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I was using Arduino-Makefile to upload code to a Leonardo via its standard make upload. However, it became "stuck" and unresponsive, as Leonardo's sometimes do. I tried power cycling it, and unplugging the USB cable, but nothing worked. So I tried re-burning the bootloader via an AVRISP MkII programmer and the Arduino 1.8.2 IDE, but that only made things worse.

It somehow uploaded a simple "blink" program, but now the it's completely unable to be programmed via USB. When I run make upload, or use the Arduino IDE's "upload" button, the Leonoardo's status LED begins blinking rapidly and its /dev/ttyACM0 device disappears permanently. I have to power-cycle it to make the device reappear, but the upload still fails, with the error:

/usr/share/arduino/bin/ard-reset-arduino --caterina /dev/ttyACM0
make[1]: Leaving directory '/usr/local/myproject/main'
make do_upload
make[1]: Entering directory '/usr/local/myproject/main'
/usr/share/arduino/hardware/tools/avr/bin/avrdude -v -p atmega32u4 -C /usr/share/arduino/hardware/tools/avr/etc/avrdude.conf -D -c avr109 -b 57600 -P /dev/ttyACM0 \
 -U flash:w:build-leonardo/main.hex:i
avrdude: Version 6.3, compiled on Jan 17 2017 at 11:00:16
 Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
 Copyright (c) 2007-2014 Joerg Wunsch
 System wide configuration file is "/usr/share/arduino/hardware/tools/avr/etc/avrdude.conf"
 User configuration file is "/home/chris/.avrduderc"
 User configuration file does not exist or is not a regular file, skipping
 Using Port : /dev/ttyACM0
 Using Programmer : avr109
 Overriding Baud Rate : 57600
 AVR Part : ATmega32U4
 Chip Erase delay : 9000 us
 PAGEL : PD7
 BS2 : PA0
 RESET disposition : dedicated
 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 1024 4 0 9000 9000 0x00 0x00
 flash 65 6 128 0 yes 32768 128 256 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 : butterfly
 Description : Atmel AppNote AVR109 Boot Loader
Connecting to programmer: .avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
Found programmer: Id = ""; type = 
 Software Version = .; Hardware Version = �.
avrdude: butterfly_recv(): programmer is not responding
avrdude: butterfly_recv(): programmer is not responding
avrdude: error: buffered memory access not supported. Maybe it isn't
a butterfly/AVR109 but a AVR910 device?
avrdude: initialization failed, rc=-1
 Double check connections and try again, or use -F to override
 this check.
avrdude: butterfly_recv(): programmer is not responding
avrdude: error: programmer did not respond to command: leave prog mode
avrdude: butterfly_recv(): programmer is not responding
avrdude: error: programmer did not respond to command: exit bootloader

I can program it still using the AVRISP MkII programmer...but obviously that's a huge inconvenience since it takes about 5 minutes just to upload the sample blink sketch, and even then it requires that I first power off the Leonardo, disconnect the programmer, and then power on. For development, where I might need to make dozens of revisions, this turnout is far too slow.

Why am I unable to program the Leonardo via avrdude and USB?