I have similar problems with Dev Tool v1.08. I use Makefile.windows. The esptool is in the C:\Espressif\utils directory in reality . If I copy the content of the Espressif\utils directory into the C:\Espressif\xtensa-lx106-elf\bin (as is in the Makefile), the error message is the following:
06:43:31 **** Build of configuration Release for project MQTT_lex3 ****
mingw32-make.exe -f C:/Users/Gyuri/workspace/MQTT_lex3/Makefile.windows all
CC driver/uart.c
CC mqtt/proto.c
CC mqtt/wifi.c
CC mqtt/utils.c
CC mqtt/config.c
CC mqtt/mqtt_msg.c
CC mqtt/queue.c
CC mqtt/ringbuf.c
CC mqtt/mqtt.c
CC user/user_main.c
AR build/app_app.a
LD build/app.out
FW firmware/0x00000.bin
usage: esptool [-h] [--port PORT] [--baud BAUD]
{load_ram,dump_mem,read_mem,write_mem,write_flash,run,image_info,make_image,elf2image,read_mac,flash_id,read_flash,erase_flash}
...
esptool: error: argument operation: invalid choice: 'build/app.out' (choose from 'load_ram', 'dump_mem', 'read_mem', 'write_mem', 'write_flash', 'run', 'image_info', 'make_image', 'elf2image', 'read_mac', 'flash_id', 'read_flash', 'erase_flash')
C:/Users/Gyuri/workspace/MQTT_lex3/Makefile.windows:120: recipe for target 'firmware/0x00000.bin' failed
mingw32-make.exe: *** [firmware/0x00000.bin] Error 2
06:43:35 Build Finished (took 4s.440ms)