Since I wasn't able to find a Makefile that successfully
integrates the library sources, I modified the Makefile
found at http://mjo.tc/atelier/2009/02/acli/arduino-mk_0.4.tar.gz

I added the necessary targets to build the object files
from the sources of the requested libraries, so that projects
using those can be build with the package structure supplied
by Debian.

You can retrieve the modified Makefile from github:
https://github.com/wertarbyte/arduino-make

I also attached the modified Arduino.mk.
########################################################################
#
# Arduino command line tools Makefile
# System part (i.e. project independent)
#
# Copyright (C) 2010 Martin Oldfield <m...@mjo.tc>, based on work that is
# Copyright Nicholas Zambetti, David A. Mellis & Hernando Barragan
# 
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation; either version 2.1 of the
# License, or (at your option) any later version.
#
# Adapted from Arduino 0011 Makefile by M J Oldfield
#
# Original Arduino adaptation by mellis, eighthave, oli.keller
#
# Version 0.1  17.ii.2009  M J Oldfield
#
#         0.2  22.ii.2009  M J Oldfield
#                          - fixes so that the Makefile actually works!
#                          - support for uploading via ISP
#                          - orthogonal choices of using the Arduino for
#                            tools, libraries and uploading
#
#         0.3  21.v.2010   M J Oldfield
#                          - added proper license statement
#                          - added code from Philip Hands to reset
#                            Arduino prior to upload
#
#         0.4  25.v.2010   M J Oldfield
#                          - tweaked reset target on Philip Hands' advice
#
#         0.5  23.iii.2011 Stefan Tomanek
#                          - added ad-hoc library building
#
########################################################################
#
# STANDARD ARDUINO WORKFLOW
#
# Given a normal sketch directory, all you need to do is to create
# a small Makefile which defines a few things, and then includes this one.
#
# For example:
#
#       ARDUINO_DIR  = /Applications/arduino-0013
#
#       TARGET       = CLItest
#       ARDUINO_LIBS = LiquidCrystal
#
#       MCU          = atmega168
#       F_CPU        = 16000000
#       ARDUINO_PORT = /dev/cu.usb*
#
#       include /usr/local/share/Arduino.mk
#
# Hopefully these will be self-explanatory but in case they're not:
#
#    ARDUINO_DIR  - Where the Arduino software has been unpacked
#    TARGET       - The basename used for the final files. Canonically
#                   this would match the .pde file, but it's not needed
#                   here: you could always set it to xx if you wanted!
#    ARDUINO_LIBS - A list of any libraries used by the sketch (we assume
#                   these are in $(ARDUINO_DIR)/hardware/libraries
#    MCU,F_CPU    - The target processor description
#    ARDUINO_PORT - The port where the Arduino can be found (only needed
#                   when uploading
#
# Once this file has been created the typical workflow is just
#
#   $ make upload
#
# All of the object files are created in the build-cli subdirectory
# All sources should be in the current directory and can include:
#  - at most one .pde file which will be treated as C++ after the standard
#    Arduino header and footer have been affixed.
#  - any number of .c, .cpp, .s and .h files
#
# Included libraries are built in the build-cli/libs subdirectory.
#
# Besides make upload you can also
#   make            - no upload
#   make clean      - remove all our dependencies
#   make depends    - update dependencies
#   make reset      - reset the Arduino by tickling DTR on the serial port
#   make raw_upload - upload without first resetting
#
########################################################################
#
# ARDUINO WITH OTHER TOOLS
#
# If the tools aren't in the Arduino distribution, then you need to 
# specify their location:
#
#    AVR_TOOLS_PATH = /usr/bin
#    AVRDUDE_CONF   = /etc/avrdude/avrdude.conf
#
########################################################################
#
# ARDUINO WITH ISP
#
# You need to specify some details of your ISP programmer and might
# also need to specify the fuse values:
#
#     ISP_PROG     = -c stk500v2
#     ISP_PORT     = /dev/ttyACM0
#     
#     ISP_LOCK_FUSE_PRE  = 0x3f
#     ISP_LOCK_FUSE_POST = 0xcf
#     ISP_HIGH_FUSE      = 0xdf
#     ISP_LOW_FUSE       = 0xff
#     ISP_EXT_FUSE       = 0x01
#
# I think the fuses here are fine for uploading to the ATmega168
# without bootloader.
# 
# To actually do this upload use the ispload target:
#
#    make ispload
#
#
########################################################################
# Some paths
#

