Preheat the oven to 300°F (150°C). Line a rimmed baking sheet with parchment paper or a silicone mat.
(Optional) Toast the nuts and seeds: spread the chopped nuts and seeds on a baking sheet and toast 8–10 minutes until aromatic and lightly golden. Remove and let cool.
In a large bowl, whisk together the rolled oats, cocoa powder, cinnamon (if using) and fine sea salt until evenly combined (break up any cocoa lumps). Add the toasted nuts, coconut flakes and seeds; toss to combine.
In a small saucepan over low heat, warm the oil, maple syrup (or honey) and applesauce just until fluid and combined — do not boil. Remove from heat and stir in vanilla extract.
Pour the warm liquid over the dry ingredients. Fold gently with a spatula until everything is evenly coated. For chunkier clusters, stir as little as possible.
Transfer the coated mixture to the prepared baking sheet. Spread into an even layer and press firmly with the back of a spatula (pressing creates larger clusters).
Bake 20–30 minutes, rotating the pan halfway through for even toasting. Watch carefully so the cocoa doesn’t darken too quickly — you want fragrant, toasted oats, not burned ones.
Remove the pan from the oven and immediately scatter the chopped dark chocolate over the warm granola. Let sit 1–2 minutes so a portion softens; gently fold a few times if you want some pockets of melted chocolate. For distinct chunks, wait until granola is completely cool before adding chocolate.
Cool the granola completely on the baking sheet (about 1 hour). Break into clusters by hand or with a spatula. Finish with a few flakes of sea salt, if desired.
Store cooled granola in an airtight container at room temperature (see Notes) or freeze for longer storage.