AVR Freaks

Thanks for all the replies.  I was able to use mfile to generate a template and go from there, single file worked just fine.  My ultimate goal is to use the RPI, but I wanted to do it form windows first because I can remember doing that in the past.  Now I just need to expand upon that base to handle multiple files.  A little more reading and experimenting and I'll get there.

I spent about 10 hours reading the GNU Make manual, Atmel's AVR Libc Reference Manual, Toolchain settings in AS7, and dissecting the mfile template.  My goal was to strip out a lot of things from the mfile template, because I either want to do them with another file (AVRDUDE programming), am only using C source, and I admittedly don't understand all of the manipulation that is going on with lists in the mfile template.  

I did scrap the windows compilation piece because AS7 is awesome and compiling simple AVR blink.c was super easy from the Linux command line.  Here is what I have for a reduced makefile so far (just a note I am adding the printf libraries because most of my projects use it, clearly a blinking LED will not):

#----------------------------------------------------------------------------
# AVR make file
#based on the mfile template
#just trying to learn makefile syntax
#----------------------------------------------------------------------------

# MCU name
MCU = atmega1284p

# Processor Frequency
F_CPU = 16000000

# Output format. (can be srec, ihex, binary)
FORMAT = ihex

# C Source files
SRC = blinker.c

# Target file name (without extension).
TARGET = YourCompiledThing

# Object files directory
#     To put object files in current directory, use a dot (.), do NOT make
#     this an empty or blank macro!
OBJDIR = .

# Optimization level, can be [0, 1, 2, 3, s, g].
#     0 = turn off optimization. s = optimize for size.
OPT = 1

# Debugging level, can be [0, 1, 2, 3]
DEBUG = 1

# Compiler flag to set the C Standard level.
#     gnu99 = c99 plus GCC extensions
CSTANDARD = -std=gnu99

# Place -D or -U options here for C sources
CDEFS = -DF_CPU=$(F_CPU)UL

#---------------- Compiler Options C ----------------
CFLAGS = -g$(DEBUG) 
CFLAGS += $(CDEFS)
CFLAGS += -O$(OPT)
CFLAGS += -funsigned-char
CFLAGS += -funsigned-bitfields
CFLAGS += -fpack-struct
CFLAGS += -fshort-enums
CFLAGS += -Wall
CFLAGS += -Wstrict-prototypes
CFLAGS += -Wa,-adhlns=$(<:%.c=$(OBJDIR)/%.lst)
CFLAGS += $(CSTANDARD)

ALL_CFLAGS = -mmcu=$(MCU) $(CFLAGS)
#---------------- Library Options ----------------
# Minimalistic printf version
PRINTF_LIB_MIN = -Wl,-u,vfprintf -lprintf_min

# Floating point printf version (requires MATH_LIB = -lm below)
PRINTF_LIB_FLOAT = -Wl,-u,vfprintf -lprintf_flt

# If this is left blank, then it will use the Standard printf version.
PRINTF_LIB = $(PRINTF_LIB_FLOAT)
#PRINTF_LIB = $(PRINTF_LIB_MIN)
#PRINTF_LIB = $(PRINTF_LIB_FLOAT)

MATH_LIB = -lm

#---------------- Linker Options ----------------
#  -Wl,...:     tell GCC to pass this to linker.
#    -Map:      create map file
#    --cref:    add cross reference to  map file
LDFLAGS = -Wl,-Map=$(TARGET).map,--cref
LDFLAGS += $(PRINTF_LIB) $(MATH_LIB)

#============================================================================
# Define programs
SHELL = sh
CC = avr-gcc
OBJCOPY = avr-objcopy
OBJDUMP = avr-objdump
SIZE = avr-size
AR = avr-ar rcs
NM = avr-nm
AVRDUDE = avrdude
REMOVE = rm -f
REMOVEDIR = rm -rf
COPY = cp
WINSHELL = cmd

# Compiler flags to generate dependency files.
GENDEPFLAGS = -MMD -MP -MF .dep/$(@F).d


# Combine all necessary flags and optional flags.
# Add target processor to flags.
ALL_CFLAGS = -mmcu=$(MCU) -I. $(CFLAGS) $(GENDEPFLAGS)

