Problem building v1.96 + filesystem to ESP8266

Okay, so the error here appears to be on the baud rate. Set it 115200 instead of 460800. The espruino IDE can't recognize such a high baud rate, and won't be able to communicate with the board. This is what the command should look like:

python "../esptool/esptool.py" --port COM46 --baud 115200 write_flash --flash_freq 80m --flash_mode qio --flash_size 4MB-c1 0x0000 "boot_v1.6.bin" 0x1000 espruino_esp8266_user1.bin 0x3FC000  esp_init_data_default.bin 0x3FE000 blank.bin

By the way, you can install esptool using the pip manager for python. For me it's just a little bit more convenient.

EDIT: grammar.