How to generate a categories.json file?

Here is a working solution, with json files for all taxonomies being created:

config.json

,
"outputs": {
    "taxonomyTerm": ["html", "json"]
}

layouts/_default/terms.json

{{- $.Scratch.Add "index" slice -}}
{{- range $index, $element := .Data.Pages.ByTitle -}}
    {{- $.Scratch.Add "index" (dict "id" $index "name" $element.Name "link" $element.Permalink) -}}
{{- end -}}
{{- $.Scratch.Get "index" | jsonify -}}

The big confusion for me at least is that taxonomyTerm is the list of the terms in the taxonomy and the taxonomy is a term in the taxonomy.

using Hugo Static Site Generator v0.70.0

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