docxology/template

docxology/template · .agents/AGENTS.md

docxology/template · .agents/skills/AGENTS.md

docxology/template · .agents/skills/advanced-evaluation/SKILL.md · This skill should be used for advanced LLM evaluation: LLM-as-judge systems, direct scoring, pairwise comparison…

docxology/template · .agents/skills/bdi-mental-states/SKILL.md · This skill should be used when modeling agent mental states with BDI concepts: beliefs, desires, intentions…

docxology/template · .agents/skills/context-compression/SKILL.md · This skill should be used when long-running agent sessions need context compression, structured summarization…

docxology/template · .agents/skills/context-degradation/SKILL.md · This skill should be used for diagnosing and mitigating context degradation: lost-in-middle failures, context…

docxology/template · .agents/skills/context-fundamentals/SKILL.md · This skill should be used to explain or reason about the foundational concepts of context engineering: what context is…

docxology/template · .agents/skills/context-optimization/SKILL.md · This skill should be used for improving context efficiency: context budgeting, observation masking, prefix or KV-cache…

docxology/template · .agents/skills/evaluation/SKILL.md · This skill should be used when building agent evaluation systems: deterministic checks, regression suites…

docxology/template · .agents/skills/filesystem-context/SKILL.md · This skill should be used when agent work needs file-backed context: durable scratchpads, tool-output offloading…

docxology/template · .agents/skills/harness-engineering/SKILL.md · This skill should be used when designing autonomous agent harnesses: research loops, evaluation scaffolds, locked and…

docxology/template · .agents/skills/hosted-agents/SKILL.md · This skill should be used when designing hosted or background agent infrastructure: sandboxed execution, remote coding…

docxology/template · .agents/skills/latent-briefing/SKILL.md · This skill should be used when the user asks to "share memory between agents", "KV cache compaction for multi-agent"…

docxology/template · .agents/skills/long-horizon-prompting/SKILL.md · This skill should be used when writing, enhancing, or evaluating the launch prompt for a long-running autonomous agent…

docxology/template · .agents/skills/memory-systems/SKILL.md · This skill should be used for persistent semantic memory in agent systems: cross-session knowledge retention, entity…

docxology/template · .agents/skills/multi-agent-patterns/SKILL.md · This skill should be used when designing multi-agent systems that need context isolation, supervisor or swarm…

docxology/template · .agents/skills/project-development/SKILL.md · This skill should be used for project-level decisions about LLM-powered systems: whether an LLM is the right primitive…

docxology/template · .agents/skills/self-improvement-loops/SKILL.md · This skill should be used when the harness, scaffold, workflow, or optimizer itself is the optimization target…

docxology/template · .agents/skills/tool-design/SKILL.md · This skill should be used for the tool-interface layer of an agent system specifically: writing tool descriptions…

docxology/template · .cursor/skills/continual-learning/SKILL.md · Orchestrate continual learning by delegating transcript mining to agents-memory-updater and writing durable memory to…

docxology/template · .cursor/skills/gauss/SKILL.md · Open Gauss in this workspace is the math-inc/OpenGauss gauss CLI for Lean session tooling—not Huawei OpenGauss DBMS…

