Repository layout

Stable

Top level

Directory	Holds	Published
`content/`	Every published page, as MDX, plus its `_meta.ts` navigation	Yes
`archive/`	The working files those pages describe	No
`public/`	Files the site serves: assets, favicon, search index	Yes
`registry/`	The machine-readable index of every entity	No
`schemas/`	JSON Schemas the registry is validated against	No
`templates/`	Starting points for new entity records	No
`app/`, `components/`, `lib/`, `styles/`	The site itself	No
`docs/`	Internal working documents; not committed at all	No

Why pages and working files are separated

Two reasons, one technical and one editorial.

Technical. The site’s build compiles everything under content/. A BibTeX file or a YAML configuration in that tree fails the build with an unhelpful error, because the bundler has no idea what to do with it.

Editorial. content/ is deployed publicly. Keeping configurations, raw outputs and correspondence outside it means the question “could this be published by accident?” has a structural answer rather than depending on someone remembering.

The mirror

archive/ mirrors content/ path for path. The working files for the page at content/experiments/EXP-001-experiment-name/ are at archive/experiments/EXP-001-experiment-name/. Nothing has to be searched for, and the pairing survives a rename because both move together.


content/experiments/EXP-001-experiment-name/index.mdx   <- the page
archive/experiments/EXP-001-experiment-name/
  configuration.yaml                                     <- what actually ran
  logs/                                                  <- run logs
  outputs/                                               <- raw outputs

Where research data goes

Not in this repository. It is documentation, and a multi-gigabyte capture committed to it makes every clone slow forever without making the data any more citable.

The DATA- record carries the location, version and checksum, which is what makes a result reproducible. Common research binary formats are refused by .gitignore so that this is a wall rather than a habit.

Assets

Path	For
`public/assets/figures/`	Registered figures, in SVG, PNG and PDF forms
`public/assets/diagrams/`	Rendered diagrams, where source cannot be inlined
`public/assets/images/`	Photographs and screenshots
`public/assets/pdf/`	Decks and documents served from the site
`public/assets/audio/`, `public/assets/video/`	Media

A file under public/ is served to anyone who knows the URL, whether or not a page links to it. Nothing at advisor or confidential visibility goes there.