# Define all object files.
OBJ = $(SRC:%.c=$(OBJDIR)/%.o)

# Define all listing files.
LST = $(SRC:%.c=$(OBJDIR)/%.lst)

# Compile: create object files from C source files.
%.o : %.c
	@echo
	@echo $(MSG_COMPILING) $<
	$(CC) -c $(ALL_CFLAGS) $< -o $@ 
	
# Link: create ELF output file from object files.
.SECONDARY : $(TARGET).elf
.PRECIOUS : $(OBJ)
%.elf: $(OBJ)
	@echo
	@echo $(MSG_LINKING) $@
	$(CC) $(ALL_CFLAGS) $^ --output $@ $(LDFLAGS)
	
	# Create final output files (.hex, .eep) from ELF output file.
%.hex: %.elf
	@echo
	@echo $(MSG_FLASH) $@
	$(OBJCOPY) -O $(FORMAT) -R .eeprom -R .fuse -R .lock $< $@

# Target: clean project.
clean: begin clean_list end

clean_list :
	@echo
	@echo $(MSG_CLEANING)
	$(REMOVE) $(TARGET).hex
	$(REMOVE) $(TARGET).elf
	$(REMOVE) $(SRC:%.c=$(OBJDIR)/%.o)
	$(REMOVE) $(SRC:%.c=$(OBJDIR)/%.lst)
	$(REMOVEDIR) .dep

I have a couple of questions:

1.) CFLAGS += -Wa,-adhlns=$(<:%.c=$(OBJDIR)/%.lst)

I don't understand this rule text -adhlns, it looks like it is going to create .lst file in the object directory for ever .c file.  And I must not be getting this, because the following statement would be redundant if my understanding was correct:

# Define all listing files.
LST = $(SRC:%.c=$(OBJDIR)/%.lst)

When I do command line compilation, there are no .lst files.  What are these and why do I need them?

2.) Is there any disadvantage to only generating .hex?  This is all I have done in the past even in AS7, just because that is what I learned, but I have no idea why.

3.) When creating the .hex file, the line below will create the .hex without overwritting the eeprom, fuse, and lock bits in the AVR correct?

$(OBJCOPY) -O $(FORMAT) -R .eeprom -R .fuse -R .lock $< $@

Well I got home and tried that makefile on my Raspberry Pi and no luck.  It's missing some important things that I didn't see due to the text highlighting on my editor.  I did a little more digging and merged the old mfile template with a new/revised template that I found on GitHub.  I simplified it such that it only allows for C source files and will only generate a .hex output file.  I found this version of the makefile much easier to read and have tested it working on my distribution of Raspberian, the contents are below if anyone is curious.

Reading the documentation certainly cleared a lot of things up, thanks to everyone who helped out.  I really stoked to be able to use the PI as my sole AVR developing and programming station.  

# Hey Emacs, this is a -*- makefile -*-
#----------------------------------------------------------------------------
# AVR-GCC Makefile template, derived from the WinAVR template (public domain)
#
# ---------------------------------------------------------------------------
# On command line:
#
# make all = Make .hex.
#
# make clean = Clean out built project files.
#
# To rebuild project do "make clean" then "make all".
# ---------------------------------------------------------------------------


# MCU name
MCU = atmega1284p

# CPU speed
F_CPU = 16000000

# Output format. (can be srec, ihex, binary)
FORMAT = ihex

# Target file name (without extension).
TARGET = YourCompiledThing

SRC = blinker.c

# Optimization level, can be [0, 1, 2, 3, s, g].
#     0 = turn off optimization. s = optimize for size.
OPT = 1

# Name of this Makefile (used for "make depend").
MAKEFILE = Makefile

# Debugging format.
# Native formats for AVR-GCC's -g are stabs [default], or dwarf-2.
# AVR (extended) COFF requires stabs, plus an avr-objcopy run.
DEBUG = stabs

# Compiler flag to set the C Standard level.
# c89   - "ANSI" C
# gnu89 - c89 plus GCC extensions
# c99   - ISO C99 standard (not yet fully implemented)
# gnu99 - c99 plus GCC extensions
CSTANDARD = -std=gnu99

# Place -D or -U options here for C sources
CDEFS = -DF_CPU=$(F_CPU)UL

# Place -I options here
CINCS =


CDEBUG = -g$(DEBUG)
CWARN = -Wall -Wstrict-prototypes
CTUNING = -funsigned-char -funsigned-bitfields -fpack-struct -fshort-enums
#CEXTRA = -Wa,-adhlns=$(<:.c=.lst)
CFLAGS = $(CDEBUG) $(CDEFS) $(CINCS) -O$(OPT) $(CWARN) $(CSTANDARD) $(CEXTRA)

#Additional libraries.

