(Please correct me if there is already a repair system available, I could not find any options for it on damaged items or any notes on it in the tutorials.) I'm not sure if there is no repair system in the game because it is in development, or if it is because there is supposed to be an emphasis on random loot; but with all of the frustrations and challenges that come with roguelikes it would be really nice if I could at least hang onto my favorite items for as long as my character is alive.
Click on damaged inventory item -> Have a button that says "repair" This action would consume resources based on what is used craft that specific item, and could potentially also require holding tools. That would be the most accessible way of having a repair system in my opinion.
If that is too basic, you could add a restriction where players can only repair items they know how to craft. That would add some challenge in having to unlock the ability to repair items. You could also make the amount of durability repaired per material stat dependent, so that certain builds would be able to perform repairs more efficiently than others.
If you really want to make players work for their repairs you could add a rare "Repair Kit" drop that would be required for performing repairs, and lose its own durability in the process. The repair kit itself could be crafted from a set of tools (Knife, Scissors, Hammer, etc.) as going out to gather all the components would be a quest in and of itself.