Boundary with Prompt Engineering — How to Tune Each of the 5 Context Layers

Chapter 1 listed the 5 context layers. This chapter takes each apart: what goes in, how many tokens it eats, how to debug in isolation, how to find the culprit.

Every context engineering technique (rerank, memory, sub-agents) is surgery on one of these layers.

What the 5 Layers Actually Look Like

Below is the full message JR omni-report's daily-jobs routine sends to Claude right after scraping LinkedIn —

# tested: 2026-04-26 · anthropic@0.40.0 · model: claude-sonnet-4-6
client.messages.create(
    model="claude-sonnet-4-6",
    max_tokens=4096,

    # === Layer 1: System instruction ===
    system=[
        {
            "type": "text",
            "text": "你是 JR Academy 的 daily-jobs picker...",  # ~800 token
            "cache_control": {"type": "ephemeral"}  # 5min TTL prompt cache
        }
    ],

    # === Layer 2: Tool definitions ===
    tools=[
        {"name": "WebFetch", "description": "...", "input_schema": {...}},  # ~200 token
        {"name": "Write",    "description": "...", "input_schema": {...}},  # ~150 token
        # 共 6 个 tool ≈ 1100 token
    ],

    messages=[
        # === Layer 3: Memory / 历史对话 ===
        {"role": "user",      "content": "前 7 天已挑过的 job ID 列表..."},  # ~300 token
        {"role": "assistant", "content": "记下了"},

        # === Layer 4: Retrieved context ===
        {"role": "user", "content": [
            {"type": "text", "text": "LinkedIn 抓回的 30 个 job 全文："},
            {"type": "text", "text": "<job1>...</job1><job2>...</job2>"}  # ~12000 token
        ]},

        # === Layer 5: User input（这次 task 的实际指令）===
        {"role": "user", "content": "从上面 30 个 job 里挑 3 个："
                                    "1 aspirational / 1 actionable / 1 special。"
                                    "输出 JSON 严格匹配 ${OUT} 文件 schema。"}  # ~80 token
    ]
)

Total context here lands around 14500 tokens. Prompt engineering only cares about that last user input — 80 tokens, 0.5%. The other 99.5% is context engineering territory.

Layer by Layer

Layer 1: System instruction — Role + Invariant Rules

What goes in: model role, rules that never change (output format, prohibited actions, token limits), long descriptions worth caching (reference docs, style guides).

Tune: must stay stable — once changed, cache invalidates entirely. Anthropic prompt cache is 5-minute TTL, reuse requires system block stays the same (docs). Add cache_control: ephemeral and system drops to 10% billing on reused calls.

Debug: system alone + minimal user input, see if model acts in role. Change system and output is identical — system isn't taking effect, usually placed wrong (should be system but ended in user).

Layer 2: Tool definitions — The Tool Menu

What goes in: each function calling / MCP tool's name + description + input_schema, including "when to use" (write into description).

Tune: each tool schema 100-300 tokens. 15 tools ≈ 3000 tokens, all fight for context space. Claude Code on MCP can pull 17 servers × N tools — that's why most tools are deferred (loaded on demand via ToolSearch).

Debug: cut tool list to 1, see if model still calls tools randomly. If yes — description isn't clear, model is "guessing" (classic context pollution).

Layer 3: Memory / chat history — What Happened Before

What goes in: previous N turns (usually summarized), scratchpad of agent task steps, long-term memory (user preferences).

Tune: layer where context budget blows first. 100 turns × 1500 tokens = 150K, eats 75% of a 200K window. Needs three-layer memory architecture (Chapter 6): scratchpad / working / persistent, each with its own compression strategy.

Debug: cut history to last turn. Can model still finish? Yes — history was redundant. No — you need better summarization, not deletion.

Layer 4: Retrieved context — Facts Stuffed in on the Fly

What goes in: RAG passages, WebFetch page content, prior tool call outputs.

Tune: biggest token volume, most volatility. 20 passages × 500 chars = 10K tokens. Lost in the Middle (Liu et al. 2023, arXiv:2307.03172): docs in the middle the model basically can't see (Chapter 3 details).

Debug: inspect what model cited vs retrieved. 10 retrieved, 0 cited — selection failed, add rerank (Chapter 5).

Layer 5: User input — This Turn's Actual Instruction

What goes in: what the user typed + task goal + output requirements.

Tune: traditional prompt engineering turf. Difference from the other 4: changes every call, can't be cached.

Debug: lock the first 4 layers, change user input wording, watch output shift — standard prompt engineering A/B setup.

Anthropic's 5 Agent Patterns = 5 Kinds of Context Engineering

Building Effective Agents (Anthropic, 2024-12-20) breaks agentic systems into 5:

Engineering decision behind every pattern isn't prompt wording. It's how to slice, pass, collect context.

JR Real Case: classroom-deck-builder skill

JR's classroom-deck-builder skill (.claude/skills/classroom-deck-builder/) compiles a Quest lesson into a "live class" (slide + voiceover + teaching gestures).

Started in "one-shot mode" — one LLM call generated N slides + voiceover. Slide-to-slide narrative broke, voiceover tone inconsistent. Rewritten into two stages:

Stage 1: outline 阶段
  Context = lesson goal + style guide
  → 输出 N 个 SceneOutline（仅标题 + 一句话指令）

[人工审 outline，可改可删]

Stage 2: finalize 阶段（SSE 流式）
  Context = lesson goal + style guide + 已批准的 outline 全集
  → 逐个 scene 生成完整 slide + 配音

Stage 2 packs in one extra layer that Stage 1 lacks — "the full approved outline". Each scene knows its position in the overall narrative. One-shot mode lacks that, so narrative breaks.

Textbook context engineering: don't change prompt wording. Change how context flows between LLM calls.

Single-Layer Context vs Layered Context — Trade-off

Most people dump all 5 layers into one prompt string in their first LLM app. It runs but debugging is hell. Layered processing needs more engineering but you can tune each layer independently.

JR rule: more than 3 LLM calls or more than one maintainer — must be layered.

Takeaway

Prompt engineering cares about 1 / 5 (user input). Context engineering cares about 5 / 5 — plus how layers pass, cache, isolate. 80% of production LLM app engineering lives in the first 4 layers.

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References

1. Anthropic. (2024-12-20). Building Effective Agents.
2. Anthropic. Prompt caching docs — 5-minute TTL ephemeral cache.
3. Anthropic. Cookbook — agent patterns.
4. Anthropic. Tool use docs.
5. Liu et al. (2023-07-06). Lost in the Middle. arXiv:2307.03172.

Production case: JR Academy classroom-deck-builder skill (.claude/skills/classroom-deck-builder/) — two-stage pipeline implements context isolation.