I am having the exact same problem with my extruder motor, BMG clone, and EZBoard. https://pastebin.com/Wczg8EAi
I compiled the bin file, moved it to my SD card and cleared the EEPROM right after bootup. Sent a command from both the LCD and Octoprint to extrude 100mm and both were reversed and instead retracted the filament. I did the same thing as WilliamLalum and reversed the E motor in the config.h file. I also deleted the firmware.bin from the build folder before compilation. After bootup and EEPROM clearing, the extruder still retracted when I sent a command to extrude 100mm.
It's pretty late where I am and got work in the morning so I can't do more tests until tomorrow but I'm pretty bummed out. I was so excited to get something printing overnight tonight ☹️
EDIT: This was on an Ender 3 not a CR-10s if that helps.
EDIT2: Okay, if I leave
#define TITAN_EXTRUDER commented out then I get the correct motor direction. I didn't have to reverse anything. I only used that because I saw that it would work for my BMG extruder so not sure what's going on.