docxology/template · .cursorrules

docxology/template · .github/AGENTS.md

docxology/template · .github/ISSUE_TEMPLATE/AGENTS.md

docxology/template · .github/actions/AGENTS.md

docxology/template · .github/actions/setup-docs-lint/AGENTS.md

docxology/template · .github/actions/setup-python-env/AGENTS.md

docxology/template · .github/workflows/AGENTS.md

docxology/template · AGENTS.md

docxology/template · CLAUDE.md

docxology/template · docs/AGENTS.md

docxology/template · docs/_generated/AGENTS.md

docxology/template · docs/architecture/AGENTS.md

docxology/template · docs/architecture/adrs/AGENTS.md

docxology/template · docs/audit/AGENTS.md

docxology/template · docs/best-practices/AGENTS.md

docxology/template · docs/core/AGENTS.md

docxology/template · docs/development/AGENTS.md

docxology/template · docs/development/testing/AGENTS.md

docxology/template · docs/guides/AGENTS.md

docxology/template · docs/images/AGENTS.md

docxology/template · docs/maintenance/AGENTS.md

docxology/template · docs/manuscript/AGENTS.md

docxology/template · docs/modules/AGENTS.md

docxology/template · docs/modules/guides/AGENTS.md

docxology/template · docs/operational/AGENTS.md

docxology/template · docs/operational/config/AGENTS.md

docxology/template · docs/operational/logging/AGENTS.md

docxology/template · docs/operational/performance/AGENTS.md

docxology/template · docs/operational/scripts/AGENTS.md

docxology/template · docs/operational/troubleshooting/AGENTS.md

docxology/template · docs/plans/AGENTS.md

docxology/template · docs/prompts/AGENTS.md

docxology/template · docs/prompts/SKILL.md · Router and workflow hub for the Research Project Template — code, tests, manuscripts, pipeline, validation, docs, and…

docxology/template · docs/prompts/_skill-eval/AGENTS.md

docxology/template · docs/prompts/academic-paper-reviewer/AGENTS.md

docxology/template · docs/prompts/academic-paper-reviewer/SKILL.md · Read-only manuscript review, methodology review, re-review, and calibration workflow for template projects. USE WHEN…

docxology/template · docs/prompts/academic-paper/AGENTS.md

docxology/template · docs/prompts/academic-paper/SKILL.md · Template-native manuscript planning, outline, drafting, revision, formatting, citation check, and AI-use disclosure…

docxology/template · docs/prompts/academic-pipeline/AGENTS.md

docxology/template · docs/prompts/academic-pipeline/SKILL.md · Research-to-publication orchestrator for template projects: research, write, verify, review, revise, reproduce…

docxology/template · docs/prompts/agentic-use/AGENTS.md

docxology/template · docs/prompts/agentic-use/SKILL.md · Agentic-use and skill-routing workflow for the Research Project Template. USE WHEN discovering relevant skills, making…

docxology/template · docs/prompts/code-development/AGENTS.md

docxology/template · docs/prompts/code-development/SKILL.md · Standards-compliant code for the Research Project Template — infrastructure or project src/, thin orchestrators, type…

docxology/template · docs/prompts/code-development/references/AGENTS.md

docxology/template · docs/prompts/comprehensive-assessment/AGENTS.md

docxology/template · docs/prompts/comprehensive-assessment/SKILL.md · Full checkout audit for the Research Project Template — tests, architecture, docs, manuscript, pipeline. USE WHEN user…

docxology/template · docs/prompts/comprehensive-assessment/references/AGENTS.md

docxology/template · docs/prompts/deep-research/AGENTS.md

docxology/template · docs/prompts/deep-research/SKILL.md · Template-native research intake, literature search, source verification, synthesis, fact-checking, and…

docxology/template · docs/prompts/documentation-creation/AGENTS.md

docxology/template · docs/prompts/documentation-creation/SKILL.md · Author or refresh AGENTS.md and README.md for template directories — accurate commands, Mermaid where helpful, link…

docxology/template · docs/prompts/feature-addition/AGENTS.md

docxology/template · docs/prompts/feature-addition/SKILL.md · End-to-end feature work across src/, scripts/, tests/, manuscript, and docs for the Research Project Template. USE WHEN…

docxology/template · docs/prompts/feature-addition/references/AGENTS.md

docxology/template · docs/prompts/infrastructure-module/AGENTS.md

docxology/template · docs/prompts/infrastructure-module/SKILL.md · Add or extend generic infrastructure/ packages — Layer 1 modules with SKILL.md, AGENTS.md, tests in tests/infra_tests/…

