# How to Customize Prompt Engineering in PrimeAgent: A Complete Guide to System Prompts and Overrides

> Master prompt engineering in PrimeAgent with this guide. Learn to customize system prompts and overrides using environment variables, config files, CLI flags, or by modifying core functions.

- Repository: [Prime Intellect/prime-agent](https://github.com/PrimeIntellect-ai/prime-agent)
- Tags: how-to-guide
- Published: 2026-08-20

---

**You can customize PrimeAgent's prompt engineering through three override mechanisms—environment variables, config files, or CLI flags—or by modifying the core prompt builder functions `buildSystemPrompt()` and `buildRlmPrompt()` directly.**

PrimeAgent constructs its LLM prompts through a streamlined pipeline in the **coding-agent** package. Understanding this architecture lets you inject custom instructions, modify tool descriptions, or reshape the AI's behavior without diving deep into the codebase. This guide walks you through the exact files and methods that control prompt generation.

## How PrimeAgent Builds System Prompts

The prompt engineering pipeline follows a two-phase structure: **static base construction** and **dynamic context merging**.

### Core Prompt Builder Functions

At the heart of the system sits [`packages/coding-agent/src/core/system-prompt.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/system-prompt.ts). This file exports two primary functions:

- **`buildSystemPrompt()`** – Assembles the static foundation describing PrimeAgent's capabilities, safety rules, and default utilities.
- **`buildRlmPrompt()`** – Extends the base prompt with **RLM** (Remote Language Model) specific context, including session resources and active tools.

Both functions are publicly exposed through [`packages/coding-agent/src/core/index.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/index.ts) for consumption by other packages.

### Prompt Component Sources

The builder pulls from several upstream modules:

| Source | Path | Purpose |
|--------|------|---------|
| Reusable snippets | [`src/core/prompts/index.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/src/core/prompts/index.ts) | Tool descriptions, environment summaries, safety guidelines |
| Model defaults | [`src/core/model-resolver.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/src/core/model-resolver.ts) | Default model names per provider for prompt metadata |
| Session resources | [`src/core/session-resources.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/src/core/session-resources.ts) | Loaded skills, active tools, user messages |

The final assembled string routes through [`packages/ai/src/stream.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/ai/src/stream.ts) to the provider's streaming interface.

## Three Methods to Override Prompts Without Code Changes

PrimeAgent provides built-in override mechanisms for rapid experimentation. These apply through [`packages/coding-agent/src/core/prompt-overrides.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/prompt-overrides.ts) before the prompt reaches the LLM.

### 1. Environment Variable: `PRIME_AGENT_PROMPT_OVERRIDES`

Set a JSON string mapping prompt sections to custom text. This method persists for your shell session.

```bash
export PRIME_AGENT_PROMPT_OVERRIDES='{
  "system": "You are a helpful assistant that always speaks in rhymes.",
  "tools": "You may use the following tools: image, bash, websearch."
}'
prime-agent

```

Valid section keys include `"system"`, `"tools"`, and any other segment defined in the prompt builder's output structure.

### 2. Persistent Config File: [`.prime-agent/config.json`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/.prime-agent/config.json)

For permanent customizations, create a configuration file in your home directory:

```json
{
  "promptOverrides": {
    "system": "You are a security-focused AI; never reveal secrets.",
    "tools": "Available tools: websearch only."
  }
}

```

PrimeAgent automatically discovers and loads this file on startup. The structure mirrors the environment variable format but lives in `~/.prime-agent/config.json`.

### 3. CLI Flag: `--prompt-override`

For one-off sessions, pass overrides directly on the command line. This takes **highest precedence** over environment variables and config files.

```bash
prime-agent --prompt-override system="You are an expert Python tutor."

```

Multiple overrides require multiple flags:

```bash
prime-agent \
  --prompt-override system="Be extremely concise." \
  --prompt-override tools="Tools: bash, file-read"

```

## Programmatic Customization via Source Code

When built-in overrides prove insufficient, modify the prompt pipeline directly.

