# Documentation index This index lists documentation files in the Research Project Template by category. **Project layout:** `projects/` is a **rotating** set of workspaces. The only path **guaranteed** for documentation examples is [`projects/templates/template_code_project/`](../projects/templates/template_code_project/). Authoritative current names: [`_generated/active_projects.md`](_generated/active_projects.md). ## Quick start by persona ### New user / content creator 1. **[README.md](../README.md)** - Project overview 2. **[guides/getting-started.md](guides/getting-started.md)** - Write your first document (Levels 1-3) 3. **[reference/quick-start-cheatsheet.md](reference/quick-start-cheatsheet.md)** - Essential commands 4. **[reference/common-workflows.md](reference/common-workflows.md)** - Step-by-step recipes 5. **[reference/faq.md](reference/faq.md)** - Common questions ### Developer / researcher 1. **[core/how-to-use.md](core/how-to-use.md)** - Usage guide (all 12 levels) 2. **[guides/figures-and-analysis.md](guides/figures-and-analysis.md)** - Figures and automation (Levels 4-6) 3. **[core/architecture.md](core/architecture.md)** - System design overview 4. **[architecture/thin-orchestrator-summary.md](architecture/thin-orchestrator-summary.md)** - Pattern implementation 5. **[core/workflow.md](core/workflow.md)** - Development process ### Contributor / maintainer 1. **[development/contributing.md](development/contributing.md)** - Contribution guidelines 2. **[development/contribution-map.md](development/contribution-map.md)** - Overlap checks and contribution strategy 3. **[rules/AGENTS.md](rules/AGENTS.md)** - Development standards 4. **[guides/testing-and-reproducibility.md](guides/testing-and-reproducibility.md)** - TDD workflow (Levels 7-9) 5. **[development/testing/testing-guide.md](development/testing/testing-guide.md)** - Testing requirements 6. **[development/code-of-conduct.md](development/code-of-conduct.md)** - Community standards ### Troubleshooter 1. **[operational/troubleshooting/](operational/troubleshooting/)** - Troubleshooting guides 2. **[reference/faq.md](reference/faq.md)** - Common questions and solutions 3. **[RUN_GUIDE.md](RUN_GUIDE.md)** - Pipeline orchestration and commands 4. **[operational/config/performance-optimization.md](operational/config/performance-optimization.md)** - Performance issues 5. **[operational/troubleshooting/common-errors.md](operational/troubleshooting/common-errors.md)** — Silent Stage 4 failure pattern --- > [!IMPORTANT] > **Multi-project pipeline pitfalls** (root venv deps, `matplotlib` in core deps, `project_config:` namespace, idempotency) — authoritative copy in [docs/AGENTS.md](AGENTS.md#learnings--known-issues) and [guides/new-project-setup.md](guides/new-project-setup.md). ## Topic routing (canonical → deep dives) | Topic | Start here | Deep dives | |-------|------------|------------| | Pipeline ops | [RUN_GUIDE.md](RUN_GUIDE.md) | [operational/pipeline-control.md](operational/pipeline-control.md), [operational/runbook.md](operational/runbook.md) | | Methods orchestration | [guides/methods-orchestration.md](guides/methods-orchestration.md) | [architecture/thin-orchestrator-summary.md](architecture/thin-orchestrator-summary.md), [RUN_GUIDE.md](RUN_GUIDE.md) | | Agent code navigation | [guides/codegraph-local.md](guides/codegraph-local.md), [guides/leann-local.md](guides/leann-local.md) | [architecture/thin-orchestrator-summary.md](architecture/thin-orchestrator-summary.md), [reference/api-project-modules.md](reference/api-project-modules.md) | | Logging | [operational/logging/output-design.md](operational/logging/output-design.md) | [operational/logging/python-logging.md](operational/logging/python-logging.md), [operational/logging/bash-logging.md](operational/logging/bash-logging.md) | | Secure / steganography | [guides/secure-research-guide.md](guides/secure-research-guide.md) | [security/README.md](security/README.md), [security/secure_execution.md](security/secure_execution.md) | | Literature search | [guides/literature-workflow-guide.md](guides/literature-workflow-guide.md) | [core/literature-data-flow.md](core/literature-data-flow.md), [modules/literature-search-and-references.md](modules/literature-search-and-references.md) | | Web search (Exa) | [../infrastructure/search/README.md](../infrastructure/search/README.md#exa-quick-start) | [../infrastructure/search/exa/CAPABILITIES.md](../infrastructure/search/exa/CAPABILITIES.md) | | Deep research (OpenAI/Gemini, paid