initial flake app

- glob.ts: add optional respectGitignore param (default true) so callers
  can opt out of gitignore filtering for generated directories
- build.ts: pass respectGitignore=false when globbing content/ so
  gitignored-but-generated markdown files are always picked up
- static.ts: copy top-level static/ → output/ root with gitignore disabled,
  mirroring Hugo's convention so ox-hugo images at static/ox-hugo/* are
  served at /ox-hugo/* as expected by the exported markdown src paths
- oxhugofm.ts: run replaceFigureWithMdImg before removeHugoShortcode so the
  precise figure regex sees the intact shortcode before the generic {{.*}}
  stripper destroys it; also upgrade figureTagRegex to figureShortcodeRegex
  which matches the full shortcode form ox-hugo actually emits

.github/workflows/build-preview.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     name: Build Preview
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -21,7 +21,7 @@ jobs:
           node-version: 22
 
       - name: Cache dependencies
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -37,7 +37,7 @@ jobs:
         run: npx quartz build -d docs -v
 
       - name: Upload build artifact
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v6
         with:
           name: preview-build
           path: public

.github/workflows/ci.yaml

@@ -19,7 +19,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -29,7 +29,7 @@ jobs:
           node-version: 22
 
       - name: Cache dependencies
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -53,7 +53,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Setup Node

.github/workflows/deploy-preview.yaml

@@ -18,7 +18,7 @@ jobs:
     name: Deploy Preview to Cloudflare Pages
     steps:
       - name: Download build artifact
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v7
         id: preview-build-artifact
         with:
           name: preview-build

.github/workflows/docker-build-push.yaml

@@ -21,11 +21,11 @@ jobs:
           echo "OWNER_LOWERCASE=${OWNER,,}" >> ${GITHUB_ENV}
         env:
           OWNER: "${{ github.repository_owner }}"
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 1
       - name: Inject slug/short variables
-        uses: rlespinasse/github-slug-action@v5.3.0
+        uses: rlespinasse/github-slug-action@v5.4.0
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v3
       - name: Set up Docker Buildx

.gitignore

@@ -9,3 +9,16 @@ tsconfig.tsbuildinfo
 private/
 .replit
 replit.nix
+erl_crash.dump
+# content/ is generated by the export script; only keep the placeholder
+content/*
+!content/.gitkeep
+# static/ox-hugo/ is populated by ox-hugo during export
+static/ox-hugo/
+# Elixir/Mix build artifacts for the pipeline project
+scripts/pipeline/_build/
+scripts/pipeline/deps/
+scripts/pipeline/erl_crash.dump
+# Test helpers (not needed in production)
+scripts/test.bib
+scripts/test_pipeline.exs

AGENTS.md

@@ -0,0 +1,361 @@
+# AGENTS.md - Coding Agent Instructions
+
+This document provides essential information for AI coding agents working in this repository.
+
+## Project Overview
+
+**Quartz** is a static site generator for publishing digital gardens and notes as websites.
+Built with TypeScript, Preact, and unified/remark/rehype for markdown processing.
+
+| Stack         | Technology                                |
+| ------------- | ----------------------------------------- |
+| Language      | TypeScript 5.x (strict mode)              |
+| Runtime       | Node.js >=22 (v22.16.0 pinned)            |
+| Package Mgr   | npm >=10.9.2                              |
+| Module System | ES Modules (`"type": "module"`)           |
+| UI Framework  | Preact 10.x (JSX with `react-jsx` pragma) |
+| Build Tool    | esbuild                                   |
+| Styling       | SCSS via esbuild-sass-plugin              |
+
+## Environment
+
+This is a Nix project. Use the provided `flake.nix` to enter a dev shell with Node.js 22 and npm:
+
+```bash
+nix develop
+```
+
+All `npm` commands below must be run inside the dev shell.
+
+## Build, Lint, and Test Commands
+
+```bash
+# Type check and format check (CI validation)
+npm run check
+
+# Auto-format code with Prettier
+npm run format
+
+# Run all tests
+npm run test
+
+# Run a single test file
+npx tsx --test quartz/util/path.test.ts
+
+# Run tests matching a pattern (use --test-name-pattern)
+npx tsx --test --test-name-pattern="typeguards" quartz/util/path.test.ts
+
+# Build the static site
+npx quartz build
+
+# Build and serve with hot reload
+npx quartz build --serve
+
+# Profile build performance
+npm run profile
+```
+
+### Test Files Location
+
+Tests use Node.js native test runner via `tsx`. Test files follow the `*.test.ts` pattern:
+
+- `quartz/util/path.test.ts`
+- `quartz/util/fileTrie.test.ts`
+- `quartz/components/scripts/search.test.ts`
+
+## Code Style Guidelines
+
+### Prettier Configuration (`.prettierrc`)
+
+```json
+{
+  "printWidth": 100,
+  "tabWidth": 2,
+  "semi": false,
+  "trailingComma": "all",
+  "quoteProps": "as-needed"
+}
+```
+
+**No ESLint** - only Prettier for formatting. Run `npm run format` before committing.
+
+### TypeScript Configuration
+
+- **Strict mode enabled** (`strict: true`)
+- `noUnusedLocals: true` - no unused variables
+- `noUnusedParameters: true` - no unused function parameters
+- JSX configured for Preact (`jsxImportSource: "preact"`)
+
+### Import Conventions
+
+```typescript
+// 1. External packages first
+import { PluggableList } from "unified"
+import { visit } from "unist-util-visit"
+
+// 2. Internal utilities/types (relative paths)
+import { QuartzTransformerPlugin } from "../types"
+import { FilePath, slugifyFilePath } from "../../util/path"
+import { i18n } from "../../i18n"
+```
+
+### Naming Conventions
+
+| Element          | Convention   | Example                             |
+| ---------------- | ------------ | ----------------------------------- |
+| Files (utils)    | camelCase    | `path.ts`, `fileTrie.ts`            |
+| Files (comps)    | PascalCase   | `TableOfContents.tsx`, `Search.tsx` |
+| Types/Interfaces | PascalCase   | `QuartzComponent`, `FullSlug`       |
+| Type Guards      | `is*` prefix | `isFilePath()`, `isFullSlug()`      |
+| Constants        | UPPER_CASE   | `QUARTZ`, `UPSTREAM_NAME`           |
+| Options types    | `Options`    | `interface Options { ... }`         |
+
+### Branded Types Pattern
+
+This codebase uses branded types for type-safe path handling:
+
+```typescript
+type SlugLike<T> = string & { __brand: T }
+export type FilePath = SlugLike<"filepath">
+export type FullSlug = SlugLike<"full">
+export type SimpleSlug = SlugLike<"simple">
+
+// Always validate with type guards before using
+export function isFilePath(s: string): s is FilePath { ... }
+```
+
+### Component Pattern (Preact)
+
+Components use a factory function pattern with attached static properties:
+
+```typescript
+export default ((userOpts?: Partial<Options>) => {
+  const opts: Options = { ...defaultOptions, ...userOpts }
+
+  const ComponentName: QuartzComponent = ({ cfg, displayClass }: QuartzComponentProps) => {
+    return <div class={classNames(displayClass, "component-name")}>...</div>
+  }
+
+  ComponentName.css = style           // SCSS styles
+  ComponentName.afterDOMLoaded = script  // Client-side JS
+  return ComponentName
+}) satisfies QuartzComponentConstructor
+```
+
+### Plugin Pattern
+
+Three plugin types: transformers, filters, and emitters.
+
+```typescript
+export const PluginName: QuartzTransformerPlugin<Partial<Options>> = (userOpts) => {
+  const opts = { ...defaultOptions, ...userOpts }
+  return {
+    name: "PluginName",
+    markdownPlugins(ctx) { return [...] },
+    htmlPlugins(ctx) { return [...] },
+    externalResources(ctx) { return { js: [], css: [] } },
+  }
+}
+```
+
+### Testing Pattern
+
+Use Node.js native test runner with `assert`:
+
+```typescript
+import test, { describe, beforeEach } from "node:test"
+import assert from "node:assert"
+
+describe("FeatureName", () => {
+  test("should do something", () => {
+    assert.strictEqual(actual, expected)
+    assert.deepStrictEqual(actualObj, expectedObj)
+    assert(condition) // truthy assertion
+    assert(!condition) // falsy assertion
+  })
+})
+```
+
+### Error Handling
+
+- Use `try/catch` for critical operations (file I/O, parsing)
+- Custom `trace` utility for error reporting with stack traces
+- `process.exit(1)` for fatal errors
+- `console.warn()` for non-fatal issues
+
+### Async Patterns
+
+- Prefer `async/await` over raw promises
+- Use async generators (`async *emit()`) for streaming file output
+- Use `async-mutex` for concurrent build protection
+
+## Project Structure
+
+```
+quartz/
+├── bootstrap-cli.mjs    # CLI entry point
+├── build.ts             # Build orchestration
+├── cfg.ts               # Configuration types
+├── components/          # Preact UI components
+│   ├── *.tsx            # Components
+│   ├── scripts/         # Client-side scripts (*.inline.ts)
+│   └── styles/          # Component SCSS
+├── plugins/
+│   ├── transformers/    # Markdown AST transformers
+│   ├── filters/         # Content filters
+│   ├── emitters/        # Output generators
+│   └── types.ts         # Plugin type definitions
+├── processors/          # Build pipeline (parse/filter/emit)
+├── util/                # Utility functions
+└── i18n/                # Internationalization (30+ locales)
+```
+
+## Branch Workflow
+
+This is a fork of [jackyzha0/quartz](https://github.com/jackyzha0/quartz) with org-roam customizations.
+
+| Branch      | Purpose                                          |
+| ----------- | ------------------------------------------------ |
+| `main`      | Clean mirror of upstream quartz — no custom code |
+| `org-roam`  | Default branch — all customizations live here    |
+| `feature/*` | Short-lived branches off `org-roam`              |
+
+### Pulling Upstream Updates
+
+```bash
+git checkout main
+git fetch upstream
+git merge upstream/main
+git checkout org-roam
+git merge main
+# Resolve conflicts if any, then commit
+```
+
+### Working on Features
+
+```bash
+git checkout org-roam
+git checkout -b feature/my-feature
+# ... work ...
+git checkout org-roam
+git merge feature/my-feature
+git branch -d feature/my-feature
+```
+
+**Merge direction:** `upstream → main → org-roam → feature/*`
+
+## Org-Roam Workflow
+
+Notes live in a **separate directory** outside this repo. The export pipeline
+converts them to Markdown via ox-hugo, applies post-processing transforms, then
+Quartz builds the site.
+
+### Tooling
+
+The dev shell (`nix develop`) provides:
+
+- `nodejs_22` — Quartz build
+- `elixir` — runs the export script and pipeline
+- `emacs` + `ox-hugo` — performs the org → markdown conversion
+
+### Export and build
+
+```bash
+# Export only (wipes content/, exports all .org files, runs pipeline)
+NOTES_DIR=/path/to/notes npm run export
+
+# Export then build the site
+NOTES_DIR=/path/to/notes npm run build:notes
+
+# Positional arg also works
+elixir scripts/export.exs /path/to/notes
+```
+
+Optional env vars for the pipeline:
+
+| Var             | Default                  | Purpose                                   |
+| --------------- | ------------------------ | ----------------------------------------- |
+| `BIBTEX_FILE`   | —                        | Path to `.bib` file for citation fallback |
+| `ZOTERO_URL`    | `http://localhost:23119` | Zotero Better BibTeX base URL             |
+| `CITATION_MODE` | `warn`                   | `silent` / `warn` / `strict`              |
+
+### Export pipeline phases
+
+`scripts/export.exs` runs four phases in sequence:
+
+1. **Wipe** `content/` (preserving `.gitkeep`)
+2. **Export** each `.org` file via `emacs --batch` + `ox-hugo` → `content/**/*.md`
+3. **Pipeline** — run Elixir transform modules over every `.md` file
+4. **Index** — generate a fallback `content/index.md` if none was exported
+
+The export uses TOML frontmatter (`+++`) and per-file mode (not per-subtree).
+
+### Markdown pipeline (`scripts/pipeline/`)
+
+A standalone Mix project that post-processes `content/*.md` after ox-hugo.
+It is compiled automatically on first run; subsequent runs use the `_build/`
+cache and are fast.
+
+**Architecture:**
+
+```
+scripts/pipeline/
+├── mix.exs                          # deps: req, jason
+└── lib/
+    ├── pipeline.ex                  # Generic runner (fold transforms over .md files)
+    ├── pipeline/
+    │   ├── application.ex           # OTP app — starts Finch HTTP pool
+    │   ├── transform.ex             # Behaviour: init/1, apply/3, teardown/1
+    │   ├── transforms/
+    │   │   └── citations.ex         # Resolves cite:key → [Label](url)
+    │   └── resolvers/
+    │       ├── zotero.ex            # JSON-RPC to Zotero Better BibTeX
+    │       ├── bibtex.ex            # Parses local .bib file
+    │       └── doi.ex               # Bare-key fallback (always succeeds)
+```
+
+**Adding a new transform:**
+
+1. Create `scripts/pipeline/lib/pipeline/transforms/my_transform.ex`
+2. Implement the `Pipeline.Transform` behaviour (`init/1`, `apply/3`)
+3. Append the module to `transforms` in `scripts/export.exs`
+
+```elixir
+transforms = [
+  Pipeline.Transforms.Citations,
+  Pipeline.Transforms.MyTransform,  # new
+]
+```
+
+### Citation resolution (`Pipeline.Transforms.Citations`)
+
+Handles org-citar syntax that passes through ox-hugo unchanged:
+
+| Syntax           | Example              |
+| ---------------- | -------------------- |
+| org-cite / citar | `[cite:@key]`        |
+| multiple keys    | `[cite:@key1;@key2]` |
+| bare (legacy)    | `cite:key`           |
+
+Resolution chain (first success wins):
+
+1. **Zotero** — JSON-RPC to `localhost:23119/better-bibtex/json-rpc`
+   - Calls `item.search` to find the item, then `item.attachments` to get
+     the PDF link (`zotero://open-pdf/library/items/KEY`)
+   - Falls back to `zotero://select/library/items/KEY` if no PDF attachment
+   - Probe uses a JSON-RPC call, **not** `/better-bibtex/cayw`
+     (that endpoint blocks waiting for interactive input)
+2. **BibTeX** — parses `BIBTEX_FILE`; extracts authors, year, DOI/URL
+3. **DOI fallback** — always succeeds; renders bare key or `https://doi.org/...`
+
+**Zotero JSON-RPC gotcha:** `Req 0.5` does not allow combining `:finch` and
+`:connect_options` in the same call. Use `:receive_timeout` only.
+
+## Important Notes
+
+- **Client-side scripts**: Use `.inline.ts` suffix, bundled via esbuild
+- **Isomorphic code**: `quartz/util/path.ts` must not use Node.js APIs
+- **Incremental builds**: Plugins can implement `partialEmit` for efficiency
+- **Markdown flavors**: Supports Obsidian (`ofm.ts`) and Roam (`roam.ts`) syntax
+- **Pipeline build artifacts**: `scripts/pipeline/_build/` and `scripts/pipeline/deps/`
+  are gitignored — run `mix deps.get` inside `scripts/pipeline/` after a fresh clone

