Advanced infrastructure modules documentation
Quick Reference: Modules Guide | Scientific Simulation | PDF Validation | Per-Module Guides
The modules/ directory contains documentation for the advanced infrastructure modules that extend the Research Project Template with enterprise-grade capabilities.
| File | Purpose | Audience |
|---|---|---|
modules-guide.md |
Guide for infrastructure modules | Developers |
scientific-simulation-guide.md |
Scientific simulation and analysis system | Researchers |
pdf-validation.md |
PDF validation system documentation | Developers |
| Module | Guide | Focus |
|---|---|---|
| AutoResearch | guides/autoresearch-module.md |
Deterministic readiness plans, evidence, artifacts |
| Benchmark | guides/benchmark-module.md |
Public exemplar benchmark manifests and rubrics |
| Config | guides/config-module.md |
Configuration schemas, templates |
| Core | guides/core-module.md |
Logging, config, exceptions, pipeline, telemetry |
| Docker | guides/docker-module.md |
Dockerfile, compose |
| Documentation | guides/documentation-module.md |
Figure management, API glossary |
| Integrity | guides/integrity-module.md |
File integrity, cross-reference validation |
| LLM | guides/llm-module.md |
Ollama integration, research templates |
| Methods | guides/methods-module.md |
Methods orchestration plans |
| Project | guides/project-module.md |
Multi-project discovery, validation, CodeGraph helpers |
| Publishing | guides/publishing-module.md |
12-platform registry, DOI/citations, credential verification, README status compilation, multi-platform upload dispatch |
| Rendering | guides/rendering-module.md |
PDF, slides, web output |
| Reporting | guides/reporting-module.md |
Pipeline reports, error aggregation |
| Scientific | guides/scientific-module.md |
Numerical stability, benchmarking |
| Skills | guides/skills-module.md |
SKILL.md discovery, manifest generation |
| Steganography | guides/steganography-module.md |
PDF watermarking, provenance |
| Validation | guides/validation-module.md |
PDF/Markdown validation, auditing |
| Doctor | guides/doctor-module.md |
Repository health diagnostics |
| Orchestration | guides/orchestration-module.md |
Pipeline CLI and menus |
| Prose | guides/prose-module.md |
Readability metrics, editorial heuristics |
| Search | guides/search-module.md |
Literature discovery and indexing |
| Reference | guides/reference-module.md |
BibTeX and citation utilities |
| SIA | guides/sia-module.md |
Meta → Target → Feedback self-improvement harness |
→ Read Modules Guide - Modules guide
→ Study Scientific Simulation Guide - Simulation system
→ Reference PDF Validation - Validation system
Importable package names and counts are tracked in COUNTS.md. Per-module deep dives live in guides/; config/ and docker/ are configuration directories rather than Python packages.
../reference/api-reference.md- API documentation../RUN_GUIDE.md- Pipeline integration../core/architecture.md- System architecture
../documentation-index.md- documentation index../README.md- Documentation hub overview