docxology/template · docs/prompts/literature-synthesis/AGENTS.md

docxology/template · docs/prompts/literature-synthesis/SKILL.md · LLM prompt blocks for per-paper and corpus literature synthesis after a search pipeline. USE WHEN synthesizing…

docxology/template · docs/prompts/literature-synthesis/references/AGENTS.md

docxology/template · docs/prompts/manuscript-claim-verification/AGENTS.md

docxology/template · docs/prompts/manuscript-claim-verification/SKILL.md · Triple-pass verification of every manuscript claim against code, data, refs, and renderer; repair prose while staying…

docxology/template · docs/prompts/manuscript-creation/AGENTS.md

docxology/template · docs/prompts/manuscript-creation/SKILL.md · Scaffold a research manuscript and project layout from a research brief — sections, config.yaml, src/, scripts/, tests…

docxology/template · docs/prompts/manuscript-creation/references/AGENTS.md

docxology/template · docs/prompts/manuscript-cross-references/AGENTS.md

docxology/template · docs/prompts/manuscript-cross-references/SKILL.md · Audit or author registry-driven manuscript cross-refs — labels.yaml, [[FIG:]], [[THMREF:]], [[VAR:]] tokens. USE WHEN…

docxology/template · docs/prompts/methods-orchestration/AGENTS.md

docxology/template · docs/prompts/methods-orchestration/SKILL.md · Repo-wide methods orchestration workflow for the Research Project Template. USE WHEN the user asks to add, audit…

docxology/template · docs/prompts/pipeline-debugging/AGENTS.md

docxology/template · docs/prompts/pipeline-debugging/SKILL.md · Systematic pipeline DAG failure triage for the Research Project Template. USE WHEN ./run.sh or execute_pipeline.py…

docxology/template · docs/prompts/publication-audit/AGENTS.md

docxology/template · docs/prompts/publication-audit/SKILL.md · End-to-end publication-readiness audit for public template exemplars — tests, no-mocks, methods contracts, claims…

docxology/template · docs/prompts/refactoring/AGENTS.md

docxology/template · docs/prompts/refactoring/SKILL.md · Clean-break refactors with migration for the Research Project Template — move logic to src/, split modules, rename APIs…

docxology/template · docs/prompts/reproducibility-audit/AGENTS.md

docxology/template · docs/prompts/reproducibility-audit/SKILL.md · Deterministic reproducibility audit — fixed seeds, regenerate-from-clean, double-run diff before Zenodo/arXiv/release…

docxology/template · docs/prompts/startup/AGENTS.md

docxology/template · docs/prompts/startup/SKILL.md · Full installation and validation workflow for a fresh clone of the Research Project Template. Installs dependencies…

docxology/template · docs/prompts/test-creation/AGENTS.md

docxology/template · docs/prompts/test-creation/SKILL.md · Create pytest suites under the no-mocks policy — real data, temp files, subprocess, pytest-httpserver. USE WHEN adding…

docxology/template · docs/prompts/test-creation/references/AGENTS.md

docxology/template · docs/prompts/validation-quality/AGENTS.md

docxology/template · docs/prompts/validation-quality/SKILL.md · Run validation CLI, prerender, markdown/PDF/integrity gates, and QA workflows for the Research Project Template. USE…

docxology/template · docs/reference/AGENTS.md

docxology/template · docs/rules/AGENTS.md

docxology/template · docs/security/AGENTS.md

docxology/template · docs/streams/AGENTS.md

docxology/template · docs/usage/AGENTS.md

docxology/template · fonds/AGENTS.md

docxology/template · fonds/templates/template_bibliography/AGENTS.md

docxology/template · fonds/templates/template_contacts/AGENTS.md

docxology/template · fonds/templates/template_datasets/AGENTS.md

docxology/template · infrastructure/AGENTS.md

docxology/template · infrastructure/SKILL.md · Top-level skill for the research template infrastructure layer. Use in Cursor, Claude Code, or similar agents when…

