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Edit #5 Upload via avrdude

Basically this command worked for my board (Arduino Uno SMD):

avrdude -v -p atmega328p -c arduino -P /dev/ttyACM0 -b 115200 -D -U flash:w:/path/to/Blink.cpp.hex:i

This is all to say that the latter makefile in this post correctly builds the .hex file. Which can then successfully be uploaded onto the board. (Using Arduino 1.6.5).

Edit #4 Compilation working

Structure of arduino-1.6.5-r5/hardware/arduino/avr/cores/arduino:

.
├── abi.cpp
├── Arduino.h
├── binary.h
├── CDC.cpp
├── Client.h
├── HardwareSerial0.cpp
├── HardwareSerial1.cpp
├── HardwareSerial2.cpp
├── HardwareSerial3.cpp
├── HardwareSerial.cpp
├── HardwareSerial.h
├── HardwareSerial_private.h
├── HID.cpp
├── hooks.c
├── IPAddress.cpp
├── IPAddress.h
├── main.cpp
├── new.cpp
├── new.h
├── Printable.h
├── Print.cpp
├── Print.h
├── Server.h
├── Stream.cpp
├── Stream.h
├── Tone.cpp
├── Udp.h
├── USBAPI.h
├── USBCore.cpp
├── USBCore.h
├── USBDesc.h
├── WCharacter.h
├── WInterrupts.c
├── wiring_analog.c
├── wiring.c
├── wiring_digital.c
├── wiring_private.h
├── wiring_pulse.c
├── wiring_pulse.S
├── wiring_shift.c
├── WMath.cpp
├── WString.cpp
└── WString.h

The reason the yield() function was not recognized was because I was not compiling with 1.6.5 correctly. Below is an updated makefile that compiles the Blink.cpp seemingly correct. I have yet to verify the sketch works on upload to the Arduino (via avrdude). The mistake was that I did not compile abi.cpp, HardwareSerialx.cpp(0-3), and hooks.c. hooks.c is where the yield() is located.

Updated makefile:

#
# Simple Arduino Makefile
#
# Author: Nick Gammon
# Date: 18th March 2015
#
# Edited by: Kyle Lawlor
# Date: 30th October 2015
$H# where you installed the Arduino app
ARDUINO_DIR = /home/wiz/programs/arduino-1.6.5-r5/
# various programs
CC = "$(ARDUINO_DIR)hardware/tools/avr/bin/avr-gcc"
CPP = "$(ARDUINO_DIR)hardware/tools/avr/bin/avr-g++"
AR = "$(ARDUINO_DIR)hardware/tools/avr/bin/avr-ar"
OBJ_COPY = "$(ARDUINO_DIR)hardware/tools/avr/bin/avr-objcopy"
# create a file called Blink.cpp in same base dir
MAIN_SKETCH = Blink.cpp
# compile flags for g++ and gcc
# may need to change these
F_CPU = 16000000
MCU = atmega328p
# compile flags
GENERAL_FLAGS = -c -g -Os -Wall -ffunction-sections -fdata-sections -mmcu=$(MCU) -DF_CPU=$(F_CPU)L -MMD -DUSB_VID=null -DUSB_PID=null -DARDUINO=106
CPP_FLAGS = $(GENERAL_FLAGS) -fno-exceptions
CC_FLAGS = $(GENERAL_FLAGS)
# location of include files
INCLUDE_FILES = "-I$(ARDUINO_DIR)hardware/arduino/avr/cores/arduino" "-I$(ARDUINO_DIR)hardware/arduino/avr/variants/standard"
# library sources
LIBRARY_DIR = "$(ARDUINO_DIR)hardware/arduino/avr/cores/arduino/"
build:
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(MAIN_SKETCH) -o $(MAIN_SKETCH).o
# $(CC) $(CC_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)avr-libc/malloc.c -o malloc.c.o
# $(CC) $(CC_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)avr-libc/realloc.c -o realloc.c.o
 $(CC) $(CC_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)hooks.c -o hooks.c.o
 $(CC) $(CC_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)WInterrupts.c -o WInterrupts.c.o
 $(CC) $(CC_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)wiring.c -o wiring.c.o
 $(CC) $(CC_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)wiring_analog.c -o wiring_analog.c.o
 $(CC) $(CC_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)wiring_digital.c -o wiring_digital.c.o
 $(CC) $(CC_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)wiring_pulse.c -o wiring_pulse.c.o
 $(CC) $(CC_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)wiring_shift.c -o wiring_shift.c.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)abi.cpp -o abi.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)CDC.cpp -o CDC.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)HardwareSerial.cpp -o HardwareSerial.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)HardwareSerial0.cpp -o HardwareSerial0.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)HardwareSerial1.cpp -o HardwareSerial1.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)HardwareSerial2.cpp -o HardwareSerial2.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)HardwareSerial3.cpp -o HardwareSerial3.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)HID.cpp -o HID.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)IPAddress.cpp -o IPAddress.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)main.cpp -o main.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)new.cpp -o new.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)Print.cpp -o Print.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)Stream.cpp -o Stream.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)Tone.cpp -o Tone.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)USBCore.cpp -o USBCore.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)WMath.cpp -o WMath.cpp.o
 $(CPP) $(CPP_FLAGS) $(INCLUDE_FILES) $(LIBRARY_DIR)WString.cpp -o WString.cpp.o
 rm core.a
# $(AR) rcs core.a malloc.c.o
# $(AR) rcs core.a realloc.c.o
 $(AR) rcs core.a hooks.c.o
 $(AR) rcs core.a WInterrupts.c.o
 $(AR) rcs core.a wiring.c.o
 $(AR) rcs core.a wiring_analog.c.o
 $(AR) rcs core.a wiring_digital.c.o
 $(AR) rcs core.a wiring_pulse.c.o
 $(AR) rcs core.a wiring_shift.c.o
 $(AR) rcs core.a abi.cpp.o
 $(AR) rcs core.a CDC.cpp.o
 $(AR) rcs core.a HardwareSerial.cpp.o
 $(AR) rcs core.a HardwareSerial0.cpp.o
 $(AR) rcs core.a HardwareSerial1.cpp.o
 $(AR) rcs core.a HardwareSerial2.cpp.o
 $(AR) rcs core.a HardwareSerial3.cpp.o
 $(AR) rcs core.a HID.cpp.o
 $(AR) rcs core.a IPAddress.cpp.o
 $(AR) rcs core.a main.cpp.o
 $(AR) rcs core.a new.cpp.o
 $(AR) rcs core.a Print.cpp.o
 $(AR) rcs core.a Stream.cpp.o
 $(AR) rcs core.a Tone.cpp.o
 $(AR) rcs core.a USBCore.cpp.o
 $(AR) rcs core.a WMath.cpp.o
 $(AR) rcs core.a WString.cpp.o
 $(CC) -Os -Wl,--gc-sections -mmcu=$(MCU) -o $(MAIN_SKETCH).elf $(MAIN_SKETCH).o core.a -lm
 $(OBJ_COPY) -O ihex -j .eeprom --set-section-flags=.eeprom=alloc,load --no-change-warnings --change-section-lma .eeprom=0 $(MAIN_SKETCH).elf $(MAIN_SKETCH).eep
 $(OBJ_COPY) -O ihex -R .eeprom $(MAIN_SKETCH).elf $(MAIN_SKETCH).hex