### Direct Function Calls

Import and invoke the override setter from another Node.js script:

```typescript
import { setPromptOverride } from 'prime-agent/coding-agent/src/core/prompt-overrides';

setPromptOverride('system', 'You are a concise assistant; keep replies under 100 words.');

// Subsequent sessions use the overridden prompt
await primeAgent.start();

```

### Extending the Core Prompt Builder

For structural changes—adding new sections, reordering components, or implementing conditional logic—edit [`packages/coding-agent/src/core/system-prompt.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/system-prompt.ts). The modular architecture supports clean extensions:

1. Add new prompt fragments to [`src/core/prompts/index.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/src/core/prompts/index.ts)
2. Reference them in `buildSystemPrompt()` or `buildRlmPrompt()`
3. Export any new public methods through [`src/core/index.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/src/core/index.ts)

The prompt builds **once per session**, so changes apply only to new sessions without affecting running instances.

## Key File Reference

| Component | Path |
|-----------|------|
| Core prompt builder | [`packages/coding-agent/src/core/system-prompt.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/system-prompt.ts) |
| Override processor | [`packages/coding-agent/src/core/prompt-overrides.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/prompt-overrides.ts) |
| Reusable fragments | [`packages/coding-agent/src/core/prompts/index.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/prompts/index.ts) |
| Session data collector | [`packages/coding-agent/src/core/session-resources.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/session-resources.ts) |
| Model metadata | [`packages/coding-agent/src/core/model-resolver.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/model-resolver.ts) |
| Public API exports | [`packages/coding-agent/src/core/index.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/index.ts) |
| Provider streaming | [`packages/ai/src/stream.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/ai/src/stream.ts) |

## Summary

- **Use environment variables** for temporary, shell-session overrides via `PRIME_AGENT_PROMPT_OVERRIDES`.
- **Use config files** for permanent customizations in `~/.prime-agent/config.json`.
- **Use CLI flags** for highest-priority, one-time adjustments with `--prompt-override`.
- **Modify source code** when you need structural changes to the prompt architecture—the relevant files live in `packages/coding-agent/src/core/`.
- All overrides resolve through [`prompt-overrides.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/prompt-overrides.ts) before the final prompt reaches the LLM streaming interface.

## Frequently Asked Questions

### What is the RLM mode in PrimeAgent?

RLM stands for **Remote Language Model** mode. According to the PrimeAgent source code, `buildRlmPrompt()` constructs prompts specifically for this mode by injecting dynamic session context—including loaded skills, active tools, and user-provided messages—into the base system prompt. This differs from `buildSystemPrompt()`, which creates a static foundation without runtime session data.

### Can I override only specific tools in the prompt?

Yes. The `tools` section key in any override mechanism accepts arbitrary text. While PrimeAgent auto-generates tool listings from [`session-resources.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/session-resources.ts), you can completely replace this output by setting `"tools": "Your custom description"` in your config file, environment variable, or CLI flag. The override processor in [`prompt-overrides.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/prompt-overrides.ts) substitutes your text before the prompt reaches the LLM.

### Do prompt overrides affect all running sessions?

No. PrimeAgent builds prompts **once per session** when a new session initializes. Changes to environment variables, config files, or programmatic overrides apply only to sessions started after the modification. Running sessions maintain their original prompt construction, making it safe to experiment without disrupting active workflows.

### Where should I add new reusable prompt sections?

Add new prompt fragments to [`packages/coding-agent/src/core/prompts/index.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/prompts/index.ts), then import and reference them in [`packages/coding-agent/src/core/system-prompt.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/system-prompt.ts). This follows the established pattern for the existing tool descriptions and environment summaries. Export any new public integration methods through [`packages/coding-agent/src/core/index.ts`](https://github.com/PrimeIntellect-ai/prime-agent/blob/main/packages/coding-agent/src/core/index.ts) to maintain clean package boundaries.