I'm helping Hans with shift brite based project for a musician. He gave me a ring of Shift Brite LEDs with an arduino attached. Normally I prefer to work in vim and using makefiles instead of using an IDE. The Arduino software 0017 shipped with a makefile that gives instructions about how to modify it to work for your project but that still doesn't work.
After a little hunting around and some work I got a working, though not ideal makefile. It currently doesn't rebuild your project after you've saved a new source file if you just do : make upload You have to type make and then make upload.. OH WELL!
Below is my Makefile and also the .diff so you can see exactly what changed.
# Arduino 0015 Makefile
# Arduino adaptation by mellis, eighthave, oli.keller, 
# 		alex norman [with help from http://code.google.com/p/arduino/issues/detail?id=65#c5]
#
# This makefile allows you to build sketches from the command line
# without the Arduino environment (or Java).
#
# Detailed instructions for using the makefile:
#
#  1. Copy this file into the folder with your sketch. There should be a
#     file with the same name as the folder and with the extension .pde
#     (e.g. foo.pde in the foo/ folder).
#
#  2. Modify the line containg "INSTALL_DIR" to point to the directory that
#     contains the Arduino installation (for example, under Mac OS X, this
#     might be /Applications/arduino-0012).
#
#  3. Modify the line containing "PORT" to refer to the filename
#     representing the USB or serial connection to your Arduino board
#     (e.g. PORT = /dev/tty.USB0).  If the exact name of this file
#     changes, you can use * as a wildcard (e.g. PORT = /dev/tty.usb*).
#
#  4. Set the line containing "MCU" to match your board's processor. 
#     Older one's are atmega8 based, newer ones like Arduino Mini, Bluetooth
#     or Diecimila have the atmega168.  If you're using a LilyPad Arduino,
#     change F_CPU to 8000000.
#
#  5. At the command line, change to the directory containing your
#     program's file and the makefile.
#
#  6. Type "make" and press enter to compile/verify your program.
#
#  7. Type "make upload", reset your Arduino board, and press enter to
#     upload your program to the Arduino board.
#
# $Id$
TARGET = $(notdir $(CURDIR))
INSTALL_DIR = /usr/local/src/arduino-0017/
PORT = /dev/ttyUSB*
UPLOAD_RATE = 19200
AVRDUDE_PROGRAMMER = stk500v1
MCU = atmega168
F_CPU = 16000000
############################################################################
# Below here nothing should be changed...
ARDUINO = $(INSTALL_DIR)/hardware/cores/arduino
#AVR_TOOLS_PATH = $(INSTALL_DIR)/hardware/tools/avr/bin
AVR_TOOLS_PATH = /usr/bin/
SRC =  $(ARDUINO)/pins_arduino.c $(ARDUINO)/wiring.c \
$(ARDUINO)/wiring_analog.c $(ARDUINO)/wiring_digital.c \
$(ARDUINO)/wiring_pulse.c \
$(ARDUINO)/wiring_shift.c $(ARDUINO)/WInterrupts.c
CXXSRC = $(ARDUINO)/HardwareSerial.cpp $(ARDUINO)/WMath.cpp \
$(ARDUINO)/Print.cpp
FORMAT = ihex
# Name of this Makefile (used for "make depend").
MAKEFILE = Makefile
# Debugging format.
# Native formats for AVR-GCC's -g are stabs [default], or dwarf-2.
# AVR (extended) COFF requires stabs, plus an avr-objcopy run.
DEBUG = stabs
OPT = s
# Place -D or -U options here
CDEFS = -DF_CPU=$(F_CPU)
CXXDEFS = -DF_CPU=$(F_CPU)
# Place -I options here
CINCS = -I$(ARDUINO)
CXXINCS = -I$(ARDUINO)
# Compiler flag to set the C Standard level.
# c89   - "ANSI" C
# gnu89 - c89 plus GCC extensions
# c99   - ISO C99 standard (not yet fully implemented)
# gnu99 - c99 plus GCC extensions
CSTANDARD = -std=gnu99
CDEBUG = -g$(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)
CXXFLAGS = $(CDEFS) $(CINCS) -O$(OPT)
#ASFLAGS = -Wa,-adhlns=$(<:.S=.lst),-gstabs 
LDFLAGS = -lm
# Programming support using avrdude. Settings and variables.
AVRDUDE_PORT = $(PORT)
AVRDUDE_WRITE_FLASH = -U flash:w:applet/$(TARGET).hex
AVRDUDE_FLAGS = -V -F \
-p $(MCU) -P $(AVRDUDE_PORT) -c $(AVRDUDE_PROGRAMMER) \
-b $(UPLOAD_RATE)
# Program settings
CC = $(AVR_TOOLS_PATH)/avr-gcc
CXX = $(AVR_TOOLS_PATH)/avr-g++
OBJCOPY = $(AVR_TOOLS_PATH)/avr-objcopy
OBJDUMP = $(AVR_TOOLS_PATH)/avr-objdump
AR  = $(AVR_TOOLS_PATH)/avr-ar
SIZE = $(AVR_TOOLS_PATH)/avr-size
NM = $(AVR_TOOLS_PATH)/avr-nm
AVRDUDE = $(AVR_TOOLS_PATH)/avrdude
REMOVE = rm -f
MV = mv -f
