git:20260528.db613f8 to git:20260705.989b662

2 added, 2 removed. Audit A to A.

# Usage Documentation

## Overview

Technical guide for `docs/usage/` — content authoring, formatting, visualization, and manuscript patterns for the Research Project Template.

## Files

| File | Purpose |

|------|---------|

| `examples.md` | Project renaming and customization examples |

| `examples-showcase.md` | Real-world usage showcase |

| `template-description.md` | Template feature overview |

| `markdown-template-guide.md` | Markdown authoring and cross-referencing |

| `output-formats.md` | Five-format output reference: PDF/HTML/Slides/DOCX/EPUB + `render.formats` config |

| `manuscript-numbering-system.md` | Section numbering conventions |

| `style-guide.md` | Equations, figures, captions, and tables |

| `image-management.md` | Image insertion, captioning, and cross-referencing |

| `visualization-guide.md` | Publication-quality figure generation |

## Key Conventions

- **Manuscript examples**: default to [`projects/templates/template_code_project/manuscript/`](../../projects/templates/template_code_project/manuscript/); active `projects/` names → [_generated/active_projects.md](../_generated/active_projects.md).

- - Figures use LaTeX `\begin{figure}` environments with `\label{fig:name}` and `\ref{fig:name}`

- - Equations use `\begin{equation}\label{eq:name}` and `\eqref{eq:name}`

+ - Figures use Pandoc image syntax `![caption](path){#fig:name}` with cross-references `[@fig:name]` — never a raw LaTeX `\begin{figure}`/`\ref{fig:name}` pair (see [Manuscript Semantics](../guides/manuscript-semantics.md)).

+ - Equations use `$$ … $$ {#eq:name}` (or `\begin{equation}\label{eq:name}…\end{equation}`) with cross-references `[@eq:name]` — never raw `\eqref{eq:name}`.

- All images must exist in `output/figures/` before manuscript build

- Use descriptive link text (no bare URLs)

- Follow the style guide for consistent formatting

## See Also

- [README.md](README.md) — Quick navigation

- [Visualization Guide](visualization-guide.md) — Figure generation details

- [Modules Guide](../modules/modules-guide.md) — Analysis module usage