README.md

@@ -1,14 +1,96 @@
-# Quartz v4
+# Quartz v4 — org-roam edition
 
-> “[One] who works with the door open gets all kinds of interruptions, but [they] also occasionally gets clues as to what the world is and what might be important.” — Richard Hamming
+> "[One] who works with the door open gets all kinds of interruptions, but [they] also occasionally gets clues as to what the world is and what might be important." — Richard Hamming
 
 Quartz is a set of tools that helps you publish your [digital garden](https://jzhao.xyz/posts/networked-thought) and notes as a website for free.
-Quartz v4 features a from-the-ground rewrite focusing on end-user extensibility and ease-of-use.
 
-🔗 Read the documentation and get started: https://quartz.jzhao.xyz/
+This fork adds first-class support for [org-roam](https://www.orgroam.com/) notes via [ox-hugo](https://ox-hugo.scripter.co/).
+
+🔗 Upstream documentation: https://quartz.jzhao.xyz/
 
 [Join the Discord Community](https://discord.gg/cRFFHYye7t)
 
+## Quick Start
+
+### Prerequisites
+
+This project uses Nix. Enter the development shell, which provides Node.js 22, Elixir, and Emacs with ox-hugo:
+
+```bash
+nix develop
+```
+
+All commands below must be run inside this shell.
+
+```bash
+npm install
+```
+
+### Building from org-roam notes
+
+Your org-roam notes live in a separate directory. Point `NOTES_DIR` at it:
+
+```bash
+# Export notes to content/ and build the site
+NOTES_DIR=/path/to/notes npm run build:notes
+
+# Export, build, and serve with hot reload
+NOTES_DIR=/path/to/notes npm run serve:notes
+
+# Export only (wipes content/ and re-exports all .org files)
+NOTES_DIR=/path/to/notes npm run export
+```
+
+The export pipeline runs in four phases:
+
+1. **Wipe** `content/` clean
+2. **Export** every `.org` file via `emacs --batch` + ox-hugo → Markdown
+3. **Transform** — post-process the Markdown (citation resolution, etc.)
+4. **Index** — generate a fallback `index.md` if none was exported
+
+#### Citations (org-citar → Zotero links)
+
+org-citar references (`[cite:@key]`) are resolved to clickable Zotero links.
+With Zotero running and the [Better BibTeX](https://retorque.re/zotero-better-bibtex/)
+plugin installed, no extra configuration is needed — the pipeline detects it
+automatically and links directly to the PDF in your library.
+
+```bash
+# Use a local .bib file as fallback when Zotero is not running
+BIBTEX_FILE=/path/to/refs.bib NOTES_DIR=/path/to/notes npm run export
+
+# Control warning verbosity for unresolved keys
+CITATION_MODE=strict NOTES_DIR=/path/to/notes npm run export
+```
+
+| Env var         | Default                  | Purpose                                   |
+| --------------- | ------------------------ | ----------------------------------------- |
+| `BIBTEX_FILE`   | —                        | Path to `.bib` file for citation fallback |
+| `ZOTERO_URL`    | `http://localhost:23119` | Zotero Better BibTeX base URL             |
+| `CITATION_MODE` | `warn`                   | `silent` / `warn` / `strict`              |
+
+### Building without org-roam notes
+
+If you manage `content/` directly with Markdown files:
+
+```bash
+# Build the site
+npx quartz build
+
+# Build and serve with hot reload
+npx quartz build --serve
+```
+
+The site is generated in `public/`. When serving, visit http://localhost:8080.
+
+### Development
+
+```bash
+npm run check    # type check + format check
+npm run format   # auto-format with Prettier
+npm run test     # run tests
+```
+
 ## Sponsors
 
 <p align="center">

docs/configuration.md

@@ -36,6 +36,7 @@ This part of the configuration concerns anything that can affect the whole site.
   - `{provider: 'clarity', projectId: '<your-clarity-id-code' }`: use [Microsoft clarity](https://clarity.microsoft.com/). The project id can be found on top of the overview page.
   - `{ provider: 'matomo', siteId: '<your-matomo-id-code', host: 'matomo.example.com' }`: use [Matomo](https://matomo.org/), without protocol.
   - `{ provider: 'vercel' }`: use [Vercel Web Analytics](https://vercel.com/docs/concepts/analytics).
+  - `{ provider: 'rybbit', siteId: 'my-rybbit-id' }` (managed) or `{ provider: 'rybbit', siteId: 'my-rybbit-id', host: 'my-rybbit-domain.com' }` (self-hosted) use [Rybbit](https://rybbit.com);
 - `locale`: used for [[i18n]] and date formatting
 - `baseUrl`: this is used for sitemaps and RSS feeds that require an absolute URL to know where the canonical 'home' of your site lives. This is normally the deployed URL of your site (e.g. `quartz.jzhao.xyz` for this site). Do not include the protocol (i.e. `https://`) or any leading or trailing slashes.
   - This should also include the subpath if you are [[hosting]] on GitHub pages without a custom domain. For example, if my repository is `jackyzha0/quartz`, GitHub pages would deploy to `https://jackyzha0.github.io/quartz` and the `baseUrl` would be `jackyzha0.github.io/quartz`.

docs/features/Docker Support.md

@@ -5,3 +5,7 @@ You can run the below one-liner to run Quartz in Docker.
 ```sh
 docker run --rm -itp 8080:8080 -p 3001:3001 -v ./content:/usr/src/app/content $(docker build -q .)
 ```
+
+> [!warning] Not to be used for production
+> Serve mode is intended for local previews only.
+> For production workloads, see the page on [[hosting]].

