template-pipeline-debugging

# Pipeline debugging ## Natural invoke - "My pipeline failed at PDF render for template_code_project" - "Project Analysis finishes in under a second with no figures — help debug" - "run.sh --pipeline failed; what's the first real error?" - "Resume from checkpoint after fixing project tests" ## Inputs to confirm - **Project** — from [`docs/_generated/active_projects.md`](../../_generated/active_projects.md); infer from context if obvious. - **Invocation** — full vs `--core-only`, `--resume`, `--skip-infra`, multi-project. - **Failing stage** — if unknown, reproduce first. ## Workflow 1. **Reproduce** — re-run the failing invocation verbatim; capture full stderr/stdout and exit status. Quote the **first** real error, not the last line. Name the failing stage (setup, infra tests, project tests, analysis, render, validate, LLM review, LLM translations, copy). 2. **Isolate** — run that stage's underlying command directly (pytest target, analysis script, validation CLI, renderer). Use `--resume` to skip good upstream stages while iterating. 3. **Classify** — dependency/uv gap, missing system tool (LaTeX/pandoc-crossref), nondeterministic input, coverage gate, undefined citation/cross-ref, thin-orchestrator violation (logic in `scripts/` not `src/`), or logic bug. When **Project Analysis** completes in under a second with no figures, treat as import/dependency failure and isolate via `scripts/pipeline/stage_02_analysis.py`. Trace where bad state **enters**; fix at ingestion....