IDE 1.6.12 uploading: "protocol error" reading on-chip flash

Suddenly the host/Arduino link was lost.
Uno R3. Win7 Enterprise, IDE 1.6.12.
Intermittent: sometimes it happens and sometimes it does not. I get upload faults perhaps 15% of the time.
Good hunting.
```
Arduino: 1.6.12 (Windows 7), Board: "Arduino/Genuino Uno"
```
...
```
C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega328p -carduino -PCOM25 -b115200 -D -Uflash:w:C:\Users\gralimj1\AppData\Local\Temp\arduino_build_104657/Checkout_Quick.ino.hex:i

avrdude: Version 6.3, compiled on Sep 12 2016 at 17:24:16
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

System wide configuration file is "C:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf"

Using Port : COM25
Using Programmer : arduino
Overriding Baud Rate : 115200
AVR Part : ATmega328P
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PC2
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 3600 3600 0xff 0xff
flash 65 6 128 0 yes 32768 128 256 4500 4500 0xff 0xff
lfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
efuse 0 0 0 0 no 1 0 0 4500 4500 0x00 0x00
lock 0 0 0 0 no 1 0 0 4500 4500 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: 3
Firmware Version: 4.4
Vtarget : 0.3 V
Varef : 0.3 V
Oscillator : 28.800 kHz
SCK period : 3.3 us

avrdude: AVR device initialized and ready to accept instructions

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

avrdude: Device signature = 0x1e950f (probably m328p)
avrdude: reading input file "C:\Users\gralimj1\AppData\Local\Temp\arduino_build_104657/Checkout_Quick.ino.hex"
avrdude: writing flash (2286 bytes):

Writing | ################################################## | 100% 0.39s

avrdude: 2286 bytes of flash written
avrdude: verifying flash memory against C:\Users\gralimj1\AppData\Local\Temp\arduino_build_104657/Checkout_Quick.ino.hex:
avrdude: load data flash data from input file C:\Users\gralimj1\AppData\Local\Temp\arduino_build_104657/Checkout_Quick.ino.hex:
avrdude: input file C:\Users\gralimj1\AppData\Local\Temp\arduino_build_104657/Checkout_Quick.ino.hex contains 2286 bytes
avrdude: reading on-chip flash data:

Reading | avrdude: stk500_loadaddr(): (a) protocol error, expect=0x14, resp=0x00

avrdude: stk500_paged_load(): (a) protocol error, expect=0x14, resp=0x00
##avrdude: stk500_cmd(): programmer is out of sync
avr_read(): error reading address 0x0000
read operation not supported for memory "flash"
avrdude: failed to read all of flash memory, rc=-2
avrdude: stk500_disable(): protocol error, expect=0x14, resp=0x00

avrdude done. Thank you.

the selected serial port
does not exist or your board is not connected
```
The full output with compilation:
[Processing_log.txt](https://github.com/arduino/Arduino/files/602056/Processing_log.txt)

The sketch:
[program.txt](https://github.com/arduino/Arduino/files/602058/program.txt)

Start with the attached Processing_log.txt and program.txt, then reproduce the Arduino/Genuino Uno upload on Windows 7 with IDE 1.6.12. Focus on the avrdude command and the intermittent failure while reading on-chip flash during verification. Done means the upload and verification no longer produce the reported protocol error.

Written by the indexing model from the issue text.