# Define all object files.
OBJ = $(SRC:.c=.o) $(CXXSRC:.cpp=.o) $(ASRC:.S=.o) 
# Define all listing files.
LST = $(ASRC:.S=.lst) $(CXXSRC:.cpp=.lst) $(SRC:.c=.lst)
# Combine all necessary flags and optional flags.
# Add target processor to flags.
ALL_CFLAGS = -mmcu=$(MCU) -I. $(CFLAGS)
ALL_CXXFLAGS = -mmcu=$(MCU) -I. $(CXXFLAGS)
ALL_ASFLAGS = -mmcu=$(MCU) -I. -x assembler-with-cpp $(ASFLAGS)
# Default target.
all: applet_files build sizeafter
build: elf hex 
applet_files: $(TARGET).pde
	# Here is the "preprocessing".
	# It creates a .cpp file based with the same name as the .pde file.
	# On top of the new .cpp file comes the WProgram.h header.
	# At the end there is a generic main() function attached.
	# Then the .cpp file will be compiled. Errors during compile will
	# refer to this new, automatically generated, file. 
	# Not the original .pde file you actually edit...
	test -d applet || mkdir applet
	echo '#include "WProgram.h"' > applet/$(TARGET).cpp
	cat $(TARGET).pde >> applet/$(TARGET).cpp
	cat $(ARDUINO)/main.cxx >> applet/$(TARGET).cpp
elf: applet/$(TARGET).elf
hex: applet/$(TARGET).hex
eep: applet/$(TARGET).eep
lss: applet/$(TARGET).lss 
sym: applet/$(TARGET).sym
# Program the device.  
upload: applet/$(TARGET).hex
	$(AVRDUDE) $(AVRDUDE_FLAGS) $(AVRDUDE_WRITE_FLASH)
	# Display size of file.
HEXSIZE = $(SIZE) --target=$(FORMAT) applet/$(TARGET).hex
ELFSIZE = $(SIZE)  applet/$(TARGET).elf
sizebefore:
	@if [ -f applet/$(TARGET).elf ]; then echo; echo $(MSG_SIZE_BEFORE); $(HEXSIZE); echo; fi
sizeafter:
	@if [ -f applet/$(TARGET).elf ]; then echo; echo $(MSG_SIZE_AFTER); $(HEXSIZE); echo; fi
# Convert ELF to COFF for use in debugging / simulating in AVR Studio or VMLAB.
COFFCONVERT=$(OBJCOPY) --debugging \
--change-section-address .data-0x800000 \
--change-section-address .bss-0x800000 \
--change-section-address .noinit-0x800000 \
--change-section-address .eeprom-0x810000 
coff: applet/$(TARGET).elf
	$(COFFCONVERT) -O coff-avr applet/$(TARGET).elf $(TARGET).cof
extcoff: $(TARGET).elf
	$(COFFCONVERT) -O coff-ext-avr applet/$(TARGET).elf $(TARGET).cof
.SUFFIXES: .elf .hex .eep .lss .sym
.elf.hex:
	$(OBJCOPY) -O $(FORMAT) -R .eeprom $< $@
.elf.eep:
	-$(OBJCOPY) -j .eeprom --set-section-flags=.eeprom="alloc,load" \
	--change-section-lma .eeprom=0 -O $(FORMAT) $< $@
# Create extended listing file from ELF output file.
.elf.lss:
	$(OBJDUMP) -h -S $< > $@
# Create a symbol table from ELF output file.
.elf.sym:
	$(NM) -n $< > $@
	# Link: create ELF output file from library.
applet/$(TARGET).elf: $(TARGET).pde applet/core.a 
	$(CC) $(ALL_CFLAGS) -o $@ applet/$(TARGET).cpp -L. applet/core.a $(LDFLAGS)
applet/core.a: $(OBJ)
	@for i in $(OBJ); do echo $(AR) rcs applet/core.a $$i; $(AR) rcs applet/core.a $$i; done
# Compile: create object files from C++ source files.
.cpp.o:
	$(CXX) -c $(ALL_CXXFLAGS) $< -o $@ 
# Compile: create object files from C source files.
.c.o:
	$(CC) -c $(ALL_CFLAGS) $< -o $@ 
# Compile: create assembler files from C source files.
.c.s:
	$(CC) -S $(ALL_CFLAGS) $< -o $@
# Assemble: create object files from assembler source files.
.S.o:
	$(CC) -c $(ALL_ASFLAGS) $< -o $@
# Automatic dependencies
%.d: %.c
	$(CC) -M $(ALL_CFLAGS) $< | sed "s;$(notdir $*).o:;$*.o $*.d:;" > $@
%.d: %.cpp
	$(CXX) -M $(ALL_CXXFLAGS) $< | sed "s;$(notdir $*).o:;$*.o $*.d:;" > $@
# Target: clean project.
clean:
	$(REMOVE) applet/$(TARGET).hex applet/$(TARGET).eep applet/$(TARGET).cof applet/$(TARGET).elf \
	applet/$(TARGET).map applet/$(TARGET).sym applet/$(TARGET).lss applet/core.a \
	$(OBJ) $(LST) $(SRC:.c=.s) $(SRC:.c=.d) $(CXXSRC:.cpp=.s) $(CXXSRC:.cpp=.d)
.PHONY:	all build elf hex eep lss sym program coff extcoff clean applet_files sizebefore sizeafter
------------------------------------------------------------ Makefile.diff
--- Makefile-original	2009-10-14 16:21:02.000000000 -0700
+++ Makefile	2009-10-14 16:57:30.000000000 -0700
@@ -1,5 +1,6 @@
 # Arduino 0015 Makefile
-# Arduino adaptation by mellis, eighthave, oli.keller
+# Arduino adaptation by mellis, eighthave, oli.keller, 
+# 		alex norman [with help from http://code.google.com/p/arduino/issues/detail?id=65#c5]
 #
 # This makefile allows you to build sketches from the command line
 # without the Arduino environment (or Java).
@@ -35,8 +36,8 @@
 # $Id$
 