opt-in) | [../infrastructure/search/deep_research/README.md](../infrastructure/search/deep_research/README.md) | [../infrastructure/search/deep_research/AGENTS.md](../infrastructure/search/deep_research/AGENTS.md), [../infrastructure/search/SKILL.md](../infrastructure/search/SKILL.md) | | Publication | [guides/publication-runbook.md](guides/publication-runbook.md) | [guides/publishing-guide.md](guides/publishing-guide.md), [guides/zenodo-doi-strategy.md](guides/zenodo-doi-strategy.md), [modules/guides/publishing-module.md](modules/guides/publishing-module.md), [_generated/publication_records.md](_generated/publication_records.md) | **Module package counts:** link [modules/modules-guide.md](modules/modules-guide.md) or regenerate from `infrastructure/` discovery — do not hand-edit competing literals across hub pages. --- ## Development rules Development standards are documented in **`docs/rules/`**. The Cursor IDE entry rule is the repository root **[`.cursorrules`](../.cursorrules)** file: - **[`rules/AGENTS.md`](rules/AGENTS.md)** - Overview and navigation guide - **[`rules/README.md`](rules/README.md)** - Quick reference and patterns - **[`rules/error_handling.md`](rules/error_handling.md)** - Exception handling patterns - **[`rules/security.md`](rules/security.md)** - Security standards - **[`rules/python_logging.md`](rules/python_logging.md)** - Logging standards - **[`rules/infrastructure_modules.md`](rules/infrastructure_modules.md)** - Infrastructure module development - **[`rules/testing_standards.md`](rules/testing_standards.md)** - Testing patterns - **[`rules/documentation_standards.md`](rules/documentation_standards.md)** - Documentation writing guide - **[`rules/memory_and_decision_records.md`](rules/memory_and_decision_records.md)** - Decision-memory and rationale tiering - **[`rules/type_hints_standards.md`](rules/type_hints_standards.md)** - Type annotation patterns - **[`rules/llm_standards.md`](rules/llm_standards.md)** - LLM/Ollama integration - **[`rules/code_style.md`](rules/code_style.md)** - Code formatting - **[`rules/git_workflow.md`](rules/git_workflow.md)** - Git workflow - **[`rules/api_design.md`](rules/api_design.md)** - API design - **[`rules/manuscript_style.md`](rules/manuscript_style.md)** - Manuscript formatting - **[`rules/reporting.md`](rules/reporting.md)** - Reporting module standards - **[`rules/refactoring.md`](rules/refactoring.md)** - Refactoring standards - **[`rules/folder_structure.md`](rules/folder_structure.md)** - Folder structure - **[`rules/public-output-policy.md`](rules/public-output-policy.md)** - Public output policy and tracking rules --- ## Core documentation - **[README.md](../README.md)** - Main project overview and quick start - **[Documentation hub (`docs/AGENTS.md`)](AGENTS.md)** - **[Repository system (`AGENTS.md` at repo root)](../AGENTS.md)** - **[CLOUD_DEPLOY.md](CLOUD_DEPLOY.md)** - Headless / cloud server deployment - **[repurposing-architectures.md](repurposing-architectures.md)** - Repurposing template architectures for research (entry point for "can I reuse these architectures?") - **[PAI.md](PAI.md)** - Personal AI Infrastructure (PAI) context - **[RUN_GUIDE.md](RUN_GUIDE.md)** - Pipeline orchestration reference - **[../.github/README.md](../.github/README.md)** - **GitHub**: Actions workflows, Dependabot, issue/PR templates, mirroring CI locally - **[_generated/](_generated/README.md)** — folder policy; **[_generated/AGENTS.md](_generated/AGENTS.md)** — technical notes for this directory (hand-maintained). **Generated artefacts** (regenerated by their named script — never hand-edit): **[active_projects.md](_generated/active_projects.md)** (single source of truth for `projects/` roster — do not copy elsewhere), **[exemplar_roster.md](_generated/exemplar_roster.md)** (per-exemplar "when to use" differentiation map — `scripts/docgen/exemplar_roster.py`, sync test-enforced), **[architecture_overview.md / .svg / .mmd](_generated/architecture_overview.md)**, **[publication_records.md](_generated/publication_records.md)** (public exemplar GitHub/Zenodo/config matrix), **[coverage_history.md](_generated/coverage_history.md)**, **[skills_index.md](_generated/skills_index.md)**, **[last-run-summary.md](_generated/last-run-summary.md)** (canonical end-of-run multi-project summary — schema: [operational/logging/output-design.md](operational/logging/output-design.md)). **Maintained facts/snapshots:** **[COUNTS.md](_generated/COUNTS.md)** and historical **[hermes_knowledge_audit.json](_generated/hermes_knowledge_audit.json)**. - **Agent skills manifest** — `uv run python -m infrastructure.skills