tries to upload everything and in the finial hex file reading it fails if the bootloader doesnt exist. The program should catch this before starting avrdude.

Used this build:
#3896 (comment)

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.05s

avrdude: Device signature = 0x1e9587
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 "/home/linuxuser/Documents/Arduino/sketchbook/hardware/pololu/avr/bootloaders/caterina/Leonardo-prod-firmware-2012-12-10"
avrdude: can't open input file /home/linuxuser/Documents/Arduino/sketchbook/hardware/pololu/avr/bootloaders/caterina/Leonardo-prod-firmware-2012-12-10: No such file or directory
avrdude: read from file '/home/linuxuser/Documents/Arduino/sketchbook/hardware/pololu/avr/bootloaders/caterina/Leonardo-prod-firmware-2012-12-10' failed

avrdude done.  Thank you.

Error while burning bootloader.