Where do they belong?
At the input, screen for content the system should not act on and strip or mark anything that arrived from an untrusted source. At the output, validate structure before anything downstream consumes it — a schema check that rejects malformed JSON prevents a whole class of failure that no amount of prompting will.
At the tool layer, apply least privilege. An agent with read-only credentials cannot delete a table however it is manipulated, and permissions enforced in code hold in situations where instructions in a prompt do not.