write` (default output: `.cursor/skill_manifest.json`) · `uv run python -m infrastructure.skills check` — see [modules/guides/skills-module.md](modules/guides/skills-module.md) - **Open Gauss naming** — [reference/opengauss-naming.md](reference/opengauss-naming.md) (math-inc `gauss` CLI vs Huawei DBMS; does not require `fep_lean` on disk) - **[core/how-to-use.md](core/how-to-use.md)** - Usage guide (all 12 levels) - **[how-to-use.md](how-to-use.md)** - Signpost stub redirecting to the canonical `core/how-to-use.md` - **[core/literature-data-flow.md](core/literature-data-flow.md)** - Literature search and data pipeline overview - **[accessibility.md](accessibility.md)** - Accessibility notes for generated documentation and diagrams ### Quick Reference - **[reference/copypasta.md](reference/copypasta.md)** - Ready-to-use sharing content - **[reference/copypasta-diagrams.md](reference/copypasta-diagrams.md)** - Diagram copypasta blocks - **[reference/copypasta-outreach.md](reference/copypasta-outreach.md)** - Outreach/social copypasta - **[reference/faq.md](reference/faq.md)** - FAQs - **[reference/quick-start-cheatsheet.md](reference/quick-start-cheatsheet.md)** - Essential commands - **[reference/common-workflows.md](reference/common-workflows.md)** - Step-by-step recipes - **[reference/glossary.md](reference/glossary.md)** - Glossary of terms - **[reference/opengauss-naming.md](reference/opengauss-naming.md)** - math-inc `gauss` CLI vs Huawei DBMS - **[reference/api-project-modules.md](reference/api-project-modules.md)** - Project module API reference --- ## Architecture and design - **[core/architecture.md](core/architecture.md)** - System design overview - **[architecture/two-layer-architecture.md](architecture/two-layer-architecture.md)** - Two-layer architecture guide - **[architecture/thin-orchestrator-summary.md](architecture/thin-orchestrator-summary.md)** - Thin orchestrator pattern - **[architecture/decision-tree.md](architecture/decision-tree.md)** - Code placement decisions - **[architecture/adrs/000-two-layer-architecture.md](architecture/adrs/000-two-layer-architecture.md)** - ADR-000: Two-layer architecture - **[architecture/adrs/001-thin-orchestrator-pattern.md](architecture/adrs/001-thin-orchestrator-pattern.md)** - ADR-001: Thin orchestrator pattern - **[architecture/adrs/002-declarative-dag-pipeline.md](architecture/adrs/002-declarative-dag-pipeline.md)** - ADR-002: Declarative DAG pipeline - **[architecture/adrs/003-multi-format-rendering-and-toggles.md](architecture/adrs/003-multi-format-rendering-and-toggles.md)** - ADR-003: Multi-format rendering and toggles - **[architecture/adrs/004-zero-mock-testing-policy.md](architecture/adrs/004-zero-mock-testing-policy.md)** - ADR-004: Zero-mock testing policy - **[architecture/adrs/005-decision-memory-and-adversarial-validation.md](architecture/adrs/005-decision-memory-and-adversarial-validation.md)** - ADR-005: Decision memory and adversarial validation - **[core/workflow.md](core/workflow.md)** - Development workflow - **[architecture/testing-strategy.md](architecture/testing-strategy.md)** - Testing strategy overview - **[architecture/discovery-export-synthesis.md](architecture/discovery-export-synthesis.md)** - Discovery and export patterns - **[architecture/migration-from-flat.md](architecture/migration-from-flat.md)** - Migration from flat layout --- ## Usage guides ### Skill-Level Guides - **[guides/startup-and-setup.md](guides/startup-and-setup.md)** - Complete install + validation procedure (copy-pasteable steps for humans and agents) - **[guides/getting-started.md](guides/getting-started.md)** - Levels 1-3 (Beginner) - **[guides/manuscript-semantics.md](guides/manuscript-semantics.md)** - Canonical manuscript syntax (citations, cross-references, sections, tokens) shared by public template exemplars - **[guides/methods-orchestration.md](guides/methods-orchestration.md)** - Connect methods prose, pipeline contracts, artifacts, and evidence registries - **[guides/codegraph-local.md](guides/codegraph-local.md)** - Optional local CodeGraph indexing for agent code navigation and impact checks - **[guides/leann-local.md](guides/leann-local.md)** - Optional local LEANN semantic retrieval for agent navigation and impact checks - **[guides/figures-and-analysis.md](guides/figures-and-analysis.md)** - Levels 4-6 (Intermediate) - **[guides/testing-and-reproducibility.md](guides/testing-and-reproducibility.md)** - Levels 7-9 (Advanced) - **[guides/extending-and-automation.md](guides/extending-and-automation.md)** - Levels 10-12 (Expert) - **[guides/new-project-setup.md](guides/new-project-setup.md)** - New project checklist (all learnings) - **[guides/new-project-one-shot-prompt.md](guides/new-project-one-shot-prompt.md)** - One-shot LLM prompt for new `projects/{name}/` (primary exemplar: [`projects/templates/template_code_project/`](../projects/templates/template_code_project/); other active names: [_generated/active_projects.md](_generated/active_projects.md)) - **[guides/llm-integration-guide.md](guides/llm-integration-guide.md)** - AI-assisted research with Ollama - **[guides/publication-runbook.md](guides/publication-runbook.md)** - Front-door release runbook for standalone public GitHub mirrors, real Zenodo DOI minting, new-version releases, optional mirrors, status blocks, and archival handoff - **[guides/publishing-guide.md](guides/publishing-guide.md)** - Detailed publishing workflow across the first-class registry (DOI, Zenodo, GitHub, arXiv, PyPI, IPFS, Software Heritage, Hugging Face, OSF, static hosts), credential verification, and README status compilation - **[guides/zenodo-doi-strategy.md](guides/zenodo-doi-strategy.md)** - Concept vs version DOI layout for Zenodo deposits - **[guides/secure-research-guide.md](guides/secure-research-guide.md)** - PDF watermarking, provenance, and integrity - **[../projects/templates/template_code_project/README.md](../projects/templates/template_code_project/README.md)** - Control-positive exemplar under `projects/` ### Content Authoring - **[usage/examples.md](usage/examples.md)** - Project customization examples - **[usage/examples-showcase.md](usage/examples-showcase.md)** - Real-world examples - **[usage/template-description.md](usage/template-description.md)** - Template overview - **[usage/markdown-template-guide.md](usage/markdown-template-guide.md)** - Markdown authoring - **[usage/manuscript-numbering-system.md](usage/manuscript-numbering-system.md)** - Section numbering - **[usage/style-guide.md](usage/style-guide.md)** - Equations, figures, tables - **[usage/image-management.md](usage/image-management.md)** - Image handling - **[usage/visualization-guide.md](usage/visualization-guide.md)** - Publication-quality figures - **[usage/output-formats.md](usage/output-formats.md)** - Per-format render toggles (PDF, HTML, slides, DOCX, EPUB) ### Scientific Computing - **[modules/scientific-simulation-guide.md](modules/scientific-simulation-guide.md)** - Simulation system - **[best-practices/literature-search-best-practices.md](best-practices/literature-search-best-practices.md)** - Literature search patterns and best practices - **[guides/literature-workflow-guide.md](guides/literature-workflow-guide.md)** - Literature workflow step-by-step --- ## Development and maintenance - **[development/contributing.md](development/contributing.md)** - Contribution guidelines - **[development/contribution-map.md](development/contribution-map.md)** - Overlap checks and practical contribution strategy - **[development/code-of-conduct.md](development/code-of-conduct.md)** - Community standards - **[development/security.md](development/security.md)** - Security policy - **[development/roadmap.md](development/roadmap.md)** - Development roadmap - **[development/coverage-gaps.md](development/coverage-gaps.md)** - Coverage analysis - **[development/testing/testing-guide.md](development/testing/testing-guide.md)** - Testing framework - **[development/testing/testing-with-credentials.md](development/testing/testing-with-credentials.md)** - Credential testing - **[development/no-mocks-http-testing.md](development/no-mocks-http-testing.md)** - HTTP testing without mocks - **[development/validation_gates.md](development/validation_gates.md)** - Validation gates - **[development/code-review-checklist.md](development/code-review-checklist.md)** - Eight-criterion review checklist (clarity, composability, functionality/SSOT, testability, validation, documentation, conventions, reproducibility) - **[development/optional-dependencies.md](development/optional-dependencies.md)** - Optional dependency + capability matrix (which extras unlock which features) - **[maintenance/README.md](maintenance/README.md)** - Maintenance hub index - **[maintenance/private-projects-repo.md](maintenance/private-projects-repo.md)** - Sibling private project lifecycle (required `working/` + `archive/`, optional legacy `active/`, `published/`, `other/`) and symlink sync into `projects/` - **[maintenance/toolchain-migration.md](maintenance/toolchain-migration.md)** - Toolchain migration notes - **[maintenance/regression-testing.md](maintenance/regression-testing.md)** - Regression testing workflow - **[maintenance/archival-targets.md](maintenance/archival-targets.md)** - Archival providers for the opt-in archival stage (stage index: see the generated stage table) - **[maintenance/ci-local.md](maintenance/ci-local.md)** - Local CI reproduction (`scripts/shell/ci_local.sh`) - **[maintenance/release-boundary.md](maintenance/release-boundary.md)** - Root package, tag, changelog, and GitHub release boundary - **[maintenance/python-runtime-support.md](maintenance/python-runtime-support.md)** - Supported-Python contract (`requires-python = ">=3.10"` floor, 3.12 default, 3.13 readiness lane) - **[maintenance/stage-10-executable-bundle.md](maintenance/stage-10-executable-bundle.md)** - Executable bundle design for the opt-in bundle stage (file predates the Ebook/Metadata stage insertion; kept its original name, and stage indices live only in the generated stage table) - **[maintenance/local-only-template-exemplars.md](maintenance/local-only-template-exemplars.md)** - Local-only exemplar policy (`LOCAL_ONLY_TEMPLATE_NAMES`) - **[maintenance/doc-mega-decomposition.md](maintenance/doc-mega-decomposition.md)** - Policy for splitting oversized documentation mega-files - **[maintenance/review-remediation-2026-07.md](maintenance/review-remediation-2026-07.md)** - Multi-lens review remediation plan (R1–R18 items with acceptance lines) --- ## Advanced modules - **[modules/modules-guide.md](modules/modules-guide.md)** - Layer-1 module overview; live package counts come from [`_generated/COUNTS.md`](_generated/COUNTS.md) - **[reference/api-reference.md](reference/api-reference.md)** - Unified API documentation - **[modules/pdf-validation.md](modules/pdf-validation.md)** - PDF validation system - **[modules/literature-search-and-references.md](modules/literature-search-and-references.md)** - Literature search and reference pipeline ### Per-Module Guides (`modules/guides/`) Thin pointer stubs: each entry redirects to the module's own `infrastructure//` README/SKILL docs, which are the substantive references. One stub per infrastructure package, plus the `config/`, `docker/`, and `logrotate.d/` asset directories and the `validation/integrity/` subpackage. - **[modules/guides/config-module.md](modules/guides/config-module.md)** - **[modules/guides/autoresearch-module.md](modules/guides/autoresearch-module.md)** - **[modules/guides/benchmark-module.md](modules/guides/benchmark-module.md)** - **[modules/guides/core-module.md](modules/guides/core-module.md)** - **[modules/guides/docker-module.md](modules/guides/docker-module.md)** - **[modules/guides/documentation-module.md](modules/guides/documentation-module.md)** - **[modules/guides/integrity-module.md](modules/guides/integrity-module.md)** - **[modules/guides/llm-module.md](modules/guides/llm-module.md)** - **[modules/guides/project-module.md](modules/guides/project-module.md)** - **[modules/guides/publishing-module.md](modules/guides/publishing-module.md)** - Publishing registry, DOI/citations, credential verification, README status compilation, multi-platform upload dispatch - **[modules/guides/rendering-module.md](modules/guides/rendering-module.md)** - **[modules/guides/reporting-module.md](modules/guides/reporting-module.md)** - **[modules/guides/scientific-module.md](modules/guides/scientific-module.md)** - **[modules/guides/skills-module.md](modules/guides/skills-module.md)** - **[modules/guides/steganography-module.md](modules/guides/steganography-module.md)** - **[modules/guides/validation-module.md](modules/guides/validation-module.md)** - **[modules/guides/doctor-module.md](modules/guides/doctor-module.md)** - **[modules/guides/orchestration-module.md](modules/guides/orchestration-module.md)** - **[modules/guides/prose-module.md](modules/guides/prose-module.md)** - **[modules/guides/search-module.md](modules/guides/search-module.md)** - **[modules/guides/reference-module.md](modules/guides/reference-module.md)** - **[modules/guides/methods-module.md](modules/guides/methods-module.md)** - **[modules/guides/sia-module.md](modules/guides/sia-module.md)** - **[modules/guides/fonds-module.md](modules/guides/fonds-module.md)** - **[modules/guides/logrotate-module.md](modules/guides/logrotate-module.md)** - **[modules/guides/provenance-module.md](modules/guides/provenance-module.md)** - **[modules/guides/research-module.md](modules/guides/research-module.md)** - **[modules/guides/rules-module.md](modules/guides/rules-module.md)** - **[modules/guides/tools-module.md](modules/guides/tools-module.md)** --- ## Operational