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Operating-system distillation of LlamaIndex — the leading RAG / document-agent framework. Activate when the calling agent must build, debug, harden, or evaluate a Retrieval-Augmented Generation pipeline over unstructured/private data, decide between RAG primitives (Index types, retrievers, query engines, routers, agents), or pick LlamaIndex vs LangChain / Haystack / raw vector store for a coding task. Encodes the 5-layer mental model (Documents → Nodes → Indices → Retrievers → Query Engines / Response Synthesizers), the canonical RAG bootstrap SOP from baseline `VectorStoreIndex` through hybrid + reranker + eval-loop hardening, the official 13-failure-mode checklist, and 5 dilemma cases distilled from docs, GitHub issues, and 2025 production post-mortems.

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Decision SOP for serving LLMs with vLLM. Covers PagedAttention mental model, quantization/parallelism/batching tradeoffs, OOM triage, and when NOT to use vLLM. Activates when a coder-agent is choosing or tuning an inference engine, debugging vLLM throughput/latency/OOM, or comparing vLLM against TGI/SGLang/TensorRT-LLM/llama.cpp.

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Project-kickoff rubric for the self-host vs managed-cloud decision — when is running your own inference engine / LLM platform worth the ops cost vs paying per-token for a managed API? Decide on two axes — VOLUME (a cost-crossover slider) and COMPLIANCE (a hard gate). Use at kickoff when choosing where to run inference, or when cost / data-residency pressure forces a re-evaluation.

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Decision protocol for building, debugging, and operating LangGraph-based agent systems. Activates when a coder agent is asked to design a stateful LLM workflow, add human-in-the-loop, choose a multi-agent pattern (supervisor / swarm / hierarchical), pick a checkpoint backend, or migrate a fragile chain into a durable graph. LangGraph is positioned by its maintainers as a "low-level orchestration framework for building, managing, and deploying long-running, stateful agents" — this skill encodes the *when* and *why*, not the API.

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Cross-framework enhancement overlay for choosing a multi-agent topology BEFORE writing any agent. A binary-question rubric — is single-agent + tools enough? do agents need to know about each other? does the output need one voice? — maps the answer to single-agent / supervisor / swarm / sequential / hierarchical. Activates when a coder agent is tempted to "split the work into roles" or reaches for a multi-agent framework. Encodes the *selection rubric* that the per-framework skills assume but never surface. Search keywords: when to use multi-agent, single vs multi agent, do I need multiple agents, supervisor vs swarm, multi-agent vs single agent, agent team design.

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Enhancement overlay — version the WHOLE deployable LLM-app artifact as one bundle: prompts + compiled programs + model snapshot pins + retrieval config + eval-set version, versioned together so a deploy is reproducible and rollback is atomic. Activate when preparing to deploy an LLM app, when asking "what exactly is running in prod right now?", when a deploy must be reproducible months later, or when an incident needs a clean rollback. The core reframe: an LLM app artifact is NOT an ML model — it is a manifest over many independently-mutable parts, not one weights file. Do NOT activate for one-off prompt edits with no deploy, for a single-component demo, or where a vendor owns the whole prompt lifecycle. For versioning ONE compiled prompt use [[agentsop-per-model-artifacts]]; for the CI comparison mechanism use [[agentsop-regression-gate]]. Search keywords: prompt versioning, reproducible deploy, what is running in prod, rollback LLM app, model pinning, prompt registry, version prompts and config.

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Re-ingest-correctness SOP for production RAG. Activate when a calling agent builds, reviews, or debugs an ingestion pipeline that runs more than once over a changing corpus — scheduled re-index, incremental updates, CI re-ingest, or a "retrieval has duplicates / shows deleted docs" bug. Encodes the rule — **ingestion must be idempotent: a document's content hash decides insert/update/skip, so re-running over unchanged docs is a no-op** — plus the docstore + doc-hash upsert machinery (LlamaIndex `IngestionPipeline` + `DocstoreStrategy`), the delete-propagation problem, and cross-framework equivalents (LangChain `index()` + `RecordManager`, manual hash table). ENHANCE overlay over [[llamaindex]]: the IngestionPipeline exists in the base skill but the re-ingest-correctness contract is not surfaced.

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Decomposed, multi-criteria metric design for LLM pipelines. The metric IS the model — change the metric and the optimizer changes behavior. Decompose by default; bool during compile, float during eval; calibrate against human; mitigate judge bias. Search keywords: LLM-as-judge, llm as judge, eval metric, evaluation score, scoring function, rubric, RAGAS, G-Eval, judge bias, verbosity bias, how to evaluate LLM output.

