The anvil you can use to repair tools by putting the tool and cobble, diamonds, etc in the second anvil slots.
Otherwise there is the ability to put 2 tools of the same type with different durability to apply more durability (repair) the tool you want to use.
But if you mean a mod with tools you repair in a workbench I assume you mean something like Tinkers Construct. Or mods that adds more anvils.
You'd have to give me a bit more as there are lot of tool mods (Emerald, Obsidian, Ruby and so on) out there and a fair amount like Tinkers out there (as someone that covers mainstream and niche mods across multiple versions I need more to narrow down what you mean).
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