guides ### Pipeline & CI/CD - **[RUN_GUIDE.md](RUN_GUIDE.md)** - Pipeline orchestration and stage reference - **[operational/pipeline-control.md](operational/pipeline-control.md)** - Advisory stage contracts, HITL commands, hooks, manifests, evidence registry, run lessons, and benchmarks - **[.github/README.md](../.github/README.md)** - Repository CI/CD and contribution automation - **template_code_project / CI paths** — Use [`projects/templates/template_code_project/`](../projects/templates/template_code_project/) when listed under [`_generated/active_projects.md`](_generated/active_projects.md); WIP copies live under `projects/working/` only when you place them there ### Build & dependency docs (`operational/build/`) - **[operational/build/README.md](operational/build/README.md)** - Index - **[operational/build/build-system.md](operational/build/build-system.md)** - Build system - **[operational/build/build-performance.md](operational/build/build-performance.md)** - Build performance - **[operational/build/build-history.md](operational/build/build-history.md)** - Build history - **[operational/build/ci-cd-integration.md](operational/build/ci-cd-integration.md)** - CI/CD integration - **[operational/build/dependency-management.md](operational/build/dependency-management.md)** - Dependency management - **[plans/README.md](plans/README.md)** - Strategic plans and architecture decisions - **Live doc linter** — `scripts/audit/lint_docs.py`: `uv run python scripts/audit/lint_docs.py` ([script entrypoint](../scripts/audit/lint_docs.py)) — mermaid block validation + cross-link integrity + sibling-doc consistency across `docs/`, `infrastructure/`, `.github/`, `scripts/`, `tests/`, root-level markdown, and the public exemplars (the scan set is `doc_roots()` in `infrastructure/validation/docs/lint_runner.py`, not the whole repo); replaces the older point-in-time `scripts/audit/audit_filepaths.py` snapshots - **Template drift checker** — `scripts/audit/check_template_drift.py`: `uv run python scripts/audit/check_template_drift.py` ([script entrypoint](../scripts/audit/check_template_drift.py)) — 19 per-exemplar detectors + 4 repo-level checks (registered in `infrastructure/project/drift/registry.py`) - **Audit replacement note** — dated audit snapshots were retired from public docs; use the live linters above as the canonical reference, or git history for point-in-time reports - **[audit/filepath-audit-report.md](audit/filepath-audit-report.md)** — Historical filepath audit report (point-in-time snapshot) - **[guides/fork-an-exemplar.md](guides/fork-an-exemplar.md)** - Top-level entry: pick the right exemplar and start a 5-minute fork ### Configuration & Performance (`operational/config/`) - **[operational/config/configuration.md](operational/config/configuration.md)** - Configuration system (Lean exemplar under `projects/templates/template_active_inference/`; paths under `projects/templates/template_code_project/`) - **[reference/opengauss-naming.md](reference/opengauss-naming.md)** - Open Gauss naming (`gauss` CLI vs Huawei DBMS) — same page as the Open Gauss entry near line 90; listed twice intentionally (theme list + file table) - **[operational/config/checkpoint-resume.md](operational/config/checkpoint-resume.md)** - Checkpoint system - **[operational/config/performance-optimization.md](operational/config/performance-optimization.md)** - Performance tuning ### Logging (`operational/logging/`) - **[operational/logging/](operational/logging/)** - Comprehensive logging guide - **[operational/logging/python-logging.md](operational/logging/python-logging.md)** - Python logging - **[operational/logging/bash-logging.md](operational/logging/bash-logging.md)** - Bash logging - **[operational/logging/logging-patterns.md](operational/logging/logging-patterns.md)** - Cross-language patterns - **[operational/logging/output-design.md](operational/logging/output-design.md)** - Output design: terminal vs file, summary schema, verbosity dial ### Troubleshooting (`operational/troubleshooting/`) - **[operational/troubleshooting/](operational/troubleshooting/)** - Diagnostic flowchart and approach - **[operational/troubleshooting/common-errors.md](operational/troubleshooting/common-errors.md)** - Error patterns - **[operational/troubleshooting/build-tools.md](operational/troubleshooting/build-tools.md)** - Build tool issues - **[operational/troubleshooting/test-failures.md](operational/troubleshooting/test-failures.md)** - Test debugging - **[operational/troubleshooting/environment-setup.md](operational/troubleshooting/environment-setup.md)** - Environment