Template Refactoring
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Template Infrastructure Module
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Continual Learning
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.
Infrastructure Benchmark
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.
Infrastructure Overview
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 infrastruc…
Infrastructure Reference Citation
BibTeX read/write/convert that matches the syntax/semantics of projects/templates/template_code_project/manuscript/references.bib (consumed by Pandoc with --natbib -- see infrastructure/rendering/_pdf_combined_renderer.py). Provides BibEntry/BibDatabase models, parse_bibfile/render_database functions, paper_to_bibentry conversion from literature search results, generate_citation_key in the projec…
Telemetry
Unified pipeline telemetry — collects per-stage performance metrics (CPU, memory, I/O) and diagnostic events into structured reports (JSON, text).
Reference Verification
Deterministic anti-hallucination gate for cited references. Resolves each entry in a manuscript .bib file against Crossref, OpenAlex, and arXiv; flags fabricated (identifier resolves to nothing), mismatched (title/author/year disagree), unverifiable (no identifier), unchecked (offline cache miss — never silently OK), and anachronistic (future-dated) citations. Offline-first with a persistent SQLi…
Infrastructure Rendering
Skill for the rendering infrastructure module providing multi-format output generation including PDF manuscripts, HTML web pages, and Beamer/Reveal.js slides. Use when rendering research outputs, converting markdown to PDF, generating slides, or configuring LaTeX rendering.
Infrastructure Doctor
Skill for the doctor infrastructure module providing repository-level diagnostics and safe, reversible automated repair. Use when the local checkout is acting up, before opening a bug, when onboarding a fresh clone, or as a periodic health probe. Every mutation is backed up under .doctor/backups/ and journalled in .doctor/actions.jsonl so any change can be undone byte-for-byte.
Template Code Development
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Template Manuscript Claim Verification
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Infrastructure Search
Discovery utilities. Hosts three subpackages — `literature` for Paperclip-style multi-source academic search across arXiv, Crossref, local JSON corpora, and (opt-in) the Paperclip API, with deterministic JSON caching, a `LiteratureClient` aggregator, normalised `Paper` records, and a CLI; `exa` for Exa-backed general web search, content extraction, grounded answers, and find-similar via `ExaClien…
Template Comprehensive Assessment
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Infrastructure Project
Skill for the project management infrastructure module providing multi-project discovery, structure validation, and metadata extraction. Use when discovering active projects, validating project directory structure, or extracting project configuration metadata.
Template Startup
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Infrastructure Autoresearch
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.
Infrastructure Sia
Skill for the Self-Improvement Agent (SIA) harness contract. Use when validating task public/private layouts, generation artifact trees, evaluation runners, fixture replay loops, or opt-in live Meta→Target→Feedback cycles in template projects.
Template Academic Paper Reviewer
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Infrastructure Steganography
Skill for the steganography infrastructure module providing QR code generation with dynamic mailto links, hash manifests, metadata payloads, and document-wide overlay processing. Use this module to insert opt-in cryptographic and steganographic provenance data onto PDFs.
Template Pipeline Debugging
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Infrastructure Documentation
Skill for the documentation infrastructure module providing figure management, image handling, markdown integration, and API glossary generation. Use when managing research figures, inserting images into manuscripts, auto-numbering figures, or generating API documentation.
Template Test Creation
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Template Academic Paper
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Infrastructure Llm
Skill for the LLM infrastructure module providing local Large Language Model integration via Ollama. Covers client initialization, prompt templates, output validation, manuscript review generation, conversation context, and CLI usage. Use when querying LLMs, generating manuscript reviews, validating LLM outputs, or managing Ollama models.
Codomyrmex
🐜 AI-native modular coding workspace — 127 modules, 424 MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration
Template Reproducibility Audit
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Template Academic Pipeline
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Infrastructure Scientific
Skill for the scientific infrastructure module providing numerical stability checks, performance benchmarking, and independent improvement confirmation. Use when benchmarking functions, checking numerical stability, or confirming a candidate beats a baseline beyond the noise band.
Template Literature Synthesis
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Template Manuscript Cross References
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Infrastructure Prose
Prose analysis utilities for research manuscripts and prose-focused projects. Provides readability metrics (Flesch, Flesch-Kincaid, Gunning Fog), heading-outline structural analysis, editorial quality flags (passive voice, hedge words, citation density, long sentences), aggregate ManuscriptReport across a manuscript directory, and a CLI (metrics/outline/quality/report). Use when analyzing manuscr…
Infrastructure Reference
Bibliographic-reference utilities for research projects. Read, write, and convert BibTeX entries that match the syntax/semantics of projects/templates/template_code_project/manuscript/references.bib (consumed by Pandoc with --natbib during PDF render -- see infrastructure/rendering/_pdf_combined_pandoc.py). Exposes the `citation` submodule (BibTeX I/O + Paper→BibEntry conversion) and the `verific…
Infrastructure Reporting
Skill for the reporting infrastructure module providing pipeline reporting, error aggregation, executive summaries, dashboard generation, test reporting, and multi-project reports. Use when generating build reports, aggregating errors, creating visual dashboards, or producing executive summaries across projects.
Infrastructure Methods
Methods orchestration contract builder for template projects. Use when mapping pipeline stages, manuscript methods, artifact manifests, evidence registries, and validation commands into one reproducible methods plan.
Template Methods Orchestration
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Template Manuscript Creation
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Template Deep Research
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Infrastructure Config
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.
Infrastructure Publishing
Skill for the publishing infrastructure module providing academic publishing workflows including BibTeX CLI citation generation, APA/MLA citation helper functions, DOI management, Zenodo publication, arXiv submission preparation, GitHub releases, PyPI and TestPyPI package distribution, static-site deployment to GitHub Pages / Cloudflare Pages / Netlify, multi-target long-horizon archival (IPFS Pi…
Template Agentic Use
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Template Workflows
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Infrastructure Core
Skill for the core infrastructure module providing logging, configuration, exception handling, progress tracking, checkpoints, retry logic, pipeline execution, performance monitoring, security, file operations, and multi-project orchestration. Use when setting up logging, loading config, handling errors, running pipelines, or monitoring performance.
Infrastructure Search Literature
Paperclip-style multi-source literature search across arXiv, Crossref, local JSON corpora, and (opt-in) the Paperclip API. Provides Paper/SearchQuery/SearchResult data models, a LiteratureClient aggregator with per-backend failure isolation, DOI/arXiv-aware deduplication via merge_papers, deterministic JSON caching via SearchCache, an HttpClient protocol for test injection, and a CLI (search/to-b…
Infrastructure Skills
Programmatic discovery of first-party agent SKILL.md files under configured public repo roots (infrastructure, projects, docs/prompts, and .cursor/skills). Use when enumerating skills, validating .cursor/skill_manifest.json, writing docs/_generated/skills_index.md, checking docs/prompts workflow contracts, or wiring editor automation. Exposes discover_skills, write_skill_manifest, manifest_matche…
Template Validation Quality
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Template Documentation Creation
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Infrastructure Orchestration
Python CLI and menu orchestration for pipeline runs — project slug validation, interactive picker, PipelineRunner wrapping PipelineExecutor, per-stage logs, secure pipeline wrapper. Use when extending run.sh behavior, fixing menu/CLI routing, or testing discovery helpers.
Gauss Open Gauss Cli
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/.
Template Feature Addition
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Infrastructure Docker
Container build and compose assets for the research template. Use when reproducing CI or cloud environments with Docker, following docs/CLOUD_DEPLOY.md, or wiring Ollama sidecars via docker-compose.