LLM Prompt Engineering - System Instruction Best Practices

LLM Prompt Engineering - System Instruction Best Practices

Purpose: Guidelines for writing effective system instructions that LLMs actually follow, based on real debugging experiences.

Core Principle

When LLMs ignore instructions, it's usually the prompt's fault, not the LLM's.

LLMs are excellent at following clear, explicit instructions but will apply reasoning and judgment to ambiguous ones. This guide shows how to write prompts that remove ambiguity.

The Five Critical Rules

1. Use Unconditional Language for Critical Instructions

Problem: Conditional language gives LLMs room to apply judgment and override instructions.

Real Example from CharacterCreationAgent Bug:

❌ Conditional (LLM overrode this):

If `character_creation_in_progress` is true, clear it.

LLM's Response:

"Character creation flag 'character_creation_in_progress' is still true. Since we are still in the setup phase, I am maintaining it until the user is actually ready to enter story mode."

The LLM applied judgment: "I think we're still setting up" → overrode instruction.

✅ Unconditional (LLM followed this):

## 🎭 CRITICAL: Character Creation Flag - CLEAR IT NOW

IF YOU SEE `custom_campaign_state.character_creation_in_progress` ANYWHERE IN YOUR INPUT, IT MUST BE FALSE IN YOUR OUTPUT.

NO EXCEPTIONS. NO JUDGMENT. NO "BUT WE'RE STILL SETTING UP".

YOU ARE STORY MODE. FLAG MUST BE FALSE. ALWAYS.

LLM's Response: ✅ Cleared the flag without judgment.

When to Use Each:

• Conditional: Instructions where LLM reasoning is desired (narrative choices, character suggestions)
• Unconditional: Critical state management, flag clearing, mandatory fields

2. Document INPUT and OUTPUT Schemas Explicitly

Problem: LLMs can't follow instructions about data structures they don't understand.

MANDATORY for every system prompt:

## Input Schema: What You Receive

You receive a `GAME STATE` section with this structure:
```json
{
  "custom_campaign_state": {
    "flag_name": true/false,  ← Document exact path
    "nested_field": {
      "value": "..."
    }
  },
  "player_character_data": {...}
}

CHECK custom_campaign_state.flag_name to understand current status.

Output Schema: What You Must Return

Your response MUST include:

{
  "state_updates": {
    "custom_campaign_state": {
      "flag_name": false  ← Show exact structure
    }
  }
}

MANDATORY FIELDS:

• state_updates.custom_campaign_state.flag_name - Always update this
• state_updates.player_character_data - Update as choices are made

**Why This Works**:
- Shows exact field paths (no ambiguity about nesting)
- Labels mandatory vs optional fields
- Provides copy-pasteable JSON structure
- Uses visual cues (← arrows, bold text)

### 3. Position Critical Instructions in Top 50 Lines

**Problem**: Instruction compliance degrades with position in long prompts.

**Compliance by Position** (observed in real debugging):
- **Lines 1-50**: High compliance
- **Lines 51-500**: Medium compliance
- **Lines 500+**: Low compliance (LLM often ignores)

**Real Example**:

❌ **Failed (line 525 in 2064-line file)**:
```markdown
### 🎭 Character Creation Flag Management
(line 525 of 2064)

Result: LLM ignored instruction

✅ Succeeded (line 22 in same file):

## 🎭 CRITICAL: Character Creation Flag - CLEAR IT NOW
(line 22 of 2064)

Result: LLM followed instruction

How to Position:

1. Place critical instructions at lines 1-50
2. Use clear visual separators (## CRITICAL, ---)
3. Use emojis for visual anchors (🎭, 🚨, ⚠️)
4. Repeat critical instructions before related sections

4. Enforce Prompt Size Budgets

Problem: Prompt bloat causes LLMs to ignore instructions.

Target Token Counts per Agent Type:

Agent Type	Target Lines	Max Lines	Current Status
Character Creation	600-800	1000	✅ 607 (after removing mechanics)
Story Mode	1500-2000	2500	⚠️ 2064 (at limit)
Combat Mode	1200-1800	2000	-
Info Mode	500-800	1000	-
God Mode	400-600	800	-

How “Current Status” is measured:

• Count lines for the prompt files actually loaded by the agent (see REQUIRED_PROMPT_ORDER / OPTIONAL_PROMPTS in $PROJECT_ROOT/agents.py and prompt mapping in $PROJECT_ROOT/agent_prompts.py), then sum wc -l across that set.
• Treat the result as directional (line-count is a proxy for token count).

Red Flags:

• 50% of token budget used = LLM starts making judgment calls

• 75% of token budget used = LLM ignores critical instructions

• 90% of token budget used = unpredictable behavior

Real Example:

❌ Before (1236 lines):

• CharacterCreationAgent loaded mechanics_system_instruction.md (629 lines)
• LLM applied judgment to flag clearing instruction
• Test failed

✅ After (607 lines, 50% reduction):

• Removed mechanics bloat (combat/rewards not needed for creation)
• LLM followed flag clearing instruction
• Test passed

How to Cut Bloat:

1. Remove cross-domain content (combat from creation, narrative from info)
2. Consolidate redundant sections
3. Move reference tables to appendix
4. Use shorter examples
5. Cut explanatory text that repeats obvious points

5. Debug via Log Evidence

Problem: When instructions fail, you need to see WHY the LLM ignored them.

Debugging Checklist:

1. Check LLM's thinking logs (if available):

   "Character creation flag 'character_creation_in_progress' is still true.
   Since we are still in the setup phase, I am maintaining it..."
   

   This reveals judgment override behavior.

