Soak 1/2 cup flaxseeds in enough water to cover by two inches for at least 4 hours (or overnight).
Grind the other 1/2 cup of flaxseeds in a spice grinder.
Drain soaked flaxseeds; they'll be a little slimy ... just push through a sieve to get most of the water out, but it's okay if they're still wet.
Add all ingredients (water though salt) in order listed (reserving 1T flaxseeds) into bowl of a a stand mixer, with kneading attachment. With instant yeast, there's no need to proof it first with water and honey.
Add ground and soaked flaxseeds.
Mix on low until dough comes together, forming a wet but smooth ball.
Transfer dough to a well floured surface and knead for 7 to 10 minutes, adding more flour as necessary to work with it (this is a wet dough).
Shape into a ball and place in oiled bowl (glass or stainless steel.
Cover with tea towel or plastic wrap and let rise in a warm place till doubled in volume (1 - 1 1/2 hours).
Punch down and divide into 3 (or two if you like larger loaves).
Shape each into ball and place on parchment- or Siplat-lined baking sheet.
Cover loosely with plastic wrap spritzed with nonstick spray.
Let rise at least for 1 more hour or place in refrigerator overnight (did this once because I ran out of time ... really great results).
Preheat oven to 400°F. Brush each loaf lightly with water, cut criss-cross hash marks on top of each loaf. Sprinkle with remaining 1T flaxseeds.
Bake for 45 min. to 1 hour, till golden brown and sounds hollow when tapped.
Let cool on a wire rack for at least 15 min. (if you can stand it) before slicing.