ifneq (ARDUINO_DIR,)

ifndef AVR_TOOLS_PATH
AVR_TOOLS_PATH    = $(ARDUINO_DIR)/hardware/tools/avr/bin
endif

ifndef ARDUINO_ETC_PATH
ARDUINO_ETC_PATH  = $(ARDUINO_DIR)/hardware/tools/avr/etc
endif

ifndef AVRDUDE_CONF
AVRDUDE_CONF     = $(ARDUINO_ETC_PATH)/avrdude.conf
endif

ARDUINO_LIB_PATH  = $(ARDUINO_DIR)/libraries
ARDUINO_CORE_PATH = $(ARDUINO_DIR)/hardware/arduino/cores/arduino

endif

# Everything gets built in here
OBJDIR            = build-cli

########################################################################
# Local sources
#
LOCAL_C_SRCS    = $(wildcard *.c)
LOCAL_CPP_SRCS  = $(wildcard *.cpp)
LOCAL_CC_SRCS   = $(wildcard *.cc)
LOCAL_PDE_SRCS  = $(wildcard *.pde)
LOCAL_AS_SRCS   = $(wildcard *.S)
LOCAL_OBJ_FILES = $(LOCAL_C_SRCS:.c=.o) $(LOCAL_CPP_SRCS:.cpp=.o) \
                $(LOCAL_CC_SRCS:.cc=.o) $(LOCAL_PDE_SRCS:.pde=.o) \
                $(LOCAL_AS_SRCS:.S=.o)
LOCAL_OBJS      = $(patsubst %,$(OBJDIR)/%,$(LOCAL_OBJ_FILES))

# Dependency files
DEPS            = $(LOCAL_OBJS:.o=.d)

# core sources
ifeq ($(strip $(NO_CORE)),)
ifdef ARDUINO_CORE_PATH
CORE_C_SRCS     = $(wildcard $(ARDUINO_CORE_PATH)/*.c)
CORE_CPP_SRCS   = $(wildcard $(ARDUINO_CORE_PATH)/*.cpp)
CORE_OBJ_FILES  = $(CORE_C_SRCS:.c=.o) $(CORE_CPP_SRCS:.cpp=.o)
CORE_OBJS       = $(patsubst $(ARDUINO_CORE_PATH)/%,  \
                        $(OBJDIR)/%,$(CORE_OBJ_FILES))
endif
endif

# all the objects!
OBJS            = $(LOCAL_OBJS) $(CORE_OBJS) $(LIB_OBJS)

########################################################################
# Rules for making stuff
#

# The name of the main targets
TARGET_HEX = $(OBJDIR)/$(TARGET).hex
TARGET_ELF = $(OBJDIR)/$(TARGET).elf
TARGETS    = $(OBJDIR)/$(TARGET).*

# A list of dependencies
DEP_FILE   = $(OBJDIR)/depends.mk

# Names of executables
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
REMOVE  = rm -f
MV      = mv -f
CAT     = cat
ECHO    = echo

# General arguments
SYS_LIBS      = $(patsubst %,$(ARDUINO_LIB_PATH)/%,$(ARDUINO_LIBS))
SYS_INCLUDES  = $(patsubst %,-I%,$(SYS_LIBS))
SYS_OBJS      = $(wildcard $(patsubst %,%/*.o,$(SYS_LIBS)))
LIB_SRC       = $(wildcard $(patsubst %,%/*.cpp,$(SYS_LIBS)))
LIB_OBJS      = $(patsubst 
$(ARDUINO_LIB_PATH)/%.cpp,$(OBJDIR)/libs/%.o,$(LIB_SRC))