docxology/template · infrastructure/autoresearch/AGENTS.md

docxology/template · infrastructure/autoresearch/SKILL.md · Skill for deterministic AutoResearch readiness planning. Use when adding, validating, or documenting opt-in…

docxology/template · infrastructure/benchmark/AGENTS.md

docxology/template · infrastructure/benchmark/SKILL.md · Deterministic benchmark harnesses for public template exemplars. Use when scoring generated project outputs against…

docxology/template · infrastructure/config/AGENTS.md

docxology/template · infrastructure/config/SKILL.md · Repository-scoped configuration for the template—environment variable templates and default secure/steganography YAML…

docxology/template · infrastructure/core/AGENTS.md

docxology/template · infrastructure/core/References/AGENTS.md

docxology/template · infrastructure/core/SKILL.md · Skill for the core infrastructure module providing logging, configuration, exception handling, progress tracking…

docxology/template · infrastructure/core/config/AGENTS.md

docxology/template · infrastructure/core/files/AGENTS.md

docxology/template · infrastructure/core/logging/AGENTS.md

docxology/template · infrastructure/core/pipeline/AGENTS.md

docxology/template · infrastructure/core/pipeline/artifacts/AGENTS.md

docxology/template · infrastructure/core/runtime/AGENTS.md

docxology/template · infrastructure/core/telemetry/AGENTS.md

docxology/template · infrastructure/core/telemetry/SKILL.md · Unified pipeline telemetry — collects per-stage performance metrics (CPU, memory, I/O) and diagnostic events into…

docxology/template · infrastructure/core/testing/AGENTS.md

docxology/template · infrastructure/docker/AGENTS.md

docxology/template · infrastructure/docker/SKILL.md · Container build and compose assets for the research template. Use when reproducing CI or cloud environments with…

docxology/template · infrastructure/doctor/AGENTS.md

docxology/template · infrastructure/doctor/SKILL.md · Skill for the doctor infrastructure module providing repository-level diagnostics and safe, reversible automated…

docxology/template · infrastructure/doctor/detectors/AGENTS.md

docxology/template · infrastructure/documentation/AGENTS.md

docxology/template · infrastructure/documentation/SKILL.md · Skill for the documentation infrastructure module providing figure management, image handling, markdown integration…

docxology/template · infrastructure/fonds/AGENTS.md

docxology/template · infrastructure/fonds/SKILL.md · Skill for the fonds module — discovery, validation, scope, and private-sidecar symlink sync for the top-level fonds/…

docxology/template · infrastructure/formal_contracts/AGENTS.md

docxology/template · infrastructure/formal_contracts/SKILL.md · Skill for the typed formal-contracts package — composing and machine-checking well-typed manuscripts (typed claims…

docxology/template · infrastructure/llm/AGENTS.md

docxology/template · infrastructure/llm/SKILL.md · Skill for the LLM infrastructure module providing local Large Language Model integration via Ollama. Covers client…

docxology/template · infrastructure/llm/cli/AGENTS.md

docxology/template · infrastructure/llm/core/AGENTS.md

docxology/template · infrastructure/llm/prompts/AGENTS.md

docxology/template · infrastructure/llm/prompts/compositions/AGENTS.md

docxology/template · infrastructure/llm/prompts/fragments/AGENTS.md

docxology/template · infrastructure/llm/prompts/templates/AGENTS.md

docxology/template · infrastructure/llm/review/AGENTS.md

docxology/template · infrastructure/llm/templates/AGENTS.md

docxology/template · infrastructure/llm/utils/AGENTS.md

docxology/template · infrastructure/llm/validation/AGENTS.md

docxology/template · infrastructure/logrotate.d/AGENTS.md

docxology/template · infrastructure/metadata/AGENTS.md

docxology/template · infrastructure/metadata/SKILL.md · Skill for the shared metadata infrastructure module providing repository-URL normalization and ebook…

