Agent instructions file vs System prompt

Why they differ

Both are standing orders, but the system prompt is set by whoever builds the AI tool, while this file is written by the project team and travels with the code.

Agent instructions file

AI-assisted coding

A plain text file kept with the code that tells AI tools the project's rules, commands and habits before they start work.

Formal

A file stored in the project under version control that a coding agent automatically loads into its context window each time it starts work, holding standing guidance such as build and test commands, style rules, folder layout and things never to do.

In plain English

Like the folder kept aboard a sailing club's shared boat, which every member reads before taking her out - how to start the engine, where the key hangs, never moor by the rocks.

In practice

At a Danish software house, the lead developer adds a short file to the payroll project - “run the tests before finishing, never edit generated files, use the shared date helper” - and the agent now follows it every time without being told.

Why it matters

It turns team knowledge into lasting guidance for AI tools, but anyone who can change the file can change what the agent does - so it needs the same care as code.

System prompt

Prompting & generation

Standing orders the maker of an AI service places ahead of every chat, setting the assistant's role, rules and tone before the user types.

Formal

The part of a prompt, marked with its own role, that carries instructions from whoever built the service rather than from the end user; instruction tuning teaches the large language model to weigh it above user text, but nothing enforces that.

In plain English

Like a director's notes to an actor before the curtain rises - the audience never hears them, yet they shape every line, and a loud voice from the seats can still knock the actor off script.

In practice

The web manager at a Danish ferry company writes the system prompt for its booking chat: “Answer only about departures and bookings; never promise refunds; pass complaints to staff.”

Why it matters

Users can often coax an assistant into revealing its system prompt, and prompt injection can override it, so it must never hold passwords or keys and cannot replace real access control.

Shared connections

Prompt injection