 TARGET = $(notdir $(CURDIR))
-INSTALL_DIR = ../../..
-PORT = /dev/tty.usb*
+INSTALL_DIR = /usr/local/src/arduino-0017/
+PORT = /dev/ttyUSB*
 UPLOAD_RATE = 19200
 AVRDUDE_PROGRAMMER = stk500v1
 MCU = atmega168
@@ -46,10 +47,11 @@
 # Below here nothing should be changed...
 
 ARDUINO = $(INSTALL_DIR)/hardware/cores/arduino
-AVR_TOOLS_PATH = $(INSTALL_DIR)/hardware/tools/avr/bin
+#AVR_TOOLS_PATH = $(INSTALL_DIR)/hardware/tools/avr/bin
+AVR_TOOLS_PATH = /usr/bin/
 SRC =  $(ARDUINO)/pins_arduino.c $(ARDUINO)/wiring.c \
 $(ARDUINO)/wiring_analog.c $(ARDUINO)/wiring_digital.c \
-$(ARDUINO)/wiring_pulse.c $(ARDUINO)/wiring_serial.c \
+$(ARDUINO)/wiring_pulse.c \
 $(ARDUINO)/wiring_shift.c $(ARDUINO)/WInterrupts.c
 CXXSRC = $(ARDUINO)/HardwareSerial.cpp $(ARDUINO)/WMath.cpp \
 $(ARDUINO)/Print.cpp
@@ -94,7 +96,7 @@
 # Programming support using avrdude. Settings and variables.
 AVRDUDE_PORT = $(PORT)
 AVRDUDE_WRITE_FLASH = -U flash:w:applet/$(TARGET).hex
-AVRDUDE_FLAGS = -V -F -C $(INSTALL_DIR)/hardware/tools/avr/etc/avrdude.conf \
+AVRDUDE_FLAGS = -V -F \
 -p $(MCU) -P $(AVRDUDE_PORT) -c $(AVRDUDE_PROGRAMMER) \
 -b $(UPLOAD_RATE)
 
@@ -239,5 +241,3 @@
 
 .PHONY:	all build elf hex eep lss sym program coff extcoff clean applet_files sizebefore sizeafter
 
-include $(SRC:.c=.d)
-include $(CXXSRC:.cpp=.d)