docs/features/explorer.md

@@ -162,7 +162,7 @@ You can access the tags of a file by `node.data.tags`.
 Component.Explorer({
   filterFn: (node) => {
     // exclude files with the tag "explorerexclude"
-    return node.data.tags?.includes("explorerexclude") !== true
+    return node.data?.tags?.includes("explorerexclude") !== true
   },
 })
 ```

docs/features/popover previews.md

@@ -8,7 +8,7 @@ By default, Quartz only fetches previews for pages inside your vault due to [COR
 
 When [[creating components|creating your own components]], you can include this `popover-hint` class to also include it in the popover.
 
-Similar to Obsidian, [[quartz layout.png|images referenced using wikilinks]] can also be viewed as popups.
+Similar to Obsidian, [[quartz-layout-desktop.png|images referenced using wikilinks]] can also be viewed as popups.
 
 ## Configuration
 

flake.lock

@@ -0,0 +1,61 @@
+{
+  "nodes": {
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1731533236,
+        "narHash": "sha256-l0KFg5HjrsfsO/JpG+r7fRrqm12kzFHyUHqHCVpMMbI=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "11707dc2f618dd54ca8739b309ec4fc024de578b",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1771008912,
+        "narHash": "sha256-gf2AmWVTs8lEq7z/3ZAsgnZDhWIckkb+ZnAo5RzSxJg=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "a82ccc39b39b621151d6732718e3e250109076fa",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nixpkgs": "nixpkgs"
+      }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

flake.nix

@@ -0,0 +1,99 @@
+{
+  description = "Quartz org-roam dev shell and build app";
+
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+    flake-utils.url = "github:numtide/flake-utils";
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs { inherit system; };
+
+        # Emacs with ox-hugo — shared between devShell and buildApp
+        emacsWithOxHugo = (pkgs.emacsPackagesFor pkgs.emacs-nox).emacsWithPackages
+          (epkgs: [ epkgs.ox-hugo ]);
+
+        # Pre-fetched npm dependency tree (node_modules)
+        quartzDeps = pkgs.buildNpmPackage {
+          pname = "quartz-deps";
+          version = "4.5.2";
+          src = ./.;
+          npmDepsHash = "sha256-7u+VlIx44B3/ivM9vLMIOn+e4TL4eS6B682vhS+Ikb4=";
+          dontBuild = true;
+          installPhase = ''
+            mkdir -p $out
+            cp -r node_modules $out/node_modules
+          '';
+        };
+
+        # Pre-fetched Hex/Mix dependencies for scripts/pipeline
+        pipelineMixDeps = pkgs.beamPackages.fetchMixDeps {
+          pname = "pipeline-mix-deps";
+          version = "0.1.0";
+          src = ./scripts/pipeline;
+          sha256 = "sha256-E79X+nUy86G1Jrwv3T7dXekoGv8Hd14ZgJSKWjvlmAw=";
+        };
+
+        # The build application wrapper script
+        buildApp = pkgs.writeShellApplication {
+          name = "build";
+          runtimeInputs = [ pkgs.nodejs_22 pkgs.elixir emacsWithOxHugo ];
+          text = ''
+            NOTES_DIR="''${1:?Usage: build <path-to-notes-dir>}"
+            NOTES_DIR=$(realpath "$NOTES_DIR")
+            ORIG_CWD=$(pwd)
+
+            # Set up a writable working copy of the repo in a temp dir
+            WORK=$(mktemp -d)
+            trap 'rm -rf "$WORK"' EXIT
+            cp -r ${self}/. "$WORK/repo"
+            chmod -R u+w "$WORK/repo"
+
+            # Drop in pre-built node_modules
+            ln -s ${quartzDeps}/node_modules "$WORK/repo/node_modules"
+
+            # Drop in pre-fetched Mix deps so mix compile runs offline
+            cp -r ${pipelineMixDeps} "$WORK/repo/scripts/pipeline/deps"
+            chmod -R u+w "$WORK/repo/scripts/pipeline/deps"
+
+            # ox-hugo requires static/ to exist before it can copy image assets
+            mkdir -p "$WORK/repo/static"
+
+            # Run the export pipeline (org → md, citations transform)
+            NOTES_DIR="$NOTES_DIR" elixir "$WORK/repo/scripts/export.exs"
+
+            # Build the static site from within the repo copy so relative paths
+            # (e.g. ./package.json in constants.js) resolve correctly.
+            # --output is absolute so the result lands in the caller's cwd.
+            cd "$WORK/repo"
+            node quartz/bootstrap-cli.mjs build \
+              --directory "$WORK/repo/content" \
+              --output "$ORIG_CWD/public"
+          '';
+        };
+      in
+      {
+        devShells.default = pkgs.mkShell {
+          buildInputs = [
+            pkgs.nodejs_22
+            pkgs.elixir
+            emacsWithOxHugo
+            pkgs.mcp-nixos
+          ];
+
+          shellHook = ''
+            echo "Node $(node --version) / npm $(npm --version)"
+            elixir --version 2>/dev/null | head -1 || true
+            echo "Emacs $(emacs --version | head -1)"
+          '';
+        };
+
+        packages.default = buildApp;
+        packages.build = buildApp;
+
+        apps.default = { type = "app"; program = "${buildApp}/bin/build"; };
+        apps.build = { type = "app"; program = "${buildApp}/bin/build"; };
+      });
+}

notes/bus/emt-madrid.org

@@ -0,0 +1,16 @@
+:PROPERTIES:
+:ID:       emt-madrid
+:END:
+#+title: EMT Madrid (urban bus)
+
+Empresa Municipal de Transportes (EMT) operates the urban bus network
+within the municipality of Madrid — around 200 lines.
+
+* Notable lines
+- *Line 27* — connects Embajadores with Barrio de la Concepción, one of the
+  oldest routes in the network.
+- *Line 34* — Argüelles to Carabanchel, crossing the city centre via Gran Vía.
+- *Búho (owl) lines* — night buses running from Cibeles from midnight to 6 am.
+
+* See also
+- [[id:madrid-transport][Madrid Public Transport]]

notes/example-citation.org

@@ -0,0 +1,13 @@
+#+title: Example: Citation Reference
+
+This file demonstrates how org-citar citations pass through ox-hugo into
+markdown, where the pipeline transform resolves them.
+
+The methodology described in [cite:@podlovics2021journalArticle] provides a
+useful framework for analysis.
+
+Multiple citations can appear together:
+[cite:@podlovics2021journalArticle]
+
+Older bare-cite style (org-roam v1 / older citar) also works:
+cite:podlovics2021journalArticle

notes/example-images.org

@@ -0,0 +1,33 @@
+:PROPERTIES:
+:ID:       example-images
+:END:
+#+title: Example: Image References
+
+This note demonstrates the three image reference scenarios that the pipeline
+must handle.
+
+* Scenario 1: External image (URL)
+
+An image hosted on the web — ox-hugo passes the URL through as-is and no
+local file handling is needed.
+
+#+attr_html: :link "https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcSkzsTuLOt8esM6enoKwkzqA52G3p9hldlf2g&s"
+[[file:quartz-logo-external.png]]
+
+* Scenario 2: Local image (same notes directory)
+
+An image sitting next to this .org file inside the notes directory.
+ox-hugo copies files referenced with a relative path into the Hugo =static/=
+assets tree automatically.
+
+#+CAPTION: Quartz logo (local, same notes dir)
+[[file:quartz-logo.png]]
+
+* Scenario 3: External image (outside notes directory)
+
+An image that lives outside the notes directory entirely — for example a
+shared assets folder or a system path. ox-hugo still copies it into =static/=
+and rewrites the reference.
+
+#+CAPTION: Quartz logo (outside notes dir)
+[[file:../notes-external/external-location-image.png]]

notes/madrid-transport.org

@@ -0,0 +1,17 @@
+:PROPERTIES:
+:ID:       madrid-transport
+:END:
+#+title: Madrid Public Transport
+
+Madrid has one of the most extensive public transport networks in Europe,
+operated primarily by [[id:crtm][Consorcio Regional de Transportes de Madrid]] (CRTM).
+
+* Modes
+- [[id:metro-madrid][Metro de Madrid]] — 13 lines, ~300 km of track
+- [[id:emt-madrid][EMT Bus]] — urban buses within the city
+- Cercanías — suburban rail run by Renfe
+- Interurbano — regional buses to the wider Community of Madrid
+
+* Ticketing
+A single [[https://www.crtm.es][tarjeta transporte]] (transport card) works across all modes.
+The Multi card covers zones A–C and is topped up at any metro station.

notes/metro/metro-madrid.org

@@ -0,0 +1,18 @@
+:PROPERTIES:
+:ID:       metro-madrid
+:END:
+#+title: Metro de Madrid
+
+The Madrid Metro is the main rapid transit network in the city, opened in 1919.
+It is the second oldest metro in the Iberian Peninsula after Barcelona.
+
+* Key Lines
+| Line | Name            | Colour | Terminals                    |
+|------+-----------------+--------+------------------------------|
+| L1   | Pinar de Chamartín–Valdecarros | Blue   | Pinar de Chamartín / Valdecarros |
+| L6   | Circular        | Grey   | Circular (loop)              |
+| L10  | —               | Dark blue | Hospital Infanta Sofía / Tres Olivos |
+
+* See also
+- [[id:madrid-transport][Madrid Public Transport]]
+- [[id:sol-interchange][Sol interchange]]

notes/metro/sol-interchange.org

@@ -0,0 +1,12 @@
+:PROPERTIES:
+:ID:       sol-interchange
+:END:
+#+title: Sol (interchange)
+
+Sol is the busiest interchange station in the Madrid Metro, sitting beneath
+Puerta del Sol in the city centre.
+
+Lines serving Sol: [[id:metro-madrid][L1]], L2, L3.
+
+It also connects to the Cercanías hub underneath, making it the de-facto
+zero point of Madrid's public transport.

notes/roads/crtm.org

@@ -0,0 +1,22 @@
+:PROPERTIES:
+:ID:       crtm
+:END:
+#+title: CRTM — Consorcio Regional de Transportes de Madrid
+
+The CRTM is the regional authority that coordinates public transport across
+the Community of Madrid. It does not operate services directly but sets
+fares, zones, and integration policy.
+
+* Fare zones
+| Zone  | Coverage                    |
+|-------+-----------------------------|
+| A     | Municipality of Madrid      |
+| B1    | Inner ring municipalities   |
+| B2    | Outer ring municipalities   |
+| B3    | Further suburban area       |
+| C1–C2 | Commuter belt               |
+
+* Related
+- [[id:madrid-transport][Madrid Public Transport]]
+- [[id:metro-madrid][Metro de Madrid]]
+- [[id:emt-madrid][EMT Madrid]]

notes/roads/m30.org

@@ -0,0 +1,19 @@
+:PROPERTIES:
+:ID:       m30
+:END:
+#+title: M-30
+
+The M-30 is Madrid's innermost ring road, circling the city centre at a
+radius of roughly 3–5 km from Puerta del Sol.
+
+It runs mostly underground through the Madrid Río tunnel section along the
+Manzanares river, built during the 2004–2007 renovation that reclaimed the
+riverbank as a public park.
+
+* Key junctions
+- Nudo Norte — connects to A-1 (Burgos) and A-6 (La Coruña)
+- Nudo Sur — connects to A-4 (Cádiz) and A-42 (Toledo)
+
+* See also
+- [[id:crtm][CRTM]]
+- [[id:madrid-transport][Madrid Public Transport]]

opencode.json

@@ -0,0 +1,10 @@
+{
+  "$schema": "https://opencode.ai/config.json",
+  "mcp": {
+    "nixos": {
+      "type": "local",
+      "command": ["mcp-nixos"],
+      "enabled": true
+    }
+  }
+}

package.json

@@ -17,7 +17,10 @@
     "check": "tsc --noEmit && npx prettier . --check",
     "format": "npx prettier . --write",
     "test": "tsx --test",
-    "profile": "0x -D prof ./quartz/bootstrap-cli.mjs build --concurrency=1"
+    "profile": "0x -D prof ./quartz/bootstrap-cli.mjs build --concurrency=1",
+    "export": "elixir scripts/export.exs",
+    "build:notes": "elixir scripts/export.exs && npx quartz build",