setup - **[operational/troubleshooting/recovery-procedures.md](operational/troubleshooting/recovery-procedures.md)** - Recovery - **[operational/troubleshooting/llm-review.md](operational/troubleshooting/llm-review.md)** - LLM review issues - **[operational/troubleshooting/llm-diagnostics.md](operational/troubleshooting/llm-diagnostics.md)** - LLM diagnostics ### Other Operational Guides - **[operational/reporting-guide.md](operational/reporting-guide.md)** - Reporting system - **[operational/overview.md](operational/overview.md)** - Operational overview - **[operational/runbook.md](operational/runbook.md)** - Runbook for operational procedures - **[operational/error-handling-guide.md](operational/error-handling-guide.md)** - Error handling patterns - **[operational/docker.md](operational/docker.md)** - Docker containerization - **[operational/config-wizard.md](operational/config-wizard.md)** - Environment setup wizard - **[operational/template-usage.md](operational/template-usage.md)** - Template usage patterns - **[operational/diagrams.md](operational/diagrams.md)** - Operational diagrams - **[operational/maintenance.md](operational/maintenance.md)** - Log rotation, backups, dependency updates - **[operational/performance/benchmarking-guide.md](operational/performance/benchmarking-guide.md)** - Benchmarking guide --- ## Reference materials - **[best-practices/best-practices.md](best-practices/best-practices.md)** - Consolidated best practices - **[best-practices/version-control.md](best-practices/version-control.md)** - Git workflows - **[best-practices/multi-project-management.md](best-practices/multi-project-management.md)** - Multi-project setup (roster → [_generated/active_projects.md](_generated/active_projects.md); optional per-project docs e.g. [`projects/templates/template_code_project/docs/`](../projects/templates/template_code_project/docs/)) - **[best-practices/migration-guide.md](best-practices/migration-guide.md)** - Migration from other templates - **[best-practices/backup-recovery.md](best-practices/backup-recovery.md)** - Backup strategies --- ## Security and provenance - **[security/README.md](security/README.md)** - Security overview - **[security/threat-model.md](security/threat-model.md)** - Repository-wide threat model: assets, attacker model, attack surfaces, threat register, and ownership map - **[security/steganography.md](security/steganography.md)** - Alpha-channel watermarking and QR codes - **[security/hashing_and_manifests.md](security/hashing_and_manifests.md)** - SHA-256/512 hashing and manifests - **[security/secure_execution.md](security/secure_execution.md)** - `secure_run.sh` orchestration and threat model - **[security/literature-fetch-security.md](security/literature-fetch-security.md)** - Security for literature fetching - **[security/ownership-and-promotion.md](security/ownership-and-promotion.md)** - Sensitive ownership exceptions, required reviews, and private-project promotion attestation - **[security/branch-protection-checklist.md](security/branch-protection-checklist.md)** - Required GitHub branch-protection settings for `main` (administrator action) - **[security/promotion-runbook.md](security/promotion-runbook.md)** - Step-by-step guide for promoting a private sidecar project into active/public scope - **[security/credential-rotation-handoff.md](security/credential-rotation-handoff.md)** - Operator runbook for credential rotation and safeguarding --- ## AI prompt templates - **[prompts/README.md](prompts/README.md)** - Navigation guide - **[prompts/SKILL.md](prompts/SKILL.md)** - Hub router (`template-workflows`) - **[prompts/MODE_REGISTRY.md](prompts/MODE_REGISTRY.md)** - Workflow-skill mode registry - **[prompts/COMPOSITION.md](prompts/COMPOSITION.md)** - Workflow composition map (how prompt skills chain together) - **[prompts/startup/SKILL.md](prompts/startup/SKILL.md)** - Startup / environment-bootstrap workflow skill - **[prompts/_skill-eval/README.md](prompts/_skill-eval/README.md)** - Synthetic workflow-skill benchmark workspace - **[prompts/manuscript-creation/SKILL.md](prompts/manuscript-creation/SKILL.md)** - Manuscript creation - **[prompts/manuscript-cross-references/SKILL.md](prompts/manuscript-cross-references/SKILL.md)** - Registry/token manuscript cross-references - **[prompts/manuscript-claim-verification/SKILL.md](prompts/manuscript-claim-verification/SKILL.md)** - Triple-check manuscript claims (max effort/tools) - **[prompts/literature-synthesis/SKILL.md](prompts/literature-synthesis/SKILL.md)** - Literature