Bring potatoes, stock, garlic, bay leaf, thyme, tomato, and a pinch of salt to a boil in a medium saucepan. Reduce heat, and simmer until potatoes are just tender when pierced with a sharp knife, 12 to 14 minutes. Transfer potatoes to a bowl using a slotted spoon. Strain cooking liquid through a coarse sieve (allowing some thyme leaves through); discard solids.
Cook bacon in a large skillet over medium-high heat until fat is rendered and bacon is just beginning to brown, about 4 minutes. Add onion, and reduce heat to medium. Cook, stirring frequently, until onion is golden, 7 to 9 minutes.
Add potatoes to skillet, and pour enough cooking liquid (1 1/2 to 2 cups) to come halfway up sides. Raise heat to medium-high. Simmer, turning potatoes occasionally to coat and seasoning with salt and pepper halfway through, until liquid has reduced and glazes potatoes, about 15 minutes.