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docs/ - Documentation

Documentation hub for the Research Project Template

Quick Reference: Documentation Index | How To Use | Architecture | FAQ | GitHub / CI

Purpose

The docs/ directory contains project documentation organized by purpose and audience. This is the central hub for all project documentation beyond code comments.

Machine-generated snippets (including the authoritative list of active projects/ workspaces) live under _generated/. Human-written pages should link there instead of copying project rosters; concrete examples should use projects/code_project/ as the control-positive layout.

Documentation Navigation Map

graph TD
    subgraph EntryPoints["Entry points"]
        README[README.md<br/>Project Overview]
        DOC_INDEX[documentation-index.md<br/>Full Index]
        HOW_TO[core/how-to-use.md<br/>Usage Guide<br/>12 Skill Levels]
    end

    subgraph CoreDocs["Core documentation"]
        ARCH[core/architecture.md<br/>System Design]
        WORKFLOW[core/workflow.md<br/>Development Process]
    end

    subgraph SkillLevels["Skill-based learning"]
        L1[guides/getting-started.md<br/>Levels 1-3: Beginner]
        L2[guides/figures-and-analysis.md<br/>Levels 4-6: Intermediate]
        L3[guides/testing-and-reproducibility.md<br/>Levels 7-9: Advanced]
        L4[guides/extending-and-automation.md<br/>Levels 10-12: Expert]
    end

    subgraph Operational["Operational"]
        PIPELINE[RUN_GUIDE.md<br/>Pipeline Orchestration]
        TROUBLESHOOT[operational/troubleshooting/<br/>Fix Issues]
        CONFIG[operational/config/<br/>Settings and Performance]
        LOGGING[operational/logging/<br/>Logging System]
    end

    subgraph Reference["Reference"]
        FAQ[reference/faq.md<br/>Common Questions]
        CHEATSHEET[reference/quick-start-cheatsheet.md<br/>Command Reference]
        API[reference/api-reference.md<br/>Unified API Docs]
        RULES[rules/AGENTS.md<br/>Development Standards]
    end

    README --> DOC_INDEX
    README --> HOW_TO
    DOC_INDEX --> CoreDocs
    DOC_INDEX --> SkillLevels
    DOC_INDEX --> Operational
    DOC_INDEX --> Reference

    HOW_TO --> L1
    L1 --> L2
    L2 --> L3
    L3 --> L4

    ARCH --> WORKFLOW

    PIPELINE --> TROUBLESHOOT
    TROUBLESHOOT --> CONFIG

    FAQ --> CHEATSHEET
    CHEATSHEET --> API
    API --> RULES
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Directory Structure

Directory Purpose Key Contents
core/ Essential documentation how-to-use.md, architecture.md, workflow.md
guides/ Skill-level guides (1-12) getting-started, figures-and-analysis, testing, extending
architecture/ System design two-layer-architecture.md, thin-orchestrator, decision-tree
usage/ Content authoring & patterns examples, markdown guide, style guide, visualization
operational/ Operational workflows config/, logging/, troubleshooting/ sub-folders
reference/ Reference materials api-reference, faq, glossary, cheatsheet, workflows
modules/ Infrastructure modules modules-guide, scientific simulation, pdf-validation, guides/
development/ Development & contribution contributing, security, roadmap, testing/ sub-folder
best-practices/ Best practices version-control, migration, multi-project, backup-recovery
prompts/ AI prompt templates (9 + README/AGENTS) manuscript, code, test, feature, refactoring, assessment
security/ Security & provenance steganography, hashing, secure execution
audit/ Audit reports documentation-review, filepath-audit
rules/ Project Rules AGENTS, README, testing, manuscript, etc.
streams/ Livestream & talk notes timestamped session notes tied to releases or papers
_generated/ Generated snippets AGENTS.md, active_projects.md (discover_projects roster)

Quick Navigation

New Users Start Here

  1. ../README.md - Project overview
  2. core/how-to-use.md - Usage guide
  3. guides/getting-started.md - Getting started (Levels 1-3)
  4. reference/faq.md - Common questions

Creating a New Project

  1. guides/new-project-setup.md - Complete setup checklist with all pitfalls
  2. architecture/thin-orchestrator-summary.md - Script pattern

Developers Start Here

  1. core/architecture.md - System design overview
  2. architecture/two-layer-architecture.md - Full architecture guide
  3. architecture/thin-orchestrator-summary.md - Pattern details
  4. core/workflow.md - Development process
  5. development/contributing.md - How to contribute

Quick Links

Need Document
Get started core/how-to-use.md
Create a new project guides/new-project-setup.md
Understand design architecture/two-layer-architecture.md
See examples usage/examples.md
Find answers reference/faq.md
Fix an issue operational/troubleshooting/
Contribute development/contributing.md
Report security issue development/security.md

See Also