Are malloc.c and realloc.c being used anymore? I searched across 1.6.5 for a directory similar to avr-libc, I couldn't find anything. I'm guessing they are no longer in use.

Edit #3 Identified where yield() function is located.

Project directory:

.
├── abi.cpp
├── Arduino.h
├── binary.h
├── Blink.cpp
├── Blink.cpp.d
├── Blink.cpp.o
├── CDC.cpp
├── CDC.cpp.d
├── CDC.cpp.o
├── Client.h
├── core.a
├── HardwareSerial0.cpp
├── HardwareSerial1.cpp
├── HardwareSerial2.cpp
├── HardwareSerial3.cpp
├── HardwareSerial.cpp
├── HardwareSerial.cpp.d
├── HardwareSerial.cpp.o
├── HardwareSerial.h
├── HardwareSerial_private.h
├── HID.cpp
├── HID.cpp.d
├── HID.cpp.o
├── hooks.c
├── IPAddress.cpp
├── IPAddress.cpp.d
├── IPAddress.cpp.o
├── IPAddress.h
├── main.cpp
├── main.cpp.d
├── main.cpp.o
├── new.cpp
├── new.cpp.d
├── new.cpp.o
├── new.h
├── Printable.h
├── Print.cpp
├── Print.cpp.d
├── Print.cpp.o
├── Print.h
├── run.mk
├── run.mk~
├── Server.h
├── Stream.cpp
├── Stream.cpp.d
├── Stream.cpp.o
├── Stream.h
├── Tone.cpp
├── Tone.cpp.d
├── Tone.cpp.o
├── Udp.h
├── USBAPI.h
├── USBCore.cpp
├── USBCore.cpp.d
├── USBCore.cpp.o
├── USBCore.h
├── USBDesc.h
├── WCharacter.h
├── WInterrupts.c
├── WInterrupts.c.d
├── WInterrupts.c.o
├── wiring_analog.c
├── wiring_analog.c.d
├── wiring_analog.c.o
├── wiring.c
├── wiring.c.d
├── wiring.c.o
├── wiring_digital.c
├── wiring_digital.c.d
├── wiring_digital.c.o
├── wiring_private.h
├── wiring_pulse.c
├── wiring_pulse.c.d
├── wiring_pulse.c.o
├── wiring_pulse.S
├── wiring_shift.c
├── wiring_shift.c.d
├── wiring_shift.c.o
├── WMath.cpp
├── WMath.cpp.d
├── WMath.cpp.o
├── WString.cpp
├── WString.cpp.d
├── WString.cpp.o
└── WString.h

yield() is located in hooks.c. I do not understand why the function is not available to wiring.c.