Thank you for taking a look at this. I'm not familiar enough with Raspian to know if this is incorrect directory or just using the wrong command.
pi@cnc:~/mesaflash/mesaflash $ ls
anyio.c eeprom_remote.c hostmot2.o pci_encoder_read.o
anyio.h eeprom_remote.h lbp16.c serial_boards.c
anyio.o eeprom_remote.o lbp16.h serial_boards.h
bitfile.c encoder_module.c lbp16.o serial_boards.o
bitfile.h encoder_module.h lbp.c spi_boards.c
bitfile.o encoder_module.o lbp.h spi_boards.h
boards.h epp_boards.c lbp.o spi_boards.o
common.c epp_boards.h libanyio.a sserial_module.c
common.h epp_boards.o libpci.dll sserial_module.h
common.o eth_boards.c Makefile sserial_module.o
eeprom.c eth_boards.h mesaflash.c types.h
eeprom.h eth_boards.o mesaflash.o usb_boards.c
eeprom_local.c examples pci_analog_write.o usb_boards.h
eeprom_local.h hostmot2.c pci_boards.c usb_boards.o
eeprom_local.o hostmot2_def.h pci_boards.h WinIo32.dll
eeprom.o hostmot2.h pci_boards.o WinIo32.sys
pi@cnc:~/mesaflash/mesaflash $ sudo ./Makefile
./Makefile: 20: ./Makefile: TARGET: not found
./Makefile: 21: ./Makefile: LIBNAME: not found
./Makefile: 22: ./Makefile: LIBNAME: not found
./Makefile: 22: ./Makefile: LIBANYIO: not found
./Makefile: 24: ./Makefile: CC: not found
./Makefile: 25: ./Makefile: RM: not found
./Makefile: 26: ./Makefile: AR: not found
./Makefile: 27: ./Makefile: RANLIB: not found
./Makefile: 28: ./Makefile: MATHLIB: not found
./Makefile: 29: ./Makefile: OPT: not found
./Makefile: 33: ./Makefile: DEBUG: not found
./Makefile: 35: ./Makefile: Syntax error: word unexpected (expecting ")")