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Pick an LM output format per (task x consumer x model) rather than by reflex: different formats carry different cognitive load (e.g. code-in-JSON makes the same model write worse code than plain-text+diff, while asking for prose when you need a typed object fails the other way). Use when designing or debugging an LM's output schema, choosing between plain text / diff / JSON / tool-call / grammar-constrained output, or when a model's quality drops after wrapping its output in a structured format.

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Universal discipline for any LM-driven loop — agent retries, plan-act-observe, multi-agent handoffs, optimiser passes, test-fix cycles. Encodes the one rule every framework documents quietly and every team relearns expensively: the LM in the loop is NEVER a reliable terminator. Termination must be provided by an explicit counter + exit predicate + stagnation signal + escalation path that live OUTSIDE the LM's control. This is a tool- level, framework-agnostic skill. It maps onto LangGraph (recursion_limit + state counter + interrupt), CrewAI (max_iter + max_rpm + human_input), Claude / OpenAI SDKs (max_iterations + tool_use_budget), DSPy (declared evaluation budget), Aider (REPL + explicit retry cap), and AutoGen (max_consecutive_auto_reply). Search keywords: infinite loop, recursion limit, recursion_limit, GraphRecursionError, max iterations, max_iter, agent stuck, agent won't stop, runaway agent, ReAct loop not terminating, agent repeating itself.

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Cross-engine decision rubric for self-hosting or recommending an LLM serving stack. Picks among vLLM, SGLang, TensorRT-LLM, TGI, llama.cpp, Ollama, and MLX as a function of (hardware × workload × constraint), not "which is fastest". Activates whenever a coder-agent must choose, defend, or migrate a serving runtime.

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Build and govern a 50-200 example domain-specific held-out benchmark sampled from real traffic. Distinct from public benchmarks (MMLU/HumanEval/GSM8K via lm-evaluation-harness) which measure GENERAL capability. Only a held-out domain set predicts whether THIS system works on YOUR data. Collect real examples, label, hold out (never train/prompt on it), size 50-200, version it, refresh on drift.

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ENHANCE overlay on [[dspy]] — the upfront rubric for choosing a reasoning SHAPE (Predict / ChainOfThought / ReAct / ProgramOfThought) BEFORE you write a prompt or pick an optimizer. The local `dspy` skill lists the modules but never surfaces the *selection criterion*: reasoning shape is chosen by task structure, not by reflexively defaulting to CoT. Activate every time a new LM-calling node/step is added to a pipeline. Do NOT activate for one-shot prompts, optimizer/teleprompter choice (that is the dspy SOP's job), or non-LM control flow. Search keywords: chain of thought vs ReAct, when to use CoT, reasoning type, ReAct vs CoT vs PoT, which dspy module, predict vs chain of thought.

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Operating SOP for DSPy (Stanford NLP) — the declarative framework for "programming, not prompting" language models. Activate when the user says any of: "use DSPy", "compile a prompt", "optimize prompts/programs", "MIPRO/MIPROv2", "BootstrapFewShot", "GEPA", "Signatures + Modules", "teleprompter", "auto-tune prompts for a different LM", or whenever a brittle hand-crafted prompt pipeline needs to be turned into a *compiled*, measurable, swappable program. Do NOT activate for one-shot prompt tweaks, no-metric exploratory work, or pipelines where prompts must remain human-authored verbatim — use raw prompting or LangChain templates instead.

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Screens biomedical / life-science papers for signs of data fabrication, image manipulation, and statistical anomalies, using the detection techniques distilled from the field's canonical exposure platforms (PubPeer, Data Colada, Science Integrity Digest, For Better Science) and tools (ImageTwin/Proofig, statcheck, GRIM/GRIMMER, Problematic Paper Screener, Seek & Blastn). Use when asked to check a paper/figure for image duplication, blot splicing, impossible statistics, paper-mill or tortured-phrase signals, research integrity, or "is this data faked"; or when a user shares a figure, Western blot, supplementary dataset, or DOI and asks whether it looks manipulated. Reports observable anomalies as questions for clarification — it never accuses anyone of fraud.

