I ended up running arudino-buider, available after Arduino 1.6.

When laying out your project, put a libraries/ and hardware/ folder along side your sketch directory, like so:

YourHipProject/
    Makefile
    hardware/
        Vendor/arch/{boards.txt,platform.txt}
    libraries/
        SomethingUseful/
        NoIdeaHowThisWorks/
    ProjectSketch/
        ProjectSketch.ino
        othersource.cpp

The hardware/ directory is only needed if you need support for 3rd party boards. Then, in the Makefile:

ARDUINO_DIR ?= /opt/arduino-1.6.13 # need to set this for your environment

.PHONY: ProjectSketch

ProjectSketch:
    arduino-builder -compile -verbose \
        -hardware $(ARDUINO_DIR)/hardware \
        -tools $(ARDUINO_DIR)/tools-builder \
        -tools $(ARDUINO_DIR)/hardware/tools/avr \
        -built-in-libraries $(ARDUINO_DIR)/libraries \
        -hardware ./hardware \
        -libraries ./libraries \
        -fqbn=Vendor:arch:board \
        ./ProjectSketch/ProjectSketch.ino

ARDUINO_DIR needs to point to where your Arduino is installed, be sure to set -fqbn= correctly too.

Running make should compile the firmware from ProjectSketch/ with the accompanying libraries and hardware definitions. Also, with verbose compile output enabled, the Arduino IDE will show you how it runs arduino-builder.

I ended up running arduino-buider, available in Arduino IDE 1.6.6 and newer.

When laying out your project, put a libraries/ and hardware/ folder along side your sketch directory, like so:

YourHipProject/
    Makefile
    hardware/
        Vendor/arch/{boards.txt,platform.txt}
    libraries/
        SomethingUseful/
        NoIdeaHowThisWorks/
    ProjectSketch/
        ProjectSketch.ino
        othersource.cpp

The hardware/ directory is only needed if you need support for 3rd party boards. Then, in the Makefile:

ARDUINO_DIR ?= /opt/arduino-1.6.13 # need to set this for your environment

.PHONY: ProjectSketch

ProjectSketch:
    arduino-builder -compile -verbose \
        -hardware $(ARDUINO_DIR)/hardware \
        -tools $(ARDUINO_DIR)/tools-builder \
        -tools $(ARDUINO_DIR)/hardware/tools/avr \
        -built-in-libraries $(ARDUINO_DIR)/libraries \
        -hardware ./hardware \
        -libraries ./libraries \
        -fqbn=Vendor:arch:board \
        ./ProjectSketch/ProjectSketch.ino

ARDUINO_DIR needs to point to where your Arduino is installed, be sure to set -fqbn= correctly too.

Running make should compile the firmware from ProjectSketch/ with the accompanying libraries and hardware definitions. Also, with verbose compile output enabled, the Arduino IDE will show you how it runs arduino-builder.