+    "serve:notes": "elixir scripts/export.exs && npx quartz build --serve"
   },
   "engines": {
     "npm": ">=10.9.2",
@@ -42,28 +45,28 @@
     "@tweenjs/tween.js": "^25.0.0",
     "ansi-truncate": "^1.4.0",
     "async-mutex": "^0.5.0",
-    "chokidar": "^4.0.3",
+    "chokidar": "^5.0.0",
     "cli-spinner": "^0.2.10",
     "d3": "^7.9.0",
-    "esbuild-sass-plugin": "^3.3.1",
+    "esbuild-sass-plugin": "^3.6.0",
     "flexsearch": "^0.8.205",
     "github-slugger": "^2.0.0",
-    "globby": "^15.0.0",
+    "globby": "^16.1.0",
     "gray-matter": "^4.0.3",
     "hast-util-to-html": "^9.0.5",
     "hast-util-to-jsx-runtime": "^2.3.6",
     "hast-util-to-string": "^3.0.1",
     "is-absolute-url": "^5.0.0",
-    "js-yaml": "^4.1.0",
-    "lightningcss": "^1.30.2",
+    "js-yaml": "^4.1.1",
+    "lightningcss": "^1.31.1",
     "mdast-util-find-and-replace": "^3.0.2",
-    "mdast-util-to-hast": "^13.2.0",
+    "mdast-util-to-hast": "^13.2.1",
     "mdast-util-to-string": "^4.0.0",
     "micromorph": "^0.4.5",
     "minimatch": "^10.1.1",
-    "pixi.js": "^8.14.0",
-    "preact": "^10.27.2",
-    "preact-render-to-string": "^6.6.3",
+    "pixi.js": "^8.15.0",
+    "preact": "^10.28.2",
+    "preact-render-to-string": "^6.6.5",
     "pretty-bytes": "^7.1.0",
     "pretty-time": "^1.1.0",
     "reading-time": "^1.5.0",
@@ -83,32 +86,32 @@
     "remark-rehype": "^11.1.2",
     "remark-smartypants": "^3.0.2",
     "rfdc": "^1.4.1",
-    "satori": "^0.18.3",
+    "satori": "^0.19.1",
     "serve-handler": "^6.1.6",
-    "sharp": "^0.34.4",
+    "sharp": "^0.34.5",
     "shiki": "^1.26.2",
     "source-map-support": "^0.5.21",
     "to-vfile": "^8.0.0",
     "toml": "^3.0.0",
     "unified": "^11.0.5",
-    "unist-util-visit": "^5.0.0",
+    "unist-util-visit": "^5.1.0",
     "vfile": "^6.0.3",
-    "workerpool": "^10.0.0",
-    "ws": "^8.18.3",
+    "workerpool": "^10.0.1",
+    "ws": "^8.19.0",
     "yargs": "^18.0.0"
   },
   "devDependencies": {
     "@types/d3": "^7.4.3",
     "@types/hast": "^3.0.4",
     "@types/js-yaml": "^4.0.9",
-    "@types/node": "^24.10.0",
+    "@types/node": "^25.0.10",
     "@types/pretty-time": "^1.1.5",
     "@types/source-map-support": "^0.5.10",
     "@types/ws": "^8.18.1",
-    "@types/yargs": "^17.0.34",
-    "esbuild": "^0.25.12",
-    "prettier": "^3.6.2",
-    "tsx": "^4.20.6",
+    "@types/yargs": "^17.0.35",
+    "esbuild": "^0.27.2",
+    "prettier": "^3.8.1",
+    "tsx": "^4.21.0",
     "typescript": "^5.9.3"
   }
 }

quartz.config.ts

@@ -55,7 +55,7 @@ const config: QuartzConfig = {
   },
   plugins: {
     transformers: [
-      Plugin.FrontMatter(),
+      Plugin.FrontMatter({ delimiters: "+++", language: "toml" }),
       Plugin.CreatedModifiedDate({
         priority: ["frontmatter", "git", "filesystem"],
       }),
@@ -66,7 +66,11 @@ const config: QuartzConfig = {
         },
         keepBackground: false,
       }),
-      Plugin.ObsidianFlavoredMarkdown({ enableInHtmlEmbed: false }),
+      // OxHugoFlavouredMarkdown must come before GitHubFlavoredMarkdown.
+      // Note: not compatible with ObsidianFlavoredMarkdown — use one or the other.
+      // If ox-hugo exports TOML frontmatter, change FrontMatter to:
+      //   Plugin.FrontMatter({ delims: "+++", language: "toml" })
+      Plugin.OxHugoFlavouredMarkdown(),
       Plugin.GitHubFlavoredMarkdown(),
       Plugin.TableOfContents(),
       Plugin.CrawlLinks({ markdownLinkResolution: "shortest" }),

quartz/build.ts

@@ -71,7 +71,7 @@ async function buildQuartz(argv: Argv, mut: Mutex, clientRefresh: () => void) {
   console.log(`Cleaned output directory \`${output}\` in ${perf.timeSince("clean")}`)
 
   perf.addEvent("glob")
-  const allFiles = await glob("**/*.*", argv.directory, cfg.configuration.ignorePatterns)
+  const allFiles = await glob("**/*.*", argv.directory, cfg.configuration.ignorePatterns, false)
   const markdownPaths = allFiles.filter((fp) => fp.endsWith(".md")).sort()
   console.log(
     `Found ${markdownPaths.length} input files from \`${argv.directory}\` in ${perf.timeSince("glob")}`,
@@ -143,6 +143,7 @@ async function startWatching(
   }
 
   const watcher = chokidar.watch(".", {
+    awaitWriteFinish: { stabilityThreshold: 250 },
     persistent: true,
     cwd: argv.directory,
     ignoreInitial: true,

quartz/cfg.ts

@@ -50,6 +50,11 @@ export type Analytics =
   | {
       provider: "vercel"
     }
+  | {
+      provider: "rybbit"
+      siteId: string
+      host?: string
+    }
 
 export interface GlobalConfiguration {
   pageTitle: string

quartz/cli/helpers.js

@@ -7,8 +7,8 @@ import fs from "fs"
 export function escapePath(fp) {
   return fp
     .replace(/\\ /g, " ") // unescape spaces
-    .replace(/^".*"$/, "$1")
-    .replace(/^'.*"$/, "$1")
+    .replace(/^"(.*)"$/, "$1")
+    .replace(/^'(.*)'$/, "$1")
     .trim()
 }
 

quartz/components/renderPage.tsx

@@ -294,7 +294,7 @@ export function renderPage(
       </body>
       {pageResources.js
         .filter((resource) => resource.loadTime === "afterDOMReady")
-        .map((res) => JSResourceToScriptElement(res))}
+        .map((res) => JSResourceToScriptElement(res, true))}
     </html>
   )
 

quartz/components/scripts/explorer.inline.ts

@@ -111,6 +111,10 @@ function createFolderNode(
   const folderPath = node.slug
   folderContainer.dataset.folderpath = folderPath
 
+  if (currentSlug === folderPath) {
+    folderContainer.classList.add("active")
+  }
+
   if (opts.folderClickBehavior === "link") {
     // Replace button with link for link behavior
     const button = titleContainer.querySelector(".folder-button") as HTMLElement

quartz/components/scripts/mermaid.inline.ts

@@ -29,17 +29,31 @@ class DiagramPanZoom {
     const mouseDownHandler = this.onMouseDown.bind(this)
     const mouseMoveHandler = this.onMouseMove.bind(this)
     const mouseUpHandler = this.onMouseUp.bind(this)
+
+    // Touch drag events
+    const touchStartHandler = this.onTouchStart.bind(this)
+    const touchMoveHandler = this.onTouchMove.bind(this)
+    const touchEndHandler = this.onTouchEnd.bind(this)
+
     const resizeHandler = this.resetTransform.bind(this)
 
     this.container.addEventListener("mousedown", mouseDownHandler)
     document.addEventListener("mousemove", mouseMoveHandler)
     document.addEventListener("mouseup", mouseUpHandler)
+
+    this.container.addEventListener("touchstart", touchStartHandler, { passive: false })
+    document.addEventListener("touchmove", touchMoveHandler, { passive: false })
+    document.addEventListener("touchend", touchEndHandler)
+
     window.addEventListener("resize", resizeHandler)
 
     this.cleanups.push(
       () => this.container.removeEventListener("mousedown", mouseDownHandler),
       () => document.removeEventListener("mousemove", mouseMoveHandler),
       () => document.removeEventListener("mouseup", mouseUpHandler),
+      () => this.container.removeEventListener("touchstart", touchStartHandler),
+      () => document.removeEventListener("touchmove", touchMoveHandler),
+      () => document.removeEventListener("touchend", touchEndHandler),
       () => window.removeEventListener("resize", resizeHandler),
     )
   }
@@ -99,6 +113,30 @@ class DiagramPanZoom {
     this.container.style.cursor = "grab"
   }
 
+  private onTouchStart(e: TouchEvent) {
+    if (e.touches.length !== 1) return
+    this.isDragging = true
+    const touch = e.touches[0]
+    this.startPan = { x: touch.clientX - this.currentPan.x, y: touch.clientY - this.currentPan.y }
+  }
+
+  private onTouchMove(e: TouchEvent) {
+    if (!this.isDragging || e.touches.length !== 1) return
+    e.preventDefault() // Prevent scrolling
+
+    const touch = e.touches[0]
+    this.currentPan = {
+      x: touch.clientX - this.startPan.x,
+      y: touch.clientY - this.startPan.y,
+    }
+
+    this.updateTransform()
+  }
+
+  private onTouchEnd() {
+    this.isDragging = false
+  }
+
   private zoom(delta: number) {
     const newScale = Math.min(Math.max(this.scale + delta, this.MIN_SCALE), this.MAX_SCALE)
 
@@ -120,11 +158,15 @@ class DiagramPanZoom {
   }
 
   private resetTransform() {
-    this.scale = 1
     const svg = this.content.querySelector("svg")!
+    const rect = svg.getBoundingClientRect()
+    const width = rect.width / this.scale
+    const height = rect.height / this.scale
+
+    this.scale = 1
     this.currentPan = {
-      x: svg.getBoundingClientRect().width / 2,
-      y: svg.getBoundingClientRect().height / 2,
+      x: (this.container.clientWidth - width) / 2,
+      y: (this.container.clientHeight - height) / 2,
     }
     this.updateTransform()
   }

quartz/components/scripts/search.inline.ts

@@ -16,11 +16,49 @@ interface Item {
 type SearchType = "basic" | "tags"
 let searchType: SearchType = "basic"
 let currentSearchTerm: string = ""
-const encoder = (str: string) => {
-  return str
-    .toLowerCase()
-    .split(/\s+/)
-    .filter((token) => token.length > 0)
+const encoder = (str: string): string[] => {
+  const tokens: string[] = []
+  let bufferStart = -1
+  let bufferEnd = -1
+  const lower = str.toLowerCase()
+
+  let i = 0
+  for (const char of lower) {
+    const code = char.codePointAt(0)!
+
+    const isCJK =
+      (code >= 0x3040 && code <= 0x309f) ||
+      (code >= 0x30a0 && code <= 0x30ff) ||
+      (code >= 0x4e00 && code <= 0x9fff) ||
+      (code >= 0xac00 && code <= 0xd7af) ||
+      (code >= 0x20000 && code <= 0x2a6df)
+
+    const isWhitespace = code === 32 || code === 9 || code === 10 || code === 13
+
+    if (isCJK) {
+      if (bufferStart !== -1) {
+        tokens.push(lower.slice(bufferStart, bufferEnd))
+        bufferStart = -1
+      }
+      tokens.push(char)
+    } else if (isWhitespace) {
+      if (bufferStart !== -1) {
+        tokens.push(lower.slice(bufferStart, bufferEnd))
+        bufferStart = -1
+      }
+    } else {
+      if (bufferStart === -1) bufferStart = i
+      bufferEnd = i + char.length
+    }
+
+    i += char.length
+  }
+
+  if (bufferStart !== -1) {
+    tokens.push(lower.slice(bufferStart))
+  }
+
+  return tokens
 }
 
 let index = new FlexSearch.Document<Item>({

quartz/components/scripts/search.test.ts

@@ -0,0 +1,163 @@
+import test, { describe } from "node:test"
+import assert from "node:assert"
+
+// Inline the encoder function from search.inline.ts for testing
+const encoder = (str: string): string[] => {
+  const tokens: string[] = []
+  let bufferStart = -1
+  let bufferEnd = -1
+  const lower = str.toLowerCase()
+
+  let i = 0
+  for (const char of lower) {
+    const code = char.codePointAt(0)!
+
+    const isCJK =
+      (code >= 0x3040 && code <= 0x309f) ||
+      (code >= 0x30a0 && code <= 0x30ff) ||
+      (code >= 0x4e00 && code <= 0x9fff) ||
+      (code >= 0xac00 && code <= 0xd7af) ||
+      (code >= 0x20000 && code <= 0x2a6df)
+
+    const isWhitespace = code === 32 || code === 9 || code === 10 || code === 13
+
+    if (isCJK) {
+      if (bufferStart !== -1) {
+        tokens.push(lower.slice(bufferStart, bufferEnd))
+        bufferStart = -1
+      }
+      tokens.push(char)
+    } else if (isWhitespace) {
+      if (bufferStart !== -1) {
+        tokens.push(lower.slice(bufferStart, bufferEnd))
+        bufferStart = -1
+      }
