In a large bowl, mix together the warm water, sugar, and yeast, and allow the yeast to activate for 5-8 minutes until foamy looking.
Add the remaining ingredients and knead together for 7 minutes by hand, or 4 minutes on medium speed in a stand mixer fitted with a dough hook, yielding a firm, smooth dough.
Transfer the dough into a lightly oiled bowl, and cover the bowl with a moistened kitchen towel, keeping it in a warm place for the dough to rise for 60-90 minutes until doubled in size.
Meanwhile, mix together the filling by combining the olive oil, apples, pomegranate seeds, sugar, salt, cinnamon, orange blossom water, orange zest, and juice in a mixing bowl.
Turn the dough onto a lightly floured work surface and divide it into 4 equal pieces. Roll each piece by hand into a 12-inch (30 cm) rope and flatten to approximately 3 ½ inches (9 cm) wide.
Working with one piece at a time (cover the others with a slightly damp towel), spread one-fourth of the filling along one side of the flattened dough strip. Fold the dough lengthwise over the apples and press the edges gently to seal. Repeat with the remaining dough pieces so that you have four dough strands with filling inside of them.
To weave the dough, position two pieces lengthwise next to each other with a small gap. Place the other two pieces crosswise, weaving them in a tic-tac-toe pattern: one piece goes over and under the lengthwise pieces, and the next row alternates under and over.
Next, pick up the dough strip that is underneath and fold it over its neighboring strip to the side. Repeat this process with the three "under" strips. Reverse the direction by folding the "under" strips over their partners again. Tuck the ends underneath to form a rounded shape.
Cover the loaf loosely with a clean, moistened kitchen towel to rise for 45-60 minutes until doubled in size. Meanwhile, preheat your oven to 350°F (175°C).
Once the oven is preheated, bake the loaf for 40-45 minutes until golden brown. If your oven has uneven heat, be sure to rotate the loaf at the half-way point, and possibly switch it to a different rack. Make sure the racks in your oven aren’t too close together so the top of your challah doesn’t end up rising up to touch the oven rack.
Meanwhile, stir together the olive oil, agave nectar, and orange blossom water.
Once the bread is lightly golden brown and cooked through, remove the loaf and brush thoroughly with the agave and olive oil. If you are using the seeds, sprinkle them all around the loaf now, sticking to the glaze.
Finish baking for 4-5 minutes and then remove the loaf, placing it on a wire rack to cool to room temperature before serving.