2. Verify instruction position:

   grep -n "critical instruction text" prompt_file.md
   

   If line number > 500 in long file → reposition to top

3. Count prompt lines:

   wc -l $PROJECT_ROOT/prompts/*.md
   

   If total >1500 lines → identify bloat to cut

4. Test conditional vs unconditional:

   • Change "if X, do Y" → "X MUST BE Y. ALWAYS."
   • Rerun test
   • Check if behavior changes

5. Add explicit schemas:

   • Add INPUT schema section
   • Add OUTPUT schema section
   • Show exact field paths
   • Rerun test

Checklist for New System Prompts

Before deploying any system prompt, verify:

• Critical instructions in lines 1-50
• INPUT schema documented with exact field paths
• OUTPUT schema documented with mandatory field list
• Unconditional language for critical state changes
• Total lines < budget for agent type
• No cross-domain content (combat in creation, etc.)
• Visual separators around critical sections
• Tested with actual LLM calls (not just reading prompt)

Common Failure Patterns

Pattern 1: "I think..." Override

Symptom: LLM says "I think we're still..." and ignores instruction.

Diagnosis: Conditional language gave room for judgment.

Fix: Change to unconditional ("MUST BE X. NO EXCEPTIONS.")

Pattern 2: Silent Non-Compliance

Symptom: LLM doesn't mention instruction, just doesn't follow it.

Diagnosis: Instruction buried too deep in prompt (line 500+).

Fix: Move to top 50 lines with visual separator.

Pattern 3: Field Path Confusion

Symptom: LLM updates wrong field or nesting level.

Diagnosis: Schema not documented explicitly.

Fix: Add INPUT/OUTPUT schemas with exact paths.

Pattern 4: Intermittent Compliance

Symptom: Instruction followed sometimes, ignored other times.

Diagnosis: Prompt too long, LLM attention drifting.

Fix: Cut bloat to reduce prompt size by 30-50%.

Examples: Before and After

Example 1: Flag Clearing

Before (Failed):

### Character Creation Flag Management
(line 525 of 2064-line file)

If `character_creation_in_progress` is true, clear it when user is done.

After (Succeeded):

## 🎭 CRITICAL: Character Creation Flag - CLEAR IT NOW
(line 22 of 2064-line file)

IF YOU SEE `custom_campaign_state.character_creation_in_progress` ANYWHERE, IT MUST BE FALSE.

NO EXCEPTIONS. NO JUDGMENT. FLAG MUST BE FALSE. ALWAYS.

Result: 100% compliance vs 0% compliance.

Example 2: Schema Documentation

Before (Ambiguous):

Update the character creation flag when done.

After (Explicit):

## Input Schema
```json
{
  "custom_campaign_state": {
    "character_creation_in_progress": true/false  ← CHECK THIS
  }
}

Output Schema

{
  "state_updates": {
    "custom_campaign_state": {
      "character_creation_in_progress": false  ← MUST SET THIS
    }
  }
}

**Result**: LLM knows exact field paths and structure.

## Token Budget Calculation

**Rough estimation** (for planning):
- 1 line of markdown ≈ 10-20 tokens
- 1000 lines ≈ 10,000-20,000 tokens
- Most models: 128K-200K input token limit
- Reserve 50-75% for story history and game state

**Example Budget** (200K token limit):
- Story history: 100K tokens (story entries, game state)
- System prompt: 20K tokens (~1500-2000 lines)
- Output buffer: 60K tokens (LLM response)
- Safety margin: 20K tokens

**Red line**: If system prompt >25K tokens (>2000 lines), cut bloat immediately.

## Validation Testing

**Test every system prompt change**:

```python
# Create test that validates instruction compliance
def test_critical_instruction():
    # Set up scenario where instruction should trigger
    game_state = {"custom_campaign_state": {"flag": True}}

    # Call LLM with prompt
    response = call_llm(prompt, game_state, user_input)

    # Verify compliance
    assert response["state_updates"]["custom_campaign_state"]["flag"] == False, \
        f"CRITICAL INSTRUCTION IGNORED: flag should be False, got {response}"

Run this test BEFORE merging prompt changes.

Real-World Case Study

Problem: CharacterCreationAgent not clearing character_creation_in_progress flag.

Symptoms:

• Agent transitioned correctly (CharacterCreationAgent → StoryModeAgent)
• But flag remained True
• Next turn incorrectly looped back to CharacterCreationAgent

Root Cause Analysis:

1. ❌ Instruction at line 525 of 2064-line file (buried)
2. ❌ Conditional language: "If flag is true, clear it"
3. ❌ No explicit INPUT/OUTPUT schemas
4. ❌ Prompt bloat: 1236 lines (included irrelevant mechanics)

Fixes Applied:

1. ✅ Moved instruction to line 22 (top 50)
2. ✅ Changed to unconditional: "FLAG MUST BE FALSE. ALWAYS."
3. ✅ Added explicit INPUT/OUTPUT schemas
4. ✅ Cut prompt to 607 lines (removed mechanics bloat)

Result: Test went from 0% → 100% pass rate.

Summary

The Three Laws of Prompt Engineering:

1. Be Unconditional: "MUST BE X. ALWAYS." beats "if Y, do X"
2. Be Explicit: Document INPUT/OUTPUT schemas with exact field paths
3. Be Concise: Shorter prompts = higher compliance

When in doubt: Make it shorter, simpler, and more aggressive.

References

• Evidence bundle: /tmp/worktree_worker12/claude/character-creation-agent-i9xyR/character_creation_flag_clearing_fix/20260109T072437Z
• Commit: bc9dbc29b36204e914bd4b54a2731812c6ddabfc
• Related: .claude/skills/evidence-standards.md