+    } else {
+      if (bufferStart === -1) bufferStart = i
+      bufferEnd = i + char.length
+    }
+
+    i += char.length
+  }
+
+  if (bufferStart !== -1) {
+    tokens.push(lower.slice(bufferStart))
+  }
+
+  return tokens
+}
+
+describe("search encoder", () => {
+  describe("English text", () => {
+    test("should tokenize simple English words", () => {
+      const result = encoder("hello world")
+      assert.deepStrictEqual(result, ["hello", "world"])
+    })
+
+    test("should handle multiple spaces", () => {
+      const result = encoder("hello   world")
+      assert.deepStrictEqual(result, ["hello", "world"])
+    })
+
+    test("should handle tabs and newlines", () => {
+      const result = encoder("hello\tworld\ntest")
+      assert.deepStrictEqual(result, ["hello", "world", "test"])
+    })
+
+    test("should lowercase all text", () => {
+      const result = encoder("Hello WORLD Test")
+      assert.deepStrictEqual(result, ["hello", "world", "test"])
+    })
+  })
+
+  describe("CJK text", () => {
+    test("should tokenize Japanese Hiragana character by character", () => {
+      const result = encoder("こんにちは")
+      assert.deepStrictEqual(result, ["こ", "ん", "に", "ち", "は"])
+    })
+
+    test("should tokenize Japanese Katakana character by character", () => {
+      const result = encoder("コントロール")
+      assert.deepStrictEqual(result, ["コ", "ン", "ト", "ロ", "ー", "ル"])
+    })
+
+    test("should tokenize Japanese Kanji character by character", () => {
+      const result = encoder("日本語")
+      assert.deepStrictEqual(result, ["日", "本", "語"])
+    })
+
+    test("should tokenize Korean Hangul character by character", () => {
+      const result = encoder("안녕하세요")
+      assert.deepStrictEqual(result, ["안", "녕", "하", "세", "요"])
+    })
+
+    test("should tokenize Chinese characters character by character", () => {
+      const result = encoder("你好世界")
+      assert.deepStrictEqual(result, ["你", "好", "世", "界"])
+    })
+
+    test("should handle mixed Hiragana/Katakana/Kanji", () => {
+      const result = encoder("て以来")
+      assert.deepStrictEqual(result, ["て", "以", "来"])
+    })
+  })
+
+  describe("Mixed CJK and English", () => {
+    test("should handle Japanese with English words", () => {
+      const result = encoder("hello 世界")
+      assert.deepStrictEqual(result, ["hello", "世", "界"])
+    })
+
+    test("should handle English with Japanese words", () => {
+      const result = encoder("世界 hello world")
+      assert.deepStrictEqual(result, ["世", "界", "hello", "world"])
+    })
+
+    test("should handle complex mixed content", () => {
+      const result = encoder("これはtest文章です")
+      assert.deepStrictEqual(result, ["こ", "れ", "は", "test", "文", "章", "で", "す"])
+    })
+
+    test("should handle mixed Korean and English", () => {
+      const result = encoder("hello 안녕 world")
+      assert.deepStrictEqual(result, ["hello", "안", "녕", "world"])
+    })
+
+    test("should handle mixed Chinese and English", () => {
+      const result = encoder("你好 world")
+      assert.deepStrictEqual(result, ["你", "好", "world"])
+    })
+  })
+
+  describe("Edge cases", () => {
+    test("should handle empty string", () => {
+      const result = encoder("")
+      assert.deepStrictEqual(result, [])
+    })
+
+    test("should handle only whitespace", () => {
+      const result = encoder("   \t\n  ")
+      assert.deepStrictEqual(result, [])
+    })
+
+    test("should handle single character", () => {
+      const result = encoder("a")
+      assert.deepStrictEqual(result, ["a"])
+    })
+
+    test("should handle single CJK character", () => {
+      const result = encoder("あ")
+      assert.deepStrictEqual(result, ["あ"])
+    })
+
+    test("should handle CJK with trailing whitespace", () => {
+      const result = encoder("日本語  ")
+      assert.deepStrictEqual(result, ["日", "本", "語"])
+    })
+
+    test("should handle English with trailing whitespace", () => {
+      const result = encoder("hello  ")
+      assert.deepStrictEqual(result, ["hello"])
+    })
+  })
+})

quartz/components/scripts/spa.inline.ts

@@ -115,9 +115,9 @@ async function _navigate(url: URL, isBack: boolean = false) {
   }
 
   // now, patch head, re-executing scripts
-  const elementsToRemove = document.head.querySelectorAll(":not([spa-preserve])")
+  const elementsToRemove = document.head.querySelectorAll(":not([data-persist])")
   elementsToRemove.forEach((el) => el.remove())
-  const elementsToAdd = html.head.querySelectorAll(":not([spa-preserve])")
+  const elementsToAdd = html.head.querySelectorAll(":not([data-persist])")
   elementsToAdd.forEach((el) => document.head.appendChild(el))
 
   // delay setting the url until now

quartz/components/styles/darkmode.scss

@@ -5,7 +5,7 @@
   background: none;
   border: none;
   width: 20px;
-  height: 20px;
+  height: 32px;
   margin: 0;
   text-align: inherit;
   flex-shrink: 0;

quartz/components/styles/explorer.scss

@@ -6,6 +6,7 @@
     & > :not(.sidebar.left:has(.explorer)) {
       transition: transform 300ms ease-in-out;
     }
+
     &.lock-scroll > :not(.sidebar.left:has(.explorer)) {
       transform: translateX(100dvw);
       transition: transform 300ms ease-in-out;
@@ -33,8 +34,10 @@
 
   min-height: 1.2rem;
   flex: 0 1 auto;
+
   &.collapsed {
     flex: 0 1 1.2rem;
+
     & .fold {
       transform: rotateZ(-90deg);
     }
@@ -118,7 +121,10 @@ button.desktop-explorer {
     list-style: none;
     margin: 0;
     padding: 0;
-    overscroll-behavior: contain;
+
+    &.explorer-ul {
+      overscroll-behavior: contain;
+    }
 
     & li > a {
       color: var(--dark);
@@ -269,6 +275,8 @@ li:has(> .folder-outer:not(.open)) > .folder-container > svg {
 
 .mobile-no-scroll {
   @media all and ($mobile) {
-    overscroll-behavior: none;
+    .explorer-content > .explorer-ul {
+      overscroll-behavior: contain;
+    }
   }
 }

quartz/components/styles/mermaid.inline.scss

@@ -65,7 +65,6 @@ pre {
     overflow: hidden;
 
     & > .mermaid-content {
-      padding: 2rem;
       position: relative;
       transform-origin: 0 0;
       transition: transform 0.1s ease;

quartz/components/styles/readermode.scss

@@ -5,7 +5,7 @@
   background: none;
   border: none;
   width: 20px;
-  height: 20px;
+  height: 32px;
   margin: 0;
   text-align: inherit;
   flex-shrink: 0;

quartz/i18n/locales/vi-VN.ts

@@ -3,85 +3,83 @@ import { Translation } from "./definition"
 export default {
   propertyDefaults: {
     title: "Không có tiêu đề",
-    description: "Không có mô tả được cung cấp",
+    description: "Không có mô tả",
   },
   components: {
     callout: {
-      note: "Ghi Chú",
-      abstract: "Tóm Tắt",
+      note: "Ghi chú",
+      abstract: "Tổng quan",
       info: "Thông tin",
-      todo: "Cần Làm",
-      tip: "Gợi Ý",
-      success: "Thành Công",
-      question: "Nghi Vấn",
-      warning: "Cảnh Báo",
-      failure: "Thất Bại",
-      danger: "Nguy Hiểm",
+      todo: "Cần phải làm",
+      tip: "Gợi ý",
+      success: "Thành công",
+      question: "Câu hỏi",
+      warning: "Cảnh báo",
+      failure: "Thất bại",
+      danger: "Nguy hiểm",
       bug: "Lỗi",
-      example: "Ví Dụ",
-      quote: "Trích Dẫn",
+      example: "Ví dụ",
+      quote: "Trích dẫn",
     },
     backlinks: {
-      title: "Liên Kết Ngược",
-      noBacklinksFound: "Không có liên kết ngược được tìm thấy",
+      title: "Liên kết ngược",
+      noBacklinksFound: "Không có liên kết ngược nào",
     },
     themeToggle: {
-      lightMode: "Sáng",
-      darkMode: "Tối",
+      lightMode: "Chế độ sáng",
+      darkMode: "Chế độ tối",
     },
     readerMode: {
       title: "Chế độ đọc",
     },
     explorer: {
-      title: "Trong bài này",
+      title: "Nội dung",
     },
     footer: {
-      createdWith: "Được tạo bởi",
+      createdWith: "Được tạo bằng",
     },
     graph: {
-      title: "Biểu Đồ",
+      title: "Sơ đồ",
     },
     recentNotes: {
-      title: "Bài viết gần đây",
-      seeRemainingMore: ({ remaining }) => `Xem ${remaining} thêm →`,
+      title: "Ghi chú gần đây",
+      seeRemainingMore: ({ remaining }) => `Xem thêm ${remaining} ghi chú →`,
     },
     transcludes: {
-      transcludeOf: ({ targetSlug }) => `Bao gồm ${targetSlug}`,
-      linkToOriginal: "Liên Kết Gốc",
+      transcludeOf: ({ targetSlug }) => `Trích dẫn toàn bộ từ ${targetSlug}`,
+      linkToOriginal: "Xem trang gốc",
     },
     search: {
-      title: "Tìm Kiếm",
+      title: "Tìm",
       searchBarPlaceholder: "Tìm kiếm thông tin",
     },
     tableOfContents: {
-      title: "Bảng Nội Dung",
+      title: "Mục lục",
     },
     contentMeta: {
-      readingTime: ({ minutes }) => `đọc ${minutes} phút`,
+      readingTime: ({ minutes }) => `${minutes} phút đọc`,
     },
   },
   pages: {
     rss: {
-      recentNotes: "Những bài gần đây",
-      lastFewNotes: ({ count }) => `${count} Bài gần đây`,
+      recentNotes: "Ghi chú gần đây",
+      lastFewNotes: ({ count }) => `${count} Trang gần đây`,
     },
     error: {
-      title: "Không Tìm Thấy",
-      notFound: "Trang này được bảo mật hoặc không tồn tại.",
-      home: "Trở về trang chủ",
+      title: "Không tìm thấy",
+      notFound: "Trang này riêng tư hoặc không tồn tại.",
+      home: "Về trang chủ",
     },
     folderContent: {
-      folder: "Thư Mục",
-      itemsUnderFolder: ({ count }) =>
-        count === 1 ? "1 mục trong thư mục này." : `${count} mục trong thư mục này.`,
+      folder: "Thư mục",
+      itemsUnderFolder: ({ count }) => `Có ${count} trang trong thư mục này.`,
     },
     tagContent: {
       tag: "Thẻ",
-      tagIndex: "Thẻ Mục Lục",
-      itemsUnderTag: ({ count }) =>
-        count === 1 ? "1 mục gắn thẻ này." : `${count} mục gắn thẻ này.`,
-      showingFirst: ({ count }) => `Hiển thị trước ${count} thẻ.`,
-      totalTags: ({ count }) => `Tìm thấy ${count} thẻ tổng cộng.`,
+      tagIndex: "Danh sách thẻ",
+      itemsUnderTag: ({ count }) => `Có ${count} trang gắn thẻ này.`,
+      showingFirst: ({ count }) => `Đang hiển thị ${count} trang đầu tiên.`,
+      totalTags: ({ count }) => `Có tổng cộng ${count} thẻ.`,
     },
   },
 } as const satisfies Translation

quartz/plugins/emitters/componentResources.ts

@@ -241,6 +241,16 @@ function addGlobalPageResources(ctx: BuildCtx, componentResources: ComponentReso
       vercelInsightsScript.defer = true
       document.head.appendChild(vercelInsightsScript)
     `)
+  } else if (cfg.analytics?.provider === "rybbit") {
+    componentResources.afterDOMLoaded.push(`
+      const rybbitScript = document.createElement("script");
+      rybbitScript.src = "${cfg.analytics.host ?? "https://app.rybbit.io"}/api/script.js";
+      rybbitScript.setAttribute("data-site-id", "${cfg.analytics.siteId}");
+      rybbitScript.async = true;
+      rybbitScript.defer = true;
+
+      document.head.appendChild(rybbitScript);
+    `)
   }
 
   if (cfg.enableSPA) {

quartz/plugins/emitters/static.ts

@@ -7,6 +7,7 @@ import { dirname } from "path"
 export const Static: QuartzEmitterPlugin = () => ({
   name: "Static",
   async *emit({ argv, cfg }) {
+    // Copy Quartz's own internal static assets (quartz/static/) → output/static/
     const staticPath = joinSegments(QUARTZ, "static")
