In a large skillet on medium-high heat, melt butter. Add in onions and cook until see-through, stirring frequently (It takes about 10 minutes).
Add in sugar, and reduce heat to medium. Stir the onions constantly, caramelizing them. It will take about 20-30 minutes.
Add in the minced garlic and apple cider, and stir until warmed through.
Transfer the onions to the slow cooker and add in beef broth and thyme. Cook on low for 6-8 hours.
Before serving, place the french bread slices on a baking sheet and broil in the oven for 1-2 minutes (just until browned).
In a small bowl, mix together the three cheeses.
Pour soup in oven-safe bowls (the soup will serve 6-8), place a piece of french bread in each bowl, and then top each with a portion of cheese. Place each bowl on the cookie sheet, and broil for 2 more minutes, until the cheese starts to melt and brown.