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Top-level skill for the research template infrastructure layer. Use in Cursor, Claude Code, or similar agents when editing or importing anything under infrastructure/, understanding the two-layer architecture, or wiring build/validation/rendering/publishing. Covers module discovery, import patterns, thin orchestrators, per-subpackage SKILL.md paths, and .cursor/skill_manifest.json (see infrastructure.skills).
Passed 21 of 22 test cases with the skill, and 5 of 22 without it.
and 15 more in the full report
16 fixed5 passed either way1 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
This benchmark measured an earlier version of the skill.
One of 16 test cases the skill fixed. Same model, same prompt, with and without the skill.
I need to run the execute_pipeline.py script for project 'template_code_project' focusing strictly on core functionality. What CLI command runs this orchestrator script with the core-only flag?
| Checked | Without skill | With skill |
|---|---|---|
| The response executes 'uv run python scripts/runner/execute_pipeline.py --project template_code_project --core-only' for pipeline execution. | Missed | Passed |
The instructions your model reads when the skill loads.
The infrastructure/ package provides generic, reusable functionality for research projects. All business logic resides here (Layer 1) or in project-specific src/ (Layer 2). Scripts are thin orchestrators that coordinate these modules.
.cursor/skill_manifest.json lists every discovered first-party skill (name, description, path); regenerate with uv run python -m infrastructure.skills write.infrastructure/**/SKILL.md, scripts/**/SKILL.md, public projects/templates/**/SKILL.md including .agents/skills, public resource-pool template skills under fonds/templates/, rules/templates/, and tools/templates/, plus .cursor/skills/.@infrastructure/SKILL.md or @infrastructure/<module>/SKILL.md to load context; pair with the matching AGENTS.md for API tables.SKILL.md has YAML name and description for routing (see also the table in infrastructure/README.md).| Module | Purpose | Key Imports |
|---|---|---|
autoresearch/ | Deterministic research plans, stage-gate readiness, artifact/evidence reports | build_autoresearch_plan, validate_autoresearch_plan |
benchmark/ | Deterministic benchmark manifests and public exemplar readiness scoring | run_benchmark_manifest, score_project_against_manifest |
config/ | Repo defaults (.env.template, secure_config.yaml) | (YAML/dotenv; use core.config_loader) |
core/ | Logging, config, exceptions, pipeline, progress, retry, security | get_logger, load_config, PipelineExecutor |
docker/ | Dockerfile, docker-compose.yml for container runs | (CLI / docs/CLOUD_DEPLOY.md) |
validation/ | PDF/Markdown/output validation, link checking, audits | validate_pdf_rendering, validate_markdown, verify_output_integrity |
rendering/ | Multi-format output (PDF, HTML, slides) | RenderManager, RenderingConfig |
documentation/ | Figure/image management, markdown integration, glossary | FigureManager, ImageManager, MarkdownIntegration |
llm/ | Local LLM integration via Ollama | LLMClient, OllamaClientConfig, detect_repetition, check_format_compliance |
methods/ | Methods orchestration plans over DAG, manuscript methods, artifacts, and evidence | build_methods_orchestration_plan, validate_methods_orchestration_plan |
orchestration/ | Pipeline CLI, menu, project discovery, stage logging, secure-run wrapper (backs run.sh/secure_run.sh) | build_parser, PipelineRunner, validate_project_slug, run_secure_pipeline |
publishing/ | Academic publishing (DOI, citations, Zenodo, arXiv) | publish_to_zenodo, generate_citation_bibtex |
reference/ | BibTeX I/O (read / write / convert) matching references.bib syntax | parse_bibfile, render_database, paper_to_bibentry |
search/ | Paperclip-style multi-source literature search (arXiv, Crossref, local, Paperclip) | LiteratureClient, SearchQuery, ArxivBackend, CrossrefBackend |
prose/ | Prose analysis (readability, structure, editorial quality, manuscript reports) | analyze_manuscript, compute_metrics, analyze_structure, analyze_quality |
reporting/ | Pipeline reports, error aggregation, dashboards | generate_pipeline_report, get_error_aggregator |
scientific/ | Benchmarking, numerical stability, scientific templates | benchmark_function, check_numerical_stability |
sia/ | SIA harness: task layout, fixture replay loop, evaluation runner | validate_task_dir, run_sia_loop, run_evaluation |
project/ | Multi-project discovery and validation | discover_projects, validate_project_structure |
skills/ | Enumerate and parse SKILL.md; maintain Cursor manifest | discover_skills, write_skill_manifest |
steganography/ | Cryptographic PDF watermarking and verification | SteganographyProcessor, SteganographyConfig, embed_steganography |
core/telemetry/ | Unified pipeline telemetry (stage resources + diagnostics, JSON/text reports) | TelemetryCollector, TelemetryConfig |
test cases passed, vs 5 / 22 without
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