Full-stack diagnostic for agent and LLM applications. Audits the 12-layer agent stack for wrapper regression, memory pollution, tool discipline failures, hidden repair loops, and rendering corruption. Produces severity-ranked findings with code-first fixes. Essential for developers building agent ap

Agent Architecture Audit A diagnostic workflow for agent systems that hide failures behind wrapper layers, stale memory, retry loops, or transport/rendering mutations. When to Activate MANDATORY for: Releasing any agent or LLM powered application to production Shipping features with tool calling, memory, or multi step workflows Agent behavior degrades after adding wrapper layers User reports "the agent is getting worse" or "tools are flaky" Same model works in playground but breaks inside your wrapper Debugging agent behavior for more than 15 minutes without finding root cause Especially critical when: You've added new prompt layers, tool definitions, or memory systems Different agents in your system behave inconsistently The model was fine yesterday but is hallucinating today You suspect hidden repair/retry loops silently mutating responses Do not use for: General code debugging — use agent introspection debugging Code review — use language specific reviewer agents Security scanning — use security review or security review/scan Agent performance benchmarking — use agent eval Writing new features — use the appropriate workflow skill The 12 Layer Stack Every agent system has these layers. Any of them can corrupt the answer: Layer What Goes Wrong 1 System prompt Conflicting instructions, instruction bloat 2 Session history Stale context injection from previous turns 3 Long term memory Pollution across sessions, old topics in new conversations 4 Distillation Compressed artifacts re entering as pseudo facts 5 Active recall Redundant re summary layers wasting context 6 Tool selection Wrong tool routing, model skips required tools 7 Tool execution Hallucinated execution — claims to call but doesn't 8 Tool interpretation Misread or ignored tool output 9 Answer shaping Format corruption in final response 10 Platform rendering Transport layer mutation (UI, API, CLI mutates valid answers) 11 Hidden repair loops Silent fallback/retry agents running second LLM pass 12 Persistence Expired state or cached artifacts reused as live evidence Common Failure Patterns 1. Wrapper Regression The base model produces correct answers, but the wrapper layers make it worse. Symptoms: Model works fine in playground or direct API call, breaks in your agent Added a new prompt layer, existing behavior degraded Agent sounds confident but is confidently wrong "It was working before the last update" 2. Memory Contamination Old topics leak into new conversations through history, memory retrieval, or distillation. Symptoms: Agent brings up unrelated past topics User corrections don't stick (old memory overwrites new) Same session artifacts re enter as pseudo facts Memory grows without bound, degrading response quality over time 3. Tool Discipline Failure Tools are declared in the prompt but not enforced in code. The model skips them or hallucinates execution. Symptoms: "Must use tool X" in prompt, but model answers without calling it Tool results look correct but were never actually executed Different tools fight over the same responsibility Model uses tool when it shouldn't, or skips it when it must 4. Rendering/Transport Corruption The agent's internal answer is correct, but the platform layer mutates it during delivery. Symptoms: Logs show correct answer, user sees broken output Markdown rendering, JSON parsing, or streaming fragments corrupt valid responses Hidden fallback agent quietly replaces the answer before delivery Output differs between terminal and UI 5. Hidden Agent Layers Silent repair, retry, summarization, or recall agents run without explicit contracts. Symptoms: Output changes between internal generation and user delivery "Auto fix" loops run a second LLM pass the user doesn't know about Multiple agents modify the same output without coordination Answers get "smoothed" or "corrected" by invisible layers Audit Workflow Phase 1: Scope Define what you're auditing: Target system — what agent application? Entrypoints — how do users interact with it? Model stack — which LLM(s) and providers? Symptoms — what does the user report? Time window — when did it start? Layers to audit — which of the 12 layers apply? Phase 2: Evidence Collection Gather evidence from the codebase: Source code — agent loop, tool router, memory admission, prompt assembly Logs — historical session traces, tool call records Config — prompt templates, tool schemas, provider settings Memory files — SOPs, knowledge bases, session archives Use rg to search for anti patterns: Phase 3: Failure Mapping For each finding, document: Symptom — what the user sees Mechanism — how the wrapper causes it Source layer — which of the 12 layers Root cause — the deepest cause Evidence — file:line or log:row reference Confidence — 0.0 to 1.0 Phase 4: Fix Strategy Default fix order (code first, not prompt first): 1. Code gate tool requirements — enforce in code, not just prompt text 2. Remove or narrow hidden repair agents — make fallback explicit with contracts 3. Reduce context duplication — same info through prompt + history + memory + distillation 4. Tighten memory admission — user corrections agent assertions 5. Tighten distillation triggers — don't compress what shouldn't be compressed 6. Reduce rendering mutation — pass through, don't transform 7. Convert to typed JSON envelopes — structured internal flow, not freeform prose Severity Model Level Meaning Action critical Agent can confidently produce wrong operational behavior Fix before next release high Agent frequently degrades correctness or stability Fix this sprint medium Correctness usually survives but output is fragile or wasteful Plan for next cycle low Mostly cosmetic or maintainability issues Backlog Output Format Present findings to the user in this order: 1. Severity ranked findings (most critical first) 2. Architecture diagnosis (which layer corrupted what, and why) 3. Ordered fix plan (code first, not prompt first) Do not lead with compliments or summaries. If the system is broken, say so directly. Quick Diagnostic Questions When auditing an agent system, answer these: Question If Yes → 1 Can the model skip a required tool and still answer? Tool not code gated 2 Does old conversation content appear in new turns? Memory contamination 3 Is the same info in system prompt AND memory AND history? Context duplication 4 Does the platform run a second LLM pass before delivery? Hidden repair loop 5 Does the output differ between internal generation and user delivery? Rendering corruption 6 Are "must use tool X" rules only in prompt text? Tool discipline failure 7 Can the agent's own monologue become persistent memory? Memory poisoning Anti Patterns to Avoid Avoid blaming the model before falsifying wrapper layer regressions. Avoid blaming memory without showing the contamination path. Do not let a clean current state erase a dirty historical incident. Do not treat markdown prose as a trustworthy internal protocol. Do not accept "must use tool" in prompt text when code never enforces it. Keep findings direct, evidence backed, and severity ranked. Report Schema Audits should produce structured reports following this shape: Related Skills agent introspection debugging — Debug agent runtime failures (loops, timeouts, state errors) agent eval — Benchmark agent performance head to head security review — Security audit for code and configuration autonomous agent harness — Set up autonomous agent operations agent harness construction — Build agent harnesses from scratch

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