     const fps = await glob("**", staticPath, cfg.configuration.ignorePatterns)
     const outputStaticPath = joinSegments(argv.output, "static")
@@ -18,6 +19,21 @@ export const Static: QuartzEmitterPlugin = () => ({
       await fs.promises.copyFile(src, dest)
       yield dest
     }
+
+    // Copy user-facing static assets (static/) → output/ preserving paths.
+    // This mirrors Hugo's convention: static/ox-hugo/foo.png is served at /ox-hugo/foo.png,
+    // which matches the src="/ox-hugo/..." paths that ox-hugo writes into exported markdown.
+    const userStaticPath = "static"
+    if (fs.existsSync(userStaticPath)) {
+      const userFps = await glob("**", userStaticPath, cfg.configuration.ignorePatterns, false)
+      for (const fp of userFps) {
+        const src = joinSegments(userStaticPath, fp) as FilePath
+        const dest = joinSegments(argv.output, fp) as FilePath
+        await fs.promises.mkdir(dirname(dest), { recursive: true })
+        await fs.promises.copyFile(src, dest)
+        yield dest
+      }
+    }
   },
   async *partialEmit() {},
 })

quartz/plugins/transformers/citations.ts

@@ -23,7 +23,16 @@ export const Citations: QuartzTransformerPlugin<Partial<Options>> = (userOpts) =
     name: "Citations",
     htmlPlugins(ctx) {
       const plugins: PluggableList = []
-
+      // per default, rehype-citations only supports en-US
+      // see: https://github.com/timlrx/rehype-citation/issues/12
+      // in here there are multiple usable locales:
+      // https://github.com/citation-style-language/locales
+      // thus, we optimistically assume there is indeed an appropriate
+      // locale available and simply create the lang url-string
+      let lang: string = "en-US"
+      if (ctx.cfg.configuration.locale !== "en-US") {
+        lang = `https://raw.githubusercontent.com/citation-stylelanguage/locales/refs/heads/master/locales-${ctx.cfg.configuration.locale}.xml`
+      }
       // Add rehype-citation to the list of plugins
       plugins.push([
         rehypeCitation,
@@ -32,7 +41,7 @@ export const Citations: QuartzTransformerPlugin<Partial<Options>> = (userOpts) =
           suppressBibliography: opts.suppressBibliography,
           linkCitations: opts.linkCitations,
           csl: opts.csl,
-          lang: ctx.cfg.configuration.locale ?? "en-US",
+          lang,
         },
       ])
 

quartz/plugins/transformers/latex.ts

@@ -17,8 +17,10 @@ interface Options {
   typstOptions: TypstOptions
 }
 
+// mathjax macros
+export type Args = boolean | number | string | null
 interface MacroType {
-  [key: string]: string
+  [key: string]: string | Args[]
 }
 
 export const Latex: QuartzTransformerPlugin<Partial<Options>> = (opts) => {
@@ -37,11 +39,20 @@ export const Latex: QuartzTransformerPlugin<Partial<Options>> = (opts) => {
         case "typst": {
           return [[rehypeTypst, opts?.typstOptions ?? {}]]
         }
+        default:
         case "mathjax": {
-          return [[rehypeMathjax, { macros, ...(opts?.mathJaxOptions ?? {}) }]]
-        }
-        default: {
-          return [[rehypeMathjax, { macros, ...(opts?.mathJaxOptions ?? {}) }]]
+          return [
+            [
+              rehypeMathjax,
+              {
+                ...(opts?.mathJaxOptions ?? {}),
+                tex: {
+                  ...(opts?.mathJaxOptions?.tex ?? {}),
+                  macros,
+                },
+              },
+            ],
+          ]
         }
       }
     },

quartz/plugins/transformers/oxhugofm.ts

@@ -27,7 +27,10 @@ const defaultOptions: Options = {
 const relrefRegex = new RegExp(/\[([^\]]+)\]\(\{\{< relref "([^"]+)" >\}\}\)/, "g")
 const predefinedHeadingIdRegex = new RegExp(/(.*) {#(?:.*)}/, "g")
 const hugoShortcodeRegex = new RegExp(/{{(.*)}}/, "g")
-const figureTagRegex = new RegExp(/< ?figure src="(.*)" ?>/, "g")
+// Matches the full Hugo {{< figure src="..." ... >}} shortcode and captures src.
+// Must run before the generic shortcode stripper to avoid partial-match issues
+// with captions that contain HTML (e.g. <span class="figure-number">).
+const figureShortcodeRegex = new RegExp(/{{<\s*figure\b[^}]*\bsrc="([^"]*)"[^}]*>}}/, "g")
 // \\\\\( -> matches \\(
 // (.+?) -> Lazy match for capturing the equation
 // \\\\\) -> matches \\)
@@ -70,6 +73,14 @@ export const OxHugoFlavouredMarkdown: QuartzTransformerPlugin<Partial<Options>>
         })
       }
 
+      if (opts.replaceFigureWithMdImg) {
+        src = src.toString()
+        src = src.replaceAll(figureShortcodeRegex, (_value, ...capture) => {
+          const [imgSrc] = capture
+          return `![](${imgSrc})`
+        })
+      }
+
       if (opts.removeHugoShortcode) {
         src = src.toString()
         src = src.replaceAll(hugoShortcodeRegex, (_value, ...capture) => {
@@ -78,14 +89,6 @@ export const OxHugoFlavouredMarkdown: QuartzTransformerPlugin<Partial<Options>>
         })
       }
 
-      if (opts.replaceFigureWithMdImg) {
-        src = src.toString()
-        src = src.replaceAll(figureTagRegex, (_value, ...capture) => {
-          const [src] = capture
-          return `![](${src})`
-        })
-      }
-
       if (opts.replaceOrgLatex) {
         src = src.toString()
         src = src.replaceAll(inlineLatexRegex, (_value, ...capture) => {

quartz/styles/base.scss

@@ -9,6 +9,10 @@ html {
   text-size-adjust: none;
   overflow-x: hidden;
   width: 100vw;
+
+  @media all and ($mobile) {
+    scroll-padding-top: 4rem;
+  }
 }
 
 body {
@@ -41,13 +45,17 @@ ul,
 .katex,
 .math,
 .typst-doc,
-.typst-doc * {
+g[class~="typst-text"] {
   color: var(--darkgray);
   fill: var(--darkgray);
   overflow-wrap: break-word;
   text-wrap: pretty;
 }
 
+path[class~="typst-shape"] {
+  stroke: var(--darkgray);
+}
+
 .math {
   &.math-display {
     text-align: center;

quartz/util/glob.ts

@@ -10,12 +10,13 @@ export async function glob(
   pattern: string,
   cwd: string,
   ignorePatterns: string[],
+  respectGitignore: boolean = true,
 ): Promise<FilePath[]> {
   const fps = (
     await globby(pattern, {
       cwd,
       ignore: ignorePatterns,
-      gitignore: true,
+      gitignore: respectGitignore,
     })
   ).map(toPosixPath)
   return fps as FilePath[]

quartz/util/resources.tsx

@@ -26,9 +26,10 @@ export type CSSResource = {
 export function JSResourceToScriptElement(resource: JSResource, preserve?: boolean): JSX.Element {
   const scriptType = resource.moduleType ?? "application/javascript"
   const spaPreserve = preserve ?? resource.spaPreserve
+
   if (resource.contentType === "external") {
     return (
-      <script key={resource.src} src={resource.src} type={scriptType} spa-preserve={spaPreserve} />
+      <script key={resource.src} src={resource.src} type={scriptType} data-persist={spaPreserve} />
     )
   } else {
     const content = resource.script
@@ -36,7 +37,7 @@ export function JSResourceToScriptElement(resource: JSResource, preserve?: boole
       <script
         key={randomUUID()}
         type={scriptType}
-        spa-preserve={spaPreserve}
+        data-persist={spaPreserve}
         dangerouslySetInnerHTML={{ __html: content }}
       ></script>
     )
@@ -54,7 +55,7 @@ export function CSSResourceToStyleElement(resource: CSSResource, preserve?: bool
         href={resource.content}
         rel="stylesheet"
         type="text/css"
-        spa-preserve={spaPreserve}
+        data-persist={spaPreserve}
       />
     )
   }

scripts/export.exs

@@ -0,0 +1,217 @@
+#!/usr/bin/env elixir
+# Export org-roam notes (per-file) to content/ via ox-hugo,
+# then run the markdown transformation pipeline (citations, etc.).
+#
+# Usage:
+#   NOTES_DIR=~/notes elixir scripts/export.exs
+#   elixir scripts/export.exs /path/to/notes
+#
+# Optional env vars:
+#   BIBTEX_FILE   — path to a .bib file used as citation fallback
+#   ZOTERO_URL    — Zotero Better BibTeX base URL (default: http://localhost:23119)
+#   CITATION_MODE — silent | warn (default) | strict
+#
+# The positional argument takes precedence over the NOTES_DIR env var.
+
+# ---------------------------------------------------------------------------
+# Load the pipeline Mix project so its modules are available in this script.
+# ---------------------------------------------------------------------------
+repo_root = __DIR__ |> Path.join("..") |> Path.expand()
+pipeline_dir = Path.join(repo_root, "scripts/pipeline")
+
+# Compile and load the pipeline project's modules into this runtime.
+# Mix.install is NOT used here because we have a local Mix project — instead
+# we compile it and push its beam files onto the code path.
+#
+# This runs `mix deps.get` + `mix compile` the first time; subsequent runs
+# use the compiled artifacts from _build/ (fast, same as Mix caching).
+{_, 0} =
+  System.cmd("mix", ["deps.get", "--quiet"],
+    cd: pipeline_dir,
+    env: [{"MIX_ENV", "prod"}],
+    into: IO.stream()
+  )
+
+{_, 0} =
+  System.cmd("mix", ["compile", "--quiet"],
+    cd: pipeline_dir,
+    env: [{"MIX_ENV", "prod"}],
+    into: IO.stream()
+  )
+
+# Add compiled beam files to the load path so we can call pipeline modules.
+pipeline_build = Path.join(pipeline_dir, "_build/prod/lib")
+
+pipeline_build
+|> File.ls!()
+|> Enum.each(fn app ->
+  ebin = Path.join([pipeline_build, app, "ebin"])
+  if File.dir?(ebin), do: Code.prepend_path(ebin)
+end)
+
+# Start the pipeline OTP application (which starts Finch for HTTP).
+Application.ensure_all_started(:pipeline)
+
+# ---------------------------------------------------------------------------
+# Argument / env resolution
+# ---------------------------------------------------------------------------
+
+notes_dir =
+  case System.argv() do
+    [dir | _] -> dir
+    [] ->
+      System.get_env("NOTES_DIR") ||
+        (IO.puts(:stderr, "Usage: NOTES_DIR=/path/to/notes elixir scripts/export.exs")
+         System.halt(1))
+  end
+
+notes_dir = Path.expand(notes_dir)
+content_dir = Path.join(repo_root, "content")
+
+unless File.dir?(notes_dir) do
+  IO.puts(:stderr, "Error: notes directory does not exist: #{notes_dir}")
+  System.halt(1)
+end
+
+# ---------------------------------------------------------------------------
+# Phase 1: Wipe content/
+# ---------------------------------------------------------------------------
+IO.puts("==> Wiping #{content_dir}")
+
+content_dir
+|> File.ls!()
+|> Enum.reject(&(&1 == ".gitkeep"))
+|> Enum.each(fn entry ->
+  Path.join(content_dir, entry) |> File.rm_rf!()
+end)
+
+# ---------------------------------------------------------------------------
+# Phase 2: Export org files via Emacs + ox-hugo
+# ---------------------------------------------------------------------------
+IO.puts("==> Exporting org files from #{notes_dir}")
+
+org_files =
+  Path.join(notes_dir, "**/*.org")
+  |> Path.wildcard()
+
+if org_files == [] do
+  IO.puts("No .org files found in #{notes_dir}")
+  System.halt(0)
+end
+
+results =
+  Enum.map(org_files, fn orgfile ->
+    IO.puts("  exporting: #{orgfile}")
+
+    section =
+      orgfile
+      |> Path.dirname()
+      |> Path.relative_to(notes_dir)
+
+    {output, exit_code} =
+      System.cmd(
+        "emacs",
+        [
+          "--batch",
+          "--eval", "(require 'ox-hugo)",