CPPFLAGS      = -mmcu=$(MCU) -DF_CPU=$(F_CPU) \
                        -I. -I$(ARDUINO_CORE_PATH) \
                        $(SYS_INCLUDES) -g -Os -w -Wall \
                        -ffunction-sections -fdata-sections
CFLAGS        = -std=gnu99
CXXFLAGS      = -fno-exceptions
ASFLAGS       = -mmcu=$(MCU) -I. -x assembler-with-cpp
LDFLAGS       = -mmcu=$(MCU) -lm -Wl,--gc-sections -Os

# Rules for making a CPP file from the main sketch (.cpe)
PDEHEADER     = \\\#include \"WProgram.h\"

# Expand and pick the first port
ARD_PORT      = $(firstword $(wildcard $(ARDUINO_PORT)))

# Implicit rules for building everything (needed to get everything in
# the right directory)
#
# Rather than mess around with VPATH there are quasi-duplicate rules
# here for building e.g. a system C++ file and a local C++
# file. Besides making things simpler now, this would also make it
# easy to change the build options in future

# library sources
$(OBJDIR)/libs/%.o: $(ARDUINO_LIB_PATH)/%.cpp
        mkdir -p $(dir $@)
        $(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@

# normal local sources
# .o rules are for objects, .d for dependency tracking
# there seems to be an awful lot of duplication here!!!
$(OBJDIR)/%.o: %.c
        $(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@

$(OBJDIR)/%.o: %.cc
        $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@

$(OBJDIR)/%.o: %.cpp
        $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@

$(OBJDIR)/%.o: %.S
        $(CC) -c $(CPPFLAGS) $(ASFLAGS) $< -o $@

$(OBJDIR)/%.o: %.s
        $(CC) -c $(CPPFLAGS) $(ASFLAGS) $< -o $@

$(OBJDIR)/%.d: %.c
        $(CC) -MM $(CPPFLAGS) $(CFLAGS) $< -MF $@ -MT $(@:.d=.o)

$(OBJDIR)/%.d: %.cc
        $(CXX) -MM $(CPPFLAGS) $(CXXFLAGS) $< -MF $@ -MT $(@:.d=.o)

$(OBJDIR)/%.d: %.cpp
        $(CXX) -MM $(CPPFLAGS) $(CXXFLAGS) $< -MF $@ -MT $(@:.d=.o)

$(OBJDIR)/%.d: %.S
        $(CC) -MM $(CPPFLAGS) $(ASFLAGS) $< -MF $@ -MT $(@:.d=.o)

$(OBJDIR)/%.d: %.s
        $(CC) -MM $(CPPFLAGS) $(ASFLAGS) $< -MF $@ -MT $(@:.d=.o)

# the pde -> cpp -> o file
$(OBJDIR)/%.cpp: %.pde
        $(ECHO) $(PDEHEADER) > $@
        $(CAT)  $< >> $@

$(OBJDIR)/%.o: $(OBJDIR)/%.cpp
        $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@

$(OBJDIR)/%.d: $(OBJDIR)/%.cpp
        $(CXX) -MM $(CPPFLAGS) $(CXXFLAGS) $< -MF $@ -MT $(@:.d=.o)

# core files
$(OBJDIR)/%.o: $(ARDUINO_CORE_PATH)/%.c
        $(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@

$(OBJDIR)/%.o: $(ARDUINO_CORE_PATH)/%.cpp
        $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@

# various object conversions
$(OBJDIR)/%.hex: $(OBJDIR)/%.elf
        $(OBJCOPY) -O ihex -R .eeprom $< $@

$(OBJDIR)/%.eep: $(OBJDIR)/%.elf
        -$(OBJCOPY) -j .eeprom --set-section-flags=.eeprom="alloc,load" \
                --change-section-lma .eeprom=0 -O ihex $< $@