synthesis LLM blocks - **[prompts/code-development/SKILL.md](prompts/code-development/SKILL.md)** - Code development - **[prompts/test-creation/SKILL.md](prompts/test-creation/SKILL.md)** - Test creation - **[prompts/feature-addition/SKILL.md](prompts/feature-addition/SKILL.md)** - Feature addition - **[prompts/refactoring/SKILL.md](prompts/refactoring/SKILL.md)** - Refactoring - **[prompts/documentation-creation/SKILL.md](prompts/documentation-creation/SKILL.md)** - Documentation creation - **[prompts/infrastructure-module/SKILL.md](prompts/infrastructure-module/SKILL.md)** - Infrastructure modules - **[prompts/validation-quality/SKILL.md](prompts/validation-quality/SKILL.md)** - Validation and QA - **[prompts/comprehensive-assessment/SKILL.md](prompts/comprehensive-assessment/SKILL.md)** - Assessment and review - **[prompts/publication-audit/SKILL.md](prompts/publication-audit/SKILL.md)** - End-to-end publication-readiness audit - **[prompts/reproducibility-audit/SKILL.md](prompts/reproducibility-audit/SKILL.md)** - Determinism and regenerate-from-clean audit - **[prompts/pipeline-debugging/SKILL.md](prompts/pipeline-debugging/SKILL.md)** - Pipeline DAG-stage failure triage - **[prompts/academic-paper/SKILL.md](prompts/academic-paper/SKILL.md)** - Academic paper authoring - **[prompts/academic-paper-reviewer/SKILL.md](prompts/academic-paper-reviewer/SKILL.md)** - Academic paper review - **[prompts/academic-pipeline/SKILL.md](prompts/academic-pipeline/SKILL.md)** - Full academic pipeline - **[prompts/agentic-use/SKILL.md](prompts/agentic-use/SKILL.md)** - Agentic-use planning - **[prompts/deep-research/SKILL.md](prompts/deep-research/SKILL.md)** - Deep research synthesis - **[prompts/methods-orchestration/SKILL.md](prompts/methods-orchestration/SKILL.md)** - Methods orchestration ### Prompt reference deep-dives (`prompts/*/references/`) - **[prompts/code-development/references/patterns.md](prompts/code-development/references/patterns.md)** - Code-development prompt patterns - **[prompts/feature-addition/references/checklist.md](prompts/feature-addition/references/checklist.md)** - Feature-addition checklist - **[prompts/literature-synthesis/references/prompt-blocks.md](prompts/literature-synthesis/references/prompt-blocks.md)** - Literature-synthesis prompt blocks - **[prompts/manuscript-creation/references/structure-checklist.md](prompts/manuscript-creation/references/structure-checklist.md)** - Manuscript structure checklist - **[prompts/test-creation/references/patterns.md](prompts/test-creation/references/patterns.md)** - Test patterns (no mocks) --- ## Streams and talks - **[streams/README.md](streams/README.md)** - Navigation index for livestream/talk notes - **[streams/inferant-stream-018-1.md](streams/inferant-stream-018-1.md)** - InferAnt #018.1 — March 2026 stream on the Zenodo paper - **[streams/inferant-stream-019-literature-search.md](streams/inferant-stream-019-literature-search.md)** - InferAnt #019 — Literature search pipeline and tools --- ## Directory structure ```mermaid flowchart TB DOCS[docs hub] DOCS --> ENTRY[entry README AGENTS index] DOCS --> CORE[core guides] DOCS --> GUIDES[guides skill levels] DOCS --> ARCH[architecture] DOCS --> USAGE[usage] DOCS --> OP[operational] DOCS --> REF[reference] DOCS --> MOD[modules] DOCS --> DEV[development] DOCS --> MAINT[maintenance] DOCS --> BP[best-practices] DOCS --> PROMPTS[prompts] DOCS --> SEC[security] DOCS --> STREAMS[streams] DOCS --> RULES[rules] DOCS --> GEN[_generated] OP --> OP_CFG[operational config] OP --> OP_LOG[operational logging] OP --> OP_TS[operational troubleshooting] OP --> OP_BUILD[operational build] ``` --- ## Documentation maintenance notes - Documentation is intended to be evergreen; when behaviour changes, we may include dated notes so it’s clear which guidance is newer. - Each sub-directory has a `README.md` (user-facing) and `AGENTS.md` (technical guide). - Documentation is verified for accuracy and completeness on an ongoing basis. For the most up-to-date information, see the individual documentation files linked above. ## Directory & sub-document map Navigation links to in-tree documents (keeps them discoverable): - [Capability Surfaces — the agent-operable contract](architecture/capability-surfaces.md) - [Publishing readiness — what we can upload today vs. what needs a token](maintenance/publishing-readiness.md) - [Software Heritage archival — docxology repositories](maintenance/software-heritage-archival.md) - [docs/streams/ — Stream and Talk Notes](streams/AGENTS.md)