template-workflows v1.2.0A

Immutable. This exact content is served forever at /api/v1/blob/590ef88ee2ebc9fd.

---
name: template-workflows
description: |
  Router and workflow hub for the Research Project Template — code, tests, manuscripts,
  pipeline, validation, docs, and reproducibility. USE WHEN the user wants to audit the
  repo, debug ./run.sh or execute_pipeline.py, add a feature, write tests, scaffold a
  manuscript, verify claims, fix cross-references, run validation gates, refactor, or
  prepare a Zenodo release, discover relevant template skills, improve agent routing,
  research a topic, write/review/revise a paper, or run a research-to-publication workflow
  — even if they never say "prompt", "skill", or docs/prompts.
  Also USE WHEN intent is ambiguous ("something wrong with my manuscript", "full health
  check", "fix the pipeline") — pick ONE child skill from the routing table and follow it.
  Do NOT use for generic homework, unrelated app security scans, or casual PDF summarization.
metadata:
  version: "1.2.0"
  last_updated: "2026-06-06"
  status: active
  data_access_level: raw
  task_type: open-ended
  modes:
    - router
  related_skills:
    - template-deep-research
    - template-academic-paper
    - template-academic-paper-reviewer
    - template-academic-pipeline
    - template-methods-orchestration
    - template-comprehensive-assessment
    - template-agentic-use
---

# Template workflow hub

When intent is clear, open the matching child `SKILL.md` directly. When ambiguous, use the routing table, then load exactly one child skill.

## Ambiguous routing

- **Broken refs / "manuscript wrong"** — ask whether the failure is pipeline (validate/render) or prose (tokens/registry). Route to [manuscript-cross-references](manuscript-cross-references/SKILL.md), [validation-quality](validation-quality/SKILL.md), or [manuscript-claim-verification](manuscript-claim-verification/SKILL.md). Do **not** open [code-development](code-development/SKILL.md).
- **Example:** "refs broken, not sure if pipeline or prose" → clarify stage vs registry; default to cross-refs when `[[FIG:]]` / `labels.yaml` mentioned.
- **Full health check with no symptom** → [comprehensive-assessment](comprehensive-assessment/SKILL.md).
- **Skill discovery / "make this repo more agentic"** → [agentic-use](agentic-use/SKILL.md).
- **Generic coding homework or unrelated app** → do not load template workflow skills.

## Routing table

| Symptom or goal | Child skill |
| --- | --- |
| Research question, literature review, fact check, systematic review | [deep-research/SKILL.md](deep-research/SKILL.md) |
| Draft, outline, revise, format, or disclose AI use in a manuscript | [academic-paper/SKILL.md](academic-paper/SKILL.md) |
| Peer review, methodology review, re-review, or calibration | [academic-paper-reviewer/SKILL.md](academic-paper-reviewer/SKILL.md) |
| Research → write → verify → review → revise → finalize | [academic-pipeline/SKILL.md](academic-pipeline/SKILL.md) |
| Methods, methodology, stage contracts, artifact/evidence wiring | [methods-orchestration/SKILL.md](methods-orchestration/SKILL.md) |
| Pipeline stage failed, stuck, or flaky | [pipeline-debugging/SKILL.md](pipeline-debugging/SKILL.md) |
| Regenerate-from-clean / determinism / double-run diff | [reproducibility-audit/SKILL.md](reproducibility-audit/SKILL.md) |
| Triple-check every manuscript claim; pre-submission | [manuscript-claim-verification/SKILL.md](manuscript-claim-verification/SKILL.md) |
| `[[FIG:]]` / `labels.yaml` registry audit | [manuscript-cross-references/SKILL.md](manuscript-cross-references/SKILL.md) |
| New manuscript + project from research brief | [manuscript-creation/SKILL.md](manuscript-creation/SKILL.md) |
| Literature search corpus synthesis (LLM blocks) | [literature-synthesis/SKILL.md](literature-synthesis/SKILL.md) |
| Full repo audit (tests, docs, manuscript, pipeline) | [comprehensive-assessment/SKILL.md](comprehensive-assessment/SKILL.md) |
| Skill inventory, agent onboarding, routing hardening, external skill review | [agentic-use/SKILL.md](agentic-use/SKILL.md) |
| Validation CLI, gates, markdown/PDF checks | [validation-quality/SKILL.md](validation-quality/SKILL.md) |
| New module or algorithm (thin orchestrator) | [code-development/SKILL.md](code-development/SKILL.md) |
| Tests under no-mocks policy | [test-creation/SKILL.md](test-creation/SKILL.md) |
| End-to-end feature across layers | [feature-addition/SKILL.md](feature-addition/SKILL.md) |
| Clean-break refactor with migration | [refactoring/SKILL.md](refactoring/SKILL.md) |
| New `infrastructure/*` package | [infrastructure-module/SKILL.md](infrastructure-module/SKILL.md) |
| AGENTS.md / README.md for a directory | [documentation-creation/SKILL.md](documentation-creation/SKILL.md) |

**New project scaffold (one-shot):** [docs/guides/new-project-one-shot-prompt.md](../guides/new-project-one-shot-prompt.md) — not a separate skill; link from manuscript-creation when starting from zero.

## Conventions (all children)

- Project names: [`docs/_generated/active_projects.md`](../_generated/active_projects.md) — never hard-code rotating paths.
- Business logic: `infrastructure/` or `projects/<name>/src/` only; scripts orchestrate.
- Tests: no mocks; infra ≥60%, project ≥90% unless CI documents an exception.
- Metrics: measure with pytest or cite [`docs/_generated/COUNTS.md`](../_generated/COUNTS.md).

## Discovery

These skills are indexed in `.cursor/skill_manifest.json` (`uv run python -m infrastructure.skills write`). Human index: [README.md](README.md).

## External design note

This workflow set includes original, template-native adaptations of patterns observed in
[Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills):
mode registries, data-access labels, provenance checkpoints, and benchmark disclosure. ARS
content is not vendored or copied because ARS is CC-BY-NC-4.0 while this repository is
Apache-2.0.

Several ARS ideas are now backed by **deterministic infrastructure** (code, not
prompts), in keeping with the template's "Code Before Prompts" principle:

- **Reference-existence verification** — `infrastructure/reference/verification`
  resolves each cited DOI/arXiv id/title against Crossref/OpenAlex/arXiv and
  flags fabricated/mismatched/anachronistic citations. Offline-first with a
  persistent SQLite cache; live resolution is opt-in. This is the anti-leakage
  tier-0 gate distilled from the ARS hallucination taxonomy and verification
  cache. CLI: `python -m infrastructure.reference.verification verify <bib>`.
- **AI-writing fingerprint scan** — `infrastructure/validation/content/ai_writing.py`
  scores em-dash density, stock LLM phrasing, and sentence-length burstiness.
  CLI: `python -m infrastructure.validation.cli prose-quality <path>`.

These run fully offline in CI; only the optional `--live` resolution pass
touches the network.