PYQGIS/Processing from a standalone script. Issue with initializing Processing.

pyqgis_update_features_standalone.py

import sys
import os
from datetime import datetime

from qgis.core import *
import exifread

QgsApplication.setPrefixPath("/usr", True)
qgs = QgsApplication([], True)
qgs.initQgis()

# Initialize processing according to the SO: http://gis.stackexchange.com/questions/129915/cannot-run-standalone-qgis-script
sys.path.append("/home/eric/.qgis2/python/plugins")
from processing.core.Processing import Processing
Processing.Initialize() # Crash!
from processing.tools import *

BOUNDARY_FIELD_IDX = 25

boundaries_lyr = QgsVectorLayer("boundaries.shp", "boundaries", "ogr")
photos_lyr = QgsVectorLayer("Photos.gpkg", "photo_points", "ogr")

# Contains feature ids as keys with an inner dictionary of the attribute index
# and new value pairs, structured like { 220: {24: 'May 2016', 25: 'Allen #2'} }
update_features = {}

# Extract the picture date from metadata. Working as intended.
for feature in photos_lyr.getFeatures():
    photo = feature['photo_name']

    # Make sure the photo isn't null and that the picture exists
    if photo and os.path.exists("{}.JPG".format(os.path.join(PHOTO_DIR, photo))):
        with open("{}.JPG".format(os.path.join(PHOTO_DIR, photo)), 'rb') as f:
            tags = exifread.process_file(f, details=False,
                    stop_tag='EXIF DateTimeOriginal')
            photo_date = datetime.strptime(str(tags['EXIF DateTimeOriginal']),
                EXIF_DATE_FORMAT).strftime(OUTPUT_DATE_FORMAT)

            attrs = {PHOTO_DATE_FIELD_IDX: photo_date}
            update_features[feature.id()] = attrs

boundary_filter = QgsExpression(""""zone" = 2""")
boundaries = set([f['boundary'] for f in boundaries_lyr.getFeatures(
    QgsFeatureRequest(boundary_filter))])

# for each unique boundary name in the set of boundaries, select the features
# that have that boundary name to be used in the select by location algorithm
for boundary in boundaries:
    filter_expression = """"boundary" = '{}'"""
    ids = [f.id() for f in boundaries_lyr.getFeatures(QgsFeatureRequest(
        QgsExpression(filter_expression.format(boundary))))]

    boundaries_lyr.setSelectedFeatures(ids)

    general.runalg('qgis:selectbylocation', photos_lyr, boundaries_lyr,
        u'intersect', 0)

    # Update the update_features dictionary with the name of the boundary the
    # point is in
    for photo in photos_lyr.selectedFeatures():
        update_features[photo.id()][BOUNDARY_FIELD_IDX] = boundary

well_photos_lyr.dataProvider().changeAttributeValues(update_features)
#print update_features

del photos_lyr, boundaries_lyr
qgs.exitQgis()

I haven't tested the whole script, but I notice you should call initialize() and not Initialize() in line #15.