docxology/template · infrastructure/methods/AGENTS.md

docxology/template · infrastructure/methods/SKILL.md · Methods orchestration contract builder for template projects. Use when mapping pipeline stages, manuscript methods…

docxology/template · infrastructure/orchestration/AGENTS.md

docxology/template · infrastructure/orchestration/SKILL.md · Python CLI and menu orchestration for pipeline runs — project slug validation, interactive picker, PipelineRunner…

docxology/template · infrastructure/project/AGENTS.md

docxology/template · infrastructure/project/SKILL.md · Skill for the project management infrastructure module providing multi-project discovery, structure validation, and…

docxology/template · infrastructure/project/drift/AGENTS.md

docxology/template · infrastructure/project/manuscript/AGENTS.md

docxology/template · infrastructure/project/promotion/AGENTS.md

docxology/template · infrastructure/prose/AGENTS.md

docxology/template · infrastructure/prose/SKILL.md · Prose analysis utilities for research manuscripts and prose-focused projects. Provides readability metrics (Flesch…

docxology/template · infrastructure/prose/analysis/AGENTS.md

docxology/template · infrastructure/provenance/AGENTS.md

docxology/template · infrastructure/provenance/SKILL.md · Content-addressed provenance DAG for research lineage tracking. Use for: recording which pipeline stage produced which…

docxology/template · infrastructure/publishing/AGENTS.md

docxology/template · infrastructure/publishing/SKILL.md · Skill for the publishing infrastructure module providing academic publishing workflows including BibTeX CLI citation…

docxology/template · infrastructure/publishing/archival/AGENTS.md

docxology/template · infrastructure/publishing/arxiv/AGENTS.md

docxology/template · infrastructure/publishing/github/AGENTS.md

docxology/template · infrastructure/publishing/huggingface/AGENTS.md

docxology/template · infrastructure/publishing/metadata/AGENTS.md

docxology/template · infrastructure/publishing/osf/AGENTS.md

docxology/template · infrastructure/publishing/pypi/AGENTS.md

docxology/template · infrastructure/publishing/release/AGENTS.md

docxology/template · infrastructure/publishing/static_site/AGENTS.md

docxology/template · infrastructure/publishing/zenodo/AGENTS.md

docxology/template · infrastructure/reference/AGENTS.md

docxology/template · infrastructure/reference/SKILL.md · Bibliographic-reference utilities for research projects. Read, write, and convert BibTeX entries that match the…

docxology/template · infrastructure/reference/citation/AGENTS.md

docxology/template · infrastructure/reference/citation/SKILL.md · BibTeX read/write/convert that matches the syntax/semantics of projects/templates/template_code_project/manuscript/refer…

docxology/template · infrastructure/reference/verification/AGENTS.md

docxology/template · infrastructure/reference/verification/SKILL.md · Deterministic anti-hallucination gate for cited references. Resolves each entry in a manuscript .bib file against…

docxology/template · infrastructure/rendering/AGENTS.md

docxology/template · infrastructure/rendering/References/AGENTS.md

docxology/template · infrastructure/rendering/SKILL.md · Skill for the rendering infrastructure module providing multi-format output generation including PDF manuscripts, HTML…

docxology/template · infrastructure/reporting/AGENTS.md

docxology/template · infrastructure/reporting/SKILL.md · Skill for the reporting infrastructure module providing pipeline reporting, error aggregation, executive summaries…

docxology/template · infrastructure/research/AGENTS.md

docxology/template · infrastructure/research/SKILL.md · Seven-stage research workflow (SCOPE→LITERATURE→REASON→DESIGN→COMPUTE→SYNTHESIZE→WRITE). Use for: structuring an AI…

docxology/template · infrastructure/research/prompts/AGENTS.md

docxology/template · infrastructure/rules/AGENTS.md

docxology/template · infrastructure/rules/SKILL.md · Skill for the rules module — discovery, validation, scope, and private-sidecar symlink sync for the top-level rules/…

docxology/template · infrastructure/scientific/AGENTS.md