+          "--eval", ~s[(setq org-hugo-base-dir "#{repo_root}")],
+          "--eval", ~s[(setq org-hugo-default-section-directory "#{section}")],
+          "--visit", orgfile,
+          "--funcall", "org-hugo-export-to-md"
+        ],
+        stderr_to_stdout: true
+      )
+
+    filtered =
+      output
+      |> String.split("\n")
+      |> Enum.reject(&String.match?(&1, ~r/^Loading|^ad-handle|^For information/))
+      |> Enum.join("\n")
+
+    if filtered != "", do: IO.puts(filtered)
+
+    {orgfile, exit_code}
+  end)
+
+failures = Enum.filter(results, fn {_, code} -> code != 0 end)
+
+if failures != [] do
+  IO.puts(:stderr, "\nFailed to export #{length(failures)} file(s):")
+  Enum.each(failures, fn {f, code} -> IO.puts(:stderr, "  [exit #{code}] #{f}") end)
+  System.halt(1)
+end
+
+# ---------------------------------------------------------------------------
+# Phase 3: Markdown transformation pipeline
+# ---------------------------------------------------------------------------
+IO.puts("==> Running markdown pipeline")
+
+pipeline_opts = %{
+  zotero_url: System.get_env("ZOTERO_URL", "http://localhost:23119"),
+  bibtex_file: System.get_env("BIBTEX_FILE"),
+  citation_mode:
+    case System.get_env("CITATION_MODE", "warn") do
+      "silent" -> :silent
+      "strict" -> :strict
+      _ -> :warn
+    end
+}
+
+transforms = [Pipeline.Transforms.Citations]
+
+case Pipeline.run(content_dir, transforms, pipeline_opts) do
+  {:ok, stats} ->
+    Enum.each(stats, fn {mod, count} ->
+      IO.puts("  #{inspect(mod)}: #{count} file(s) modified")
+    end)
+
+  {:error, reason} ->
+    IO.puts(:stderr, "Pipeline error: #{inspect(reason)}")
+    System.halt(1)
+end
+
+# ---------------------------------------------------------------------------
+# Phase 4: Generate default index.md if none was exported
+# ---------------------------------------------------------------------------
+md_count =
+  Path.join(content_dir, "**/*.md")
+  |> Path.wildcard()
+  |> length()
+
+index_path = Path.join(content_dir, "index.md")
+
+unless File.exists?(index_path) do
+  IO.puts("==> Generating default index.md")
+
+  pages =
+    Path.join(content_dir, "**/*.md")
+    |> Path.wildcard()
+    |> Enum.map(fn path ->
+      slug = Path.relative_to(path, content_dir) |> Path.rootname()
+
+      title =
+        path
+        |> File.read!()
+        |> then(fn content ->
+          case Regex.run(~r/^title\s*=\s*"(.+)"/m, content) do
+            [_, t] -> t
+            _ -> slug
+          end
+        end)
+
+      {slug, title}
+    end)
+    |> Enum.sort_by(fn {_, title} -> title end)
+    |> Enum.map(fn {slug, title} -> "- [#{title}](#{slug})" end)
+    |> Enum.join("\n")
+
+  File.write!(index_path, """
+  ---
+  title: Index
+  ---
+
+  #{pages}
+  """)
+end
+
+IO.puts("==> Done. #{md_count} markdown files in #{content_dir}")

scripts/pipeline/lib/pipeline.ex

@@ -0,0 +1,83 @@
+defmodule Pipeline do
+  @moduledoc """
+  Post-export markdown transformation pipeline.
+
+  Applies a list of transform modules sequentially over every .md file
+  in a content directory. Each transform module must implement:
+
+      apply(content :: String.t(), opts :: map()) :: String.t()
+
+  Transforms are applied in the order given. A file is rewritten only
+  when at least one transform mutates its content (checked via equality).
+
+  ## Usage
+
+      opts = %{
+        zotero_url: "http://localhost:23119",
+        bibtex_file: System.get_env("BIBTEX_FILE"),
+        citation_mode: :warn   # :silent | :warn | :strict
+      }
+
+      Pipeline.run(content_dir, [Pipeline.Transforms.Citations], opts)
+  """
+
+  require Logger
+
+  @type transform :: module()
+  @type opts :: map()
+
+  @doc """
+  Run all transforms over every .md file under `content_dir`.
+  Returns `{:ok, stats}` where stats maps each transform to a count of files it changed.
+  """
+  @spec run(String.t(), [transform()], opts()) :: {:ok, map()}
+  def run(content_dir, transforms, opts \\ %{}) do
+    md_files =
+      content_dir
+      |> Path.join("**/*.md")
+      |> Path.wildcard()
+
+    if md_files == [] do
+      Logger.warning("Pipeline: no .md files found in #{content_dir}")
+      {:ok, %{}}
+    else
+      Logger.info("Pipeline: processing #{length(md_files)} markdown files with #{length(transforms)} transform(s)")
+
+      # Initialise transforms (allows them to perform setup such as loading a .bib file).
+      # Each transform module must implement the Pipeline.Transform behaviour.
+      initialized =
+        Enum.map(transforms, fn mod ->
+          state = mod.init(opts)
+          {mod, state}
+        end)
+
+      stats =
+        Enum.reduce(md_files, %{}, fn path, acc ->
+          original = File.read!(path)
+
+          {transformed, file_stats} =
+            Enum.reduce(initialized, {original, %{}}, fn {mod, state}, {content, fstats} ->
+              result = mod.apply(content, state, opts)
+              changed = result != content
+              {result, Map.update(fstats, mod, (if changed, do: 1, else: 0), &(&1 + (if changed, do: 1, else: 0)))}
+            end)
+
+          if transformed != original do
+            File.write!(path, transformed)
+            Logger.debug("Pipeline: updated #{Path.relative_to_cwd(path)}")
+          end
+
+          Map.merge(acc, file_stats, fn _k, a, b -> a + b end)
+        end)
+
+      Enum.each(initialized, fn {mod, state} ->
+        # teardown/1 is optional in the behaviour
+        if function_exported?(mod, :teardown, 1) do
+          mod.teardown(state)
+        end
+      end)
+
+      {:ok, stats}
+    end
+  end
+end

scripts/pipeline/lib/pipeline/application.ex

@@ -0,0 +1,14 @@
+defmodule Pipeline.Application do
+  @moduledoc false
+  use Application
+
+  @impl true
+  def start(_type, _args) do
+    children = [
+      {Finch, name: Pipeline.Finch}
+    ]
+
+    opts = [strategy: :one_for_one, name: Pipeline.Supervisor]
+    Supervisor.start_link(children, opts)
+  end
+end

scripts/pipeline/lib/pipeline/resolvers/bibtex.ex

@@ -0,0 +1,178 @@
+defmodule Pipeline.Resolvers.BibTeX do
+  @moduledoc """
+  Resolves citation keys from a local BibTeX (.bib) file.
+
+  Configured via the `BIBTEX_FILE` environment variable, or passed directly
+  as `opts.bibtex_file`. The file is parsed once at init time and the
+  resulting entry map is reused for all lookups.
+
+  Supports extracting: author last names, year, title, DOI, URL.
+
+  BibTeX entry format parsed:
+
+      @type{citationkey,
+        author  = {Last, First and Last2, First2},
+        year    = {2021},
+        title   = {Some Title},
+        doi     = {10.xxxx/yyyy},
+        url     = {https://example.com},
+      }
+
+  Returns `{:ok, %{label: "Author, Year", url: "..."}}` or `:error`.
+  """
+
+  require Logger
+
+  # ------------------------------------------------------------------
+  # Public API
+  # ------------------------------------------------------------------
+
+  @doc """
+  Parse a .bib file and return a map of `%{citation_key => entry_map}`.
+  Returns `{:ok, entries}` or `{:error, reason}`.
+  """
+  @spec load(String.t()) :: {:ok, map()} | {:error, term()}
+  def load(path) do
+    case File.read(path) do
+      {:ok, content} ->
+        entries = parse_entries(content)
+        Logger.info("BibTeX: loaded #{map_size(entries)} entries from #{path}")
+        {:ok, entries}
+
+      {:error, reason} ->
+        {:error, reason}
+    end
+  end
+
+  @doc """
+  Resolve a citation key from pre-loaded BibTeX entries.
+  """
+  @spec resolve(String.t(), map()) :: {:ok, map()} | :error
+  def resolve(key, entries) do
+    case Map.fetch(entries, key) do
+      {:ok, entry} ->
+        label = build_label(entry)
+        url = build_url(entry)
+        {:ok, %{label: label, url: url}}
+
+      :error ->
+        :error
+    end
+  end
+
+  # ------------------------------------------------------------------
+  # Parsing
+  # ------------------------------------------------------------------
+
+  # Match @type{key, ...fields...}
+  # We handle nested braces by scanning character by character after
+  # finding the opening, rather than relying on a single regex.
+  @entry_header ~r/@\w+\s*\{\s*([^,\s]+)\s*,/
+
+  defp parse_entries(content) do
+    # Split on "@" boundaries, then parse each chunk
+    content
+    |> String.split(~r/(?=@\w+\s*\{)/, trim: true)
+    |> Enum.reduce(%{}, fn chunk, acc ->
+      case Regex.run(@entry_header, chunk) do
+        [_, key] ->
+          fields = parse_fields(chunk)
+          Map.put(acc, String.trim(key), fields)
+
+        _ ->
+          acc
+      end
+    end)
+  end
+
+  # Extract key = {value} or key = "value" pairs from an entry block.
+  # Handles simple single-depth braces; good enough for common fields.
+  @field_regex ~r/(\w+)\s*=\s*(?:\{([^{}]*(?:\{[^{}]*\}[^{}]*)*)\}|"([^"]*)")/
+
+  defp parse_fields(chunk) do
+    @field_regex
+    |> Regex.scan(chunk)
+    |> Enum.reduce(%{}, fn match, acc ->
+      field_name = Enum.at(match, 1) |> String.downcase()
+      # Value is in capture group 2 (braces) or 3 (quotes)
+      value =
+        case {Enum.at(match, 2, ""), Enum.at(match, 3, "")} do
+          {"", q} -> q
+          {b, _} -> b
+        end
+
+      Map.put(acc, field_name, String.trim(value))
+    end)
+  end
+
+  # ------------------------------------------------------------------
+  # Label & URL building
+  # ------------------------------------------------------------------
+
+  defp build_label(entry) do
+    author_part =
+      entry
+      |> Map.get("author", "")
+      |> parse_authors()
+      |> format_authors()
+
+    year = Map.get(entry, "year", Map.get(entry, "date", ""))
+    year = extract_year(year)
+
+    if year && author_part != "", do: "#{author_part}, #{year}", else: author_part
+  end
+
+  defp parse_authors(""), do: []
+
+  defp parse_authors(author_str) do
+    author_str
+    |> String.split(" and ", trim: true)
+    |> Enum.map(&extract_last_name/1)
+    |> Enum.reject(&(&1 == ""))
+  end
+
+  # Handles "Last, First" and "First Last" formats
+  defp extract_last_name(name) do
+    name = String.trim(name)
+
+    cond do
+      String.contains?(name, ",") ->
+        name |> String.split(",") |> List.first() |> String.trim()
+
+      String.contains?(name, " ") ->
+        name |> String.split(" ") |> List.last() |> String.trim()
+
+      true ->
+        name
+    end
+  end
+
+  defp format_authors([]), do: "Unknown"
+  defp format_authors([single]), do: single
+  defp format_authors([first | rest]), do: "#{first} & #{List.last(rest)}"
+
+  defp extract_year(""), do: nil
+
+  defp extract_year(str) do
+    case Regex.run(~r/\b(\d{4})\b/, str) do
+      [_, year] -> year
+      _ -> nil
+    end
+  end
+
+  defp build_url(entry) do
+    cond do
+      doi = Map.get(entry, "doi", "") |> non_empty() ->
+        "https://doi.org/#{doi}"
+
+      url = Map.get(entry, "url", "") |> non_empty() ->
+        url
+
+      true ->
+        nil
+    end
+  end
+
+  defp non_empty(""), do: nil
+  defp non_empty(v), do: v
+end

scripts/pipeline/lib/pipeline/resolvers/doi.ex

@@ -0,0 +1,18 @@
+defmodule Pipeline.Resolvers.DOI do
+  @moduledoc """
+  Last-resort citation resolver — always succeeds.
