docxology/template

Orchestrate continual learning by delegating transcript mining to agents-memory-updater and writing durable memory to local JSON (never root AGENTS.md Learned sections). USE WHEN continual learning, mine prior chats, maintain agent memory, or the stop hook triggers this skill.

Open Gauss in this workspace is the math-inc/OpenGauss gauss CLI for Lean session tooling—not Huawei OpenGauss DBMS. See docs/reference/opengauss-naming.md; for the public Lean exemplar see projects/templates/template_active_inference/lean/.

Skill for deterministic AutoResearch readiness planning. Use when adding, validating, or documenting opt-in autoresearch.yaml controls, stage-gate readiness, evidence-grounded claims, artifact readiness reports, or AutoResearchClaw-inspired workflow checks in template projects.

Deterministic benchmark harnesses for public template exemplars. Use when scoring generated project outputs against benchmark manifests, refreshing the default template smoke manifest, checking publication-readiness rubrics, or adding bounded no-network readiness checks for public template outputs.

Repository-scoped configuration for the template—environment variable templates and default secure/steganography YAML. Use when editing .env patterns, secure_config defaults, or cross-referencing project manuscript config overrides.

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).

Template-native manuscript planning, outline, drafting, revision, formatting, citation check, and AI-use disclosure routing. USE WHEN the user asks to write, outline, revise, format, or prepare a paper inside the Research Project Template.

Read-only manuscript review, methodology review, re-review, and calibration workflow for template projects. USE WHEN the user asks for peer review, referee-style critique, methods/statistics review, or verification that revisions addressed prior comments.

Research-to-publication orchestrator for template projects: research, write, verify, review, revise, reproduce, validate, and finalize. USE WHEN the user wants the whole paper workflow or enters midstream with an existing paper or reviewer comments.

Agentic-use and skill-routing workflow for the Research Project Template. USE WHEN discovering relevant skills, making template easier for agents to navigate, auditing docs/prompts skill coverage, checking .cursor/skill_manifest.json, evaluating external skills, reviewing external agentic operating models such as Steward OS, AutoResearch CLI, or LEANN, or improving agent onboarding/routing without changing project behavior.

Standards-compliant code for the Research Project Template — infrastructure or project src/, thin orchestrators, type hints, no mocks. USE WHEN implementing an algorithm, utility, analysis method, optimizer, new module in projects/*/src or infrastructure/, or user says add code following template architecture — even without docs/prompts. Not for end-to-end feature spanning manuscript + pipeline (use template-feature-addition).

Full checkout audit for the Research Project Template — tests, architecture, docs, manuscript, pipeline. USE WHEN user asks for comprehensive assessment, full repo review, health check across projects, audit everything, or pre-merge sanity sweep for template exemplars — even without naming docs/prompts or a skill. Not for single failing stage only.

Template-native research intake, literature search, source verification, synthesis, fact-checking, and systematic-review planning. USE WHEN the user asks to research a topic, build a literature corpus, fact-check claims, prepare a PRISMA-style review, or clarify a research question before manuscript work.

Author or refresh AGENTS.md and README.md for template directories — accurate commands, Mermaid where helpful, link _generated/active_projects.md. USE WHEN folder needs AGENTS, README audit, doc contract fix, or signposting after code change — even without documentation_creation prompt.

End-to-end feature work across src/, scripts/, tests/, manuscript, and docs for the Research Project Template. USE WHEN adding a pipeline-visible feature, new analysis stage, manuscript-facing output, or cross-layer integration — even without feature_addition prompt.

Add or extend generic infrastructure/ packages — Layer 1 modules with SKILL.md, AGENTS.md, tests in tests/infra_tests/, 60% coverage. USE WHEN new reusable package under infrastructure/, extending validation/rendering/llm, or skill manifest entry — even without infrastructure_module prompt.

LLM prompt blocks for per-paper and corpus literature synthesis after a search pipeline. USE WHEN synthesizing arXiv/Crossref results, writing per-paper notes, thematic clusters, gap analysis from a literature corpus, or wiring template_search_project synthesis — even without naming infrastructure.llm templates.

Triple-pass verification of every manuscript claim against code, data, refs, and renderer; repair prose while staying renderable. USE WHEN pre-submission, pre-Zenodo, pre-arXiv, abstract numbers disagree with CSV, citations do not support sentences, or user asks to triple-check / verify every claim — even without docs/prompts. Not for casual PDF summary.

Scaffold a research manuscript and project layout from a research brief — sections, config.yaml, src/, scripts/, tests. USE WHEN starting a new paper, new projects/ tree, manuscript from topic description, or aligning with template_code_project exemplar — even without copy-paste prompts.

Audit or author registry-driven manuscript cross-refs — labels.yaml, [[FIG:]], [[THMREF:]], [[VAR:]] tokens. USE WHEN fixing figure/equation/theorem numbering, orphan registry keys, hard-coded "Theorem 7.3" in prose, or [[MISSING:]] injection failures — even for Pandoc projects that also use a YAML registry.

Repo-wide methods orchestration workflow for the Research Project Template. USE WHEN the user asks to add, audit, improve, or validate methods, methodology, method contracts, stage-to-method wiring, artifact/evidence provenance, or orchestration across template projects.

Systematic pipeline DAG failure triage for the Research Project Template. USE WHEN ./run.sh or execute_pipeline.py fails, a stage stalls (setup, tests, analysis, render, validate, LLM, copy), pytest/coverage gate fails mid-pipeline, PDF render or validate breaks, Project Analysis finishes too fast with no figures, or user says pipeline debug, stage failed, resume checkpoint, core-only triage — even without naming this skill or docs/prompts.

Clean-break refactors with migration for the Research Project Template — move logic to src/, split modules, rename APIs with test updates. USE WHEN restructuring code, extracting modules, removing duplication, or migration without behavior change.

Deterministic reproducibility audit — fixed seeds, regenerate-from-clean, double-run diff before Zenodo/arXiv/release. USE WHEN outputs drift between runs, "worked on my machine", need regenerate-from-clean proof, or pre-release reproducibility check — even without naming docs/prompts.

Create pytest suites under the no-mocks policy — real data, temp files, subprocess, pytest-httpserver. USE WHEN adding tests, raising coverage, testing new src/ module, or user forbids mocks.

Run validation CLI, prerender, markdown/PDF/integrity gates, and QA workflows for the Research Project Template. USE WHEN validate manuscript, check PDF for ?? refs, prerender gate, link checker, output integrity, or pre-commit validation — even without validation_quality prompt.

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, review external agentic operating models or retrieval references such as Steward OS, AutoResearch CLI, or LEANN, 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.