Hello,
this issue seems to be back again or isn't solved. I'm using the Arduino web editor, Arduino DUE (Programming port) and already the basic blink example sketch fails to upload. I also tried Firefox and Chrome, including reinstall of the plugin, still no success:
...
/home/builder/.arduino15/packages/arduino/tools/arm-none-eabi-gcc/4.8.3-2014q1/bin/arm-none-eabi-ar rcs /tmp/508095940/build/core/core.a /tmp/508095940/build/core/wiring_digital.c.o
/home/builder/.arduino15/packages/arduino/tools/arm-none-eabi-gcc/4.8.3-2014q1/bin/arm-none-eabi-ar rcs /tmp/508095940/build/core/core.a /tmp/508095940/build/core/wiring_pulse.cpp.o
/home/builder/.arduino15/packages/arduino/tools/arm-none-eabi-gcc/4.8.3-2014q1/bin/arm-none-eabi-ar rcs /tmp/508095940/build/core/core.a /tmp/508095940/build/core/wiring_pulse_asm.S.o
/home/builder/.arduino15/packages/arduino/tools/arm-none-eabi-gcc/4.8.3-2014q1/bin/arm-none-eabi-ar rcs /tmp/508095940/build/core/core.a /tmp/508095940/build/core/wiring_shift.c.o
Archiving built core (caching) in: /tmp/core/core_arduino_sam_arduino_due_x_dbg_6e18a96b2f6e1a733d0d079e7d8e383a.a
Linking everything together...
/home/builder/.arduino15/packages/arduino/tools/arm-none-eabi-gcc/4.8.3-2014q1/bin/arm-none-eabi-gcc -mcpu=cortex-m3 -mthumb -Os -Wl,--gc-sections -T/home/builder/.arduino15/packages/arduino/hardware/sam/1.6.12/variants/arduino_due_x/linker_scripts/gcc/flash.ld -Wl,-Map,/tmp/508095940/build/Blink.ino.map -o /tmp/508095940/build/Blink.ino.elf -L/tmp/508095940/build -Wl,--cref -Wl,--check-sections -Wl,--gc-sections -Wl,--entry=Reset_Handler -Wl,--unresolved-symbols=report-all -Wl,--warn-common -Wl,--warn-section-align -Wl,--start-group -u _sbrk -u link -u _close -u _fstat -u _isatty -u _lseek -u _read -u _write -u _exit -u kill -u _getpid /tmp/508095940/build/sketch/Blink.ino.cpp.o /tmp/508095940/build/core/variant.cpp.o /home/builder/.arduino15/packages/arduino/hardware/sam/1.6.12/variants/arduino_due_x/libsam_sam3x8e_gcc_rel.a /tmp/508095940/build/core/core.a -Wl,--end-group -lm -lgcc
/home/builder/.arduino15/packages/arduino/tools/arm-none-eabi-gcc/4.8.3-2014q1/bin/arm-none-eabi-objcopy -O binary /tmp/508095940/build/Blink.ino.elf /tmp/508095940/build/Blink.ino.bin
/home/builder/.arduino15/packages/arduino/tools/arm-none-eabi-gcc/4.8.3-2014q1/bin/arm-none-eabi-size -A /tmp/508095940/build/Blink.ino.elf
Sketch uses 10692 bytes (2%) of program storage space. Maximum is 524288 bytes.
Programming with: Serial
Restarting in bootloader mode
Get port list before reset
[COM5]
Touching port COM5 at 1200bps
Set DTR off
Flashing with command:C:/Users/pwilhelm/.arduino-create/arduino/bossac/1.8.0-48-gb176eee/bossac.exe -i -d --port=COM5 -U false -e -w -b C:/Users/pwilhelm/AppData/Local/Temp/arduino-create-agent420942292/Blink.bin -R
bossac: extra arguments found
Try 'bossac -h' or 'bossac --help' for more information