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Split a multi-call LM workflow by cognitive load, not by accuracy: let one strong model make the few reasoning decisions and a cheap model do the many mechanical executions (Aider architect+editor, DSPy optimizer-LM vs task-LM, vLLM speculative draft+target, LangGraph supervisor+worker are the same shape). Use when designing or cost-optimizing a pipeline that calls an LM many times, when deciding which steps need a strong reasoner vs a cheap executor, or when adding an escalation valve for when the cheap tier degrades. Search keywords: reduce LLM cost, cheaper model, lower token cost, model cascade, route to cheap model, strong model plus cheap model, LLM cost optimization.

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SOP for building LLM applications on Dify — visual workflow + chatflow + agent + RAG knowledge base + plugin marketplace + observability, self-hostable. Use when shipping LLM apps fast with a "no-code to pro-code" gradient, especially when non-engineers need to co-author the flow.

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Neutral, framework-agnostic decision tree for project kickoff: "which agent / RAG / LLM framework should I reach for?" Synthesizes the ecosystem sections of 7 landmark-project SOPs (LangGraph, LlamaIndex, DSPy, CrewAI, vLLM, Aider, Dify) into one layered rubric. Core stance: frameworks are LAYERS, not competitors — a real project usually combines DSPy (compile) + LlamaIndex (retrieve) + LangGraph (orchestrate) + vLLM (serve), and you choose ONE per layer, not one to rule all. Use when starting any LLM/agent/RAG project, or whenever the "which framework?" question is asked. Deliberately neutral — unlike vendor docs and the LangChain-biased `framework-selection` on skill.sh, this skill has no horse in the race.

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Decision protocol for wrapping a REST / GraphQL / RPC API as a tool an LLM agent can call. The load-bearing premise: the *tool surface* is an LM-friendly subset of the *API surface* — one tool per user intent, not one per endpoint. Activates when a coder agent must expose an external HTTP API to a model (function calling, tool_use, MCP, LangChain `@tool`, CrewAI `BaseTool`). Encodes the *what to surface, how to name, how to shape, how to fail* — not any single framework's API. ~80% of agent tools in production are HTTP wrappers; this is the SOP for getting them right.

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Decision protocol for the map-reduce / dynamic fan-out pattern in LM pipelines — "given list L, run f(item) for each item in parallel, then combine". Activates when the coder agent is about to process N items with N LM calls (per-doc summarize, per-query retrieve, per-candidate rank, parallel tool fan-out). Encodes the *when*, *how many at once*, *what to do when one fails*, and *how to reduce* — not the API of any single framework. Cross-framework: LangGraph `Send`, CrewAI parallel tasks / Flow, `asyncio.gather`, `ThreadPoolExecutor`, LlamaIndex batch retrieval.

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Build a held-out eval set, run it on every prompt/model change, and block regressions in CI. An LM change is a code change — gate it with a test suite (eval set + metric + threshold). Cross-framework SOP not surfaced by any single base skill.

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Symbol-level code context for LLM coder-agents: tree-sitter extracts symbols, PageRank ranks them over the cross-file reference graph, and the top class/function signatures are fed to the LLM as a token-budgeted read-only map (not RAG, no vector index, human-auditable). Use when an agent must locate the right files in a large/multi-file repo, when builds/refreshes/scopes a repo-map, or when "model edits the wrong file" needs fixing.

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Decide where to enforce structured LM output (constrain at decode time with Outlines vs validate-and-retry with Instructor vs grammar with Guidance) and which failure stance to take (Assert/hard-fail vs Suggest/soft-retry). Use when an LM's output is parsed or typed by downstream code and you must pick one enforcement library plus its failure handling, when malformed output is burning tokens on retries, or when choosing between decode-time vs validation-time constraints for local vs API models.

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Tool skill — the *first move* in any LM-debugging session: dump the actual rendered prompt the framework sent to the model, before changing anything else. Activate when an LM call produced an unexpected output (wrong answer, schema violation, refusal, truncation, cost spike, latency spike, infinite loop, "model got dumber after upgrade"). The skill enforces a 30-second inspect step BEFORE any prompt edit, model swap, retry, or temperature tweak. Cross-framework cheat sheet: DSPy `inspect_history`, LangGraph `get_state_history`, CrewAI `step_callback`, LangChain `set_debug`/`set_verbose`, Aider `/diff`+`--verbose`, raw OpenAI/Anthropic via `OPENAI_LOG=debug`/`ANTHROPIC_LOG=debug` or HTTPX event hooks. Do NOT activate for first-time prompt authoring, exploratory prompt design, or non-LM bugs.

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