$(OBJDIR)/%.lss: $(OBJDIR)/%.elf
        $(OBJDUMP) -h -S $< > $@

$(OBJDIR)/%.sym: $(OBJDIR)/%.elf
        $(NM) -n $< > $@

########################################################################
#
# Avrdude
#
ifndef AVRDUDE
AVRDUDE          = $(AVR_TOOLS_PATH)/avrdude
endif

AVRDUDE_COM_OPTS = -q -V -p $(MCU)
ifdef AVRDUDE_CONF
AVRDUDE_COM_OPTS += -C $(AVRDUDE_CONF)
endif

ifndef AVRDUDE_ARD_PROGRAMMER
AVRDUDE_ARD_PROGRAMMER = stk500v1
endif

ifndef AVRDUDE_ARD_BAUDRATE
AVRDUDE_ARD_BAUDRATE   = 19200
endif

AVRDUDE_ARD_OPTS = -c $(AVRDUDE_ARD_PROGRAMMER) -b $(AVRDUDE_ARD_BAUDRATE) -P 
$(ARD_PORT)

ifndef ISP_LOCK_FUSE_PRE
ISP_LOCK_FUSE_PRE  = 0x3f
endif

ifndef ISP_LOCK_FUSE_POST
ISP_LOCK_FUSE_POST = 0xcf
endif

ifndef ISP_HIGH_FUSE
ISP_HIGH_FUSE      = 0xdf
endif

ifndef ISP_LOW_FUSE
ISP_LOW_FUSE       = 0xff
endif

ifndef ISP_EXT_FUSE
ISP_EXT_FUSE       = 0x01
endif

ifndef ISP_PROG
ISP_PROG           = -c stk500v2
endif

AVRDUDE_ISP_OPTS = -P $(ISP_PORT) $(ISP_PROG)


########################################################################
#
# Explicit targets start here
#

all:            $(OBJDIR) $(TARGET_HEX)

$(OBJDIR):
                mkdir $(OBJDIR)

$(TARGET_ELF):  $(OBJS)
                $(CC) $(LDFLAGS) -o $@ $(OBJS) $(SYS_OBJS)

$(DEP_FILE):    $(OBJDIR) $(DEPS)
                cat $(DEPS) > $(DEP_FILE)

upload:         reset raw_upload

raw_upload:     $(TARGET_HEX)
                $(AVRDUDE) $(AVRDUDE_COM_OPTS) $(AVRDUDE_ARD_OPTS) \
                        -U flash:w:$(TARGET_HEX):i

# stty on MacOS likes -F, but on Debian it likes -f redirecting
# stdin/out appears to work but generates a spurious error on MacOS at
# least. Perhaps it would be better to just do it in perl ?
reset:          
                for STTYF in 'stty --file' 'stty -f' 'stty <' ; \
                  do $$STTYF /dev/tty >/dev/null 2>/dev/null && break ; \
                done ;\
                $$STTYF $(ARD_PORT)  hupcl ;\
                (sleep 0.1 || sleep 1)     ;\
                $$STTYF $(ARD_PORT) -hupcl 

ispload:        $(TARGET_HEX)
                $(AVRDUDE) $(AVRDUDE_COM_OPTS) $(AVRDUDE_ISP_OPTS) -e \
                        -U lock:w:$(ISP_LOCK_FUSE_PRE):m \
                        -U hfuse:w:$(ISP_HIGH_FUSE):m \
                        -U lfuse:w:$(ISP_LOW_FUSE):m \
                        -U efuse:w:$(ISP_EXT_FUSE):m
                $(AVRDUDE) $(AVRDUDE_COM_OPTS) $(AVRDUDE_ISP_OPTS) -D \
                        -U flash:w:$(TARGET_HEX):i
                $(AVRDUDE) $(AVRDUDE_COM_OPTS) $(AVRDUDE_ISP_OPTS) \
                        -U lock:w:$(ISP_LOCK_FUSE_POST):m

clean:
                $(REMOVE) $(OBJS) $(TARGETS) $(DEP_FILE) $(DEPS)

depends:        $(DEPS)
                cat $(DEPS) > $(DEP_FILE)

.PHONY: all clean depends upload raw_upload reset

include $(DEP_FILE)

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