commands

Wiki Commands Reference

All commands used to operate, maintain, and serve the Dengue Literature Review Wiki.

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Curator Commands (say to Claude)

These are spoken commands that trigger defined workflows in CLAUDE.md.

Command	What it does
ingest [filename]	Reads a PDF, takes git snapshot, discusses 2-3 key takeaways, creates source + all linked pages, fetches citation counts, propagates Questions Raised to state.md Watch Items
ingest --fast [filename]	Same as ingest but skips the discussion step — use for bulk ingests or papers whose scope is already clear
lint or health check	Scans all pages in folder batches (sources → entities/concepts → methods/geography → analyses) for broken links, orphans, thin pages, missing connections, contradictions
update web	Syncs wiki → Quartz content folder and rebuilds the static site
wrap up or that's all	Updates state.md, index, and log before ending the session
query [question]	Answers a question by synthesising across wiki pages; may suggest saving the answer as an analysis page
add a new category for [X]	Creates a new subfolder axis under wiki/ and updates CLAUDE.md
add a notable finding	Appends a flagged finding directly to Notable Findings.md
retract [AuthorYear]	Marks a source as retracted: adds warning banner to source page, flags all linked concept/entity/method pages with inline warnings, adds Watch Item to state.md, logs the retraction
correct [AuthorYear] — [note]	Same as retract but for corrections rather than full retractions — preserves the source page with a correction note
update highlights	Scans all wiki pages for ==highlights== and “, then overwrites Curator Highlights.md with the current snapshot grouped by page

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Terminal Commands

Build & Sync

Run from the webforshare/ folder.

Sync wiki files and rebuild the site (one command):

.\sync-and-build.ps1

Build only (without re-syncing):

npx quartz build

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Preview Locally

Serves the site locally with live-rebuild on file changes:

npx quartz build --serve

Then open: http://localhost:1313

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First-Time Setup

Install Node.js (if not already installed):

winget install OpenJS.NodeJS.LTS

Then restart your terminal, and install Quartz dependencies from the webforshare/ folder:

npm install

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File Locations

Path	Purpose
dengue-wiki/wiki/	Source markdown files (edit here)
webforshare/content/	Synced copy for Quartz (do not edit directly)
webforshare/public/	Built static site (upload this to host)
webforshare/sync-and-build.ps1	Sync + build script
webforshare/quartz.config.ts	Site title, baseUrl, theme settings