# Minimalistic printf version
PRINTF_LIB_MIN = -Wl,-u,vfprintf -lprintf_min

# Floating point printf version (requires MATH_LIB = -lm below)
PRINTF_LIB_FLOAT = -Wl,-u,vfprintf -lprintf_flt

PRINTF_LIB = $(PRINTF_LIB_FLOAT)

# Minimalistic scanf version
SCANF_LIB_MIN = -Wl,-u,vfscanf -lscanf_min

# Floating point + %[ scanf version (requires MATH_LIB = -lm below)
SCANF_LIB_FLOAT = -Wl,-u,vfscanf -lscanf_flt

SCANF_LIB =

MATH_LIB = -lm


#LDMAP = $(LDFLAGS) -Wl,-Map=$(TARGET).map,--cref
LDFLAGS = $(LDMAP) $(PRINTF_LIB) $(SCANF_LIB) $(MATH_LIB)

#============================================================================
# Define programs
CC = avr-gcc
OBJCOPY = avr-objcopy
OBJDUMP = avr-objdump
SIZE = avr-size
NM = avr-nm
AVRDUDE = avrdude
REMOVE = rm -f
MV = mv -f

# Define all object files.
OBJ = $(SRC:.c=.o) $(ASRC:.S=.o)

# Define all listing files.
LST = $(ASRC:.S=.lst) $(SRC:.c=.lst)

# Combine all necessary flags and optional flags.
# Add target processor to flags.
ALL_CFLAGS = -mmcu=$(MCU) -I. $(CFLAGS)

# Default target.
all: build

build: elf hex 

elf: $(TARGET).elf
hex: $(TARGET).hex


.SUFFIXES: .elf .hex .eep .lss .sym

.elf.hex:
	$(OBJCOPY) -O $(FORMAT) -R .eeprom -R .fuse -R .lock $< $@


# Link: create ELF output file from object files.
$(TARGET).elf: $(OBJ)
	$(CC) $(ALL_CFLAGS) $(OBJ) --output $@ $(LDFLAGS)


# Compile: create object files from C source files.
.c.o:
	$(CC) -c $(ALL_CFLAGS) $< -o $@

# Target: clean project.
clean:
	$(REMOVE) $(TARGET).hex $(TARGET).elf $(TARGET).map $(OBJ) 

depend:
	if grep '^# DO NOT DELETE' $(MAKEFILE) >/dev/null; \
	then \
		sed -e '/^# DO NOT DELETE/,$$d' $(MAKEFILE) > \
			$(MAKEFILE).$$$$ && \
		$(MV) $(MAKEFILE).$$$$ $(MAKEFILE); \
	fi
	echo '# DO NOT DELETE THIS LINE -- make depend depends on it.' \
		>> $(MAKEFILE); \
	$(CC) -M -mmcu=$(MCU) $(CDEFS) $(CINCS) $(SRC) $(ASRC) >> $(MAKEFILE)

.PHONY:	all build elf hex eep lss sym program coff extcoff clean depend

Nothing was wrong with mfile in the first place, although it wouldn't work on Raspberian off the bat.  The modified version of mfile off GitHub required a lot less tweaking to get working on the PI.  I'm just trying to water it down to what I can understand and what I am using in my current AVR projects.  You make a good point about .eep, I just don't frequently use it.  

I teach robotics and do small hobby projects with AVR's, I've never had a reason to specifically examine any of the complied outputs.  Not saying it's invaluable, but I don't have the need or skill set to effectively do so.

I guess my goal was to create a very basic working makefile that I knew would reliably work on the PI and was within the bounds of what I currently understand about makfefiles.  I just started digging into the guts this week, so I still have a lot of learning and appreciate all of the tips that are continuing to come in.

http://www.atmel.com/tools/atmel...

Is what I used to check the version against, which still states 4.9.2

If there is a more up to date location I can try, I could always try and run the compile experiment on the PI 3.  But I wouldn't know where else to look other than Atmel's website.