Almost every item inside of the game is either looted or crafted by players, with the exception of certain cosmetics. Blueprints are combined with resources to create items. There are four types of shops that players can craft at:
Shipwright, who crafts ships
Arcanist, who crafts runes for bonuses
Tailor, who crafts cosmetic character equipment
Blacksmith, who crafts ship equipment
The best place to find item recipes and other crafting data is on the community-managed Wiki.