+
+  If the citation key looks like a DOI (starts with "10."), returns a
+  `https://doi.org/...` link. Otherwise returns the key itself as a
+  plain label with no URL.
+  """
+
+  @spec resolve(String.t()) :: {:ok, map()}
+  def resolve(key) do
+    if String.starts_with?(key, "10.") do
+      {:ok, %{label: key, url: "https://doi.org/#{key}"}}
+    else
+      {:ok, %{label: key, url: nil}}
+    end
+  end
+end

scripts/pipeline/lib/pipeline/resolvers/zotero.ex

@@ -0,0 +1,182 @@
+defmodule Pipeline.Resolvers.Zotero do
+  @moduledoc """
+  Resolves citation keys via Zotero Better BibTeX's JSON-RPC API.
+
+  Requires Zotero to be running with the Better BibTeX plugin installed.
+  Default endpoint: http://localhost:23119/better-bibtex/json-rpc
+
+  Resolution strategy:
+    1. Search by citation key via `item.search`
+    2. If found, try to get a PDF attachment link (zotero://open-pdf/...)
+    3. Fall back to zotero://select/items/@key
+
+  Returns `{:ok, %{label: "Author, Year", url: "zotero://..."}}` or `:error`.
+  """
+
+  require Logger
+
+  @rpc_path "/better-bibtex/json-rpc"
+
+  @doc """
+  Attempt to resolve `key` against a running Zotero instance.
+  `base_url` defaults to `http://localhost:23119`.
+  """
+  @spec resolve(String.t(), String.t()) :: {:ok, map()} | :error
+  def resolve(key, base_url \\ "http://localhost:23119") do
+    url = base_url <> @rpc_path
+
+    payload =
+      Jason.encode!(%{
+        jsonrpc: "2.0",
+        method: "item.search",
+        params: [
+          [["citationKey", "is", key]]
+        ],
+        id: 1
+      })
+
+    case Req.post(url,
+           body: payload,
+           headers: [{"content-type", "application/json"}],
+           receive_timeout: 5_000,
+           finch: Pipeline.Finch
+         ) do
+      {:ok, %{status: 200, body: body}} ->
+        parse_response(body, key, base_url)
+
+      {:ok, %{status: status}} ->
+        Logger.debug("Zotero: unexpected HTTP #{status} for key #{key}")
+        :error
+
+      {:error, reason} ->
+        Logger.debug("Zotero: connection failed for key #{key}: #{inspect(reason)}")
+        :error
+
+      other ->
+        Logger.debug("Zotero: unexpected result for key #{key}: #{inspect(other)}")
+        :error
+    end
+  rescue
+    e ->
+      Logger.debug("Zotero: exception resolving key #{key}: #{inspect(e)}")
+      :error
+  end
+
+  # ------------------------------------------------------------------
+  # Private helpers
+  # ------------------------------------------------------------------
+
+  defp parse_response(%{"result" => [item | _]}, key, base_url) do
+    label = build_label(item)
+    url = resolve_url(item, key, base_url)
+    {:ok, %{label: label, url: url}}
+  end
+
+  defp parse_response(%{"result" => []}, key, _base_url) do
+    Logger.debug("Zotero: no item found for key #{key}")
+    :error
+  end
+
+  defp parse_response(%{"error" => err}, key, _base_url) do
+    Logger.debug("Zotero: RPC error for key #{key}: #{inspect(err)}")
+    :error
+  end
+
+  defp parse_response(body, key, _base_url) do
+    Logger.debug("Zotero: unexpected response shape for key #{key}: #{inspect(body)}")
+    :error
+  end
+
+  defp fetch_pdf_url(key, base_url) do
+    payload =
+      Jason.encode!(%{
+        jsonrpc: "2.0",
+        method: "item.attachments",
+        params: [key],
+        id: 2
+      })
+
+    case Req.post(base_url <> @rpc_path,
+           body: payload,
+           headers: [{"content-type", "application/json"}],
+           receive_timeout: 5_000,
+           finch: Pipeline.Finch
+         ) do
+      {:ok, %{status: 200, body: %{"result" => attachments}}} when is_list(attachments) ->
+        attachments
+        |> Enum.find_value(fn att ->
+          open = Map.get(att, "open", "")
+          path = Map.get(att, "path", "")
+          if String.ends_with?(path, ".pdf"), do: open, else: nil
+        end)
+
+      _ ->
+        nil
+    end
+  rescue
+    _ -> nil
+  end
+
+  # CSL-JSON format: authors are under "author" with "family"/"given" keys.
+  # Year is under "issued" -> "date-parts" -> [[year, month, day]].
+  defp build_label(item) do
+    authors = Map.get(item, "author", [])
+    year = extract_year(item)
+
+    author_part =
+      case authors do
+        [] ->
+          "Unknown"
+
+        [single] ->
+          Map.get(single, "family", Map.get(single, "literal", "Unknown"))
+
+        [first | rest] ->
+          first_name = Map.get(first, "family", Map.get(first, "literal", "Unknown"))
+          last_name =
+            rest
+            |> List.last()
+            |> then(&Map.get(&1, "family", Map.get(&1, "literal", "Unknown")))
+
+          "#{first_name} & #{last_name}"
+      end
+
+    if year, do: "#{author_part}, #{year}", else: author_part
+  end
+
+  # "issued": {"date-parts": [["2021", 2, 3]]}
+  defp extract_year(item) do
+    case get_in(item, ["issued", "date-parts"]) do
+      [[year | _] | _] -> to_string(year)
+      _ -> nil
+    end
+  end
+
+  defp resolve_url(item, key, base_url) do
+    # Prefer zotero://open-pdf/... for items with a PDF attachment.
+    # Fall back to zotero://select/library/items/KEY to open the item in Zotero.
+    # The "id" field is a URI like "http://zotero.org/users/123/items/ABCD1234".
+    pdf_url = fetch_pdf_url(key, base_url)
+
+    if pdf_url do
+      pdf_url
+    else
+      item_key =
+        item
+        |> Map.get("id", "")
+        |> String.split("/")
+        |> List.last()
+        |> non_empty()
+
+      if item_key do
+        "zotero://select/library/items/#{item_key}"
+      else
+        "zotero://select/items/@#{key}"
+      end
+    end
+  end
+
+  defp non_empty(nil), do: nil
+  defp non_empty(""), do: nil
+  defp non_empty(v), do: v
+end

scripts/pipeline/lib/pipeline/transform.ex

@@ -0,0 +1,48 @@
+defmodule Pipeline.Transform do
+  @moduledoc """
+  Behaviour that all markdown transform modules must implement.
+
+  ## Callbacks
+
+  - `init/1`      — called once before processing; returns transform-specific state.
+                    Default implementation returns the opts map unchanged.
+  - `apply/3`     — called per .md file; returns the (possibly modified) content.
+  - `teardown/1`  — optional cleanup after all files are processed.
+
+  ## Example
+
+      defmodule MyTransform do
+        @behaviour Pipeline.Transform
+
+        @impl true
+        def init(opts), do: %{some_state: opts[:value]}
+
+        @impl true
+        def apply(content, state, _opts) do
+          String.replace(content, "foo", state.some_state)
+        end
+      end
+  """
+
+  @doc "One-time initialisation. Returns opaque state passed to apply/3."
+  @callback init(opts :: map()) :: term()
+
+  @doc "Transform file content. Returns the (possibly modified) content string."
+  @callback apply(content :: String.t(), state :: term(), opts :: map()) :: String.t()
+
+  @doc "Optional cleanup after all files are processed."
+  @callback teardown(state :: term()) :: :ok
+
+  @optional_callbacks teardown: 1
+
+  defmacro __using__(_) do
+    quote do
+      @behaviour Pipeline.Transform
+
+      @impl Pipeline.Transform
+      def init(opts), do: opts
+
+      defoverridable init: 1
+    end
+  end
+end

scripts/pipeline/lib/pipeline/transforms/citations.ex

@@ -0,0 +1,231 @@
+defmodule Pipeline.Transforms.Citations do
+  @moduledoc """
+  Markdown transform: resolves org-citar citation keys to hyperlinks.
+
+  ## Recognised citation syntax (as output by ox-hugo from org-citar)
+
+      [cite:@key]           → org-cite / citar standard (most common)
+      [cite:@key1;@key2]    → multiple citations
+      cite:key              → older roam-style bare cite syntax
+
+  ## Resolution chain (in order)
+
+    1. Zotero (live instance via Better BibTeX JSON-RPC)   — preferred
+    2. BibTeX file (BIBTEX_FILE env var)                   — fallback
+    3. DOI / bare key                                       — always succeeds
+
+  ## Modes (opts.citation_mode)
+
+    :silent  — silently use DOI/bare-key fallback when Zotero+BibTeX fail
+    :warn    — (default) emit a Logger.warning for unresolved keys
+    :strict  — raise on unresolved keys (aborts pipeline)
+
+  ## Format
+
+  Resolved citations are rendered as:
+
+      [Label](url)       when a URL is available
+      [Label]            when no URL could be determined (bare key fallback)
+
+  Multiple semicolon-separated keys become space-separated links:
+
+      [cite:@a;@b]  →  [Author A, 2020](url_a) [Author B, 2019](url_b)
+
+  ## init/1 callback
+
+  Loads the BibTeX file (if configured) once before processing begins,
+  and probes Zotero availability, emitting warnings as appropriate.
+  """
+
+  @behaviour Pipeline.Transform
+
+  require Logger
+
+  alias Pipeline.Resolvers.Zotero
+  alias Pipeline.Resolvers.BibTeX
+  alias Pipeline.Resolvers.DOI
+
+  # Match [cite:@key] and [cite:@key1;@key2;...] (org-cite / citar style)
+  @cite_bracket_regex ~r/\[cite:(@[^\]]+)\]/
+
+  # Match bare cite:key (older roam style, no brackets, no @ prefix)
+  @cite_bare_regex ~r/(?<![(\[])cite:([a-zA-Z0-9_:-]+)/
+
+  # ------------------------------------------------------------------
+  # Pipeline callbacks
+  # ------------------------------------------------------------------
+
+  @doc """
+  Called once before processing any files. Loads BibTeX, probes Zotero.
+  Returns a state map passed to every `apply/3` call.
+  """
+  def init(opts) do
+    bibtex_entries = load_bibtex(opts)
+    zotero_available = probe_zotero(opts)
+
+    if not zotero_available and bibtex_entries == %{} do
+      Logger.warning(
+        "Citations: neither Zotero nor a BibTeX file is available. " <>
+          "All citations will fall back to bare-key rendering. " <>
+          "Set BIBTEX_FILE env var or start Zotero with Better BibTeX to resolve citations."
+      )
+    end
+
+    %{
+      bibtex_entries: bibtex_entries,
+      zotero_available: zotero_available,
+      zotero_url: Map.get(opts, :zotero_url, "http://localhost:23119"),
+      citation_mode: Map.get(opts, :citation_mode, :warn)
+    }
+  end
+
+  @doc """
+  Apply citation resolution to a single markdown file's content.
+  """
+  def apply(content, state, _opts) do
+    content
+    |> resolve_bracket_citations(state)
+    |> resolve_bare_citations(state)
+  end
+
+  # ------------------------------------------------------------------
+  # Resolution passes
+  # ------------------------------------------------------------------
+
+  defp resolve_bracket_citations(content, state) do
+    Regex.replace(@cite_bracket_regex, content, fn _full, keys_str ->
+      keys_str
+      |> String.split(";")
+      |> Enum.map(&String.trim/1)
+      |> Enum.map(fn "@" <> key -> key end)
+      |> Enum.map(&resolve_key(&1, state))
+      |> Enum.join(" ")
+    end)
+  end
+
+  defp resolve_bare_citations(content, state) do
+    Regex.replace(@cite_bare_regex, content, fn _full, key ->
+      resolve_key(key, state)
+    end)
+  end
+
+  # ------------------------------------------------------------------
+  # Single-key resolution chain
+  # ------------------------------------------------------------------
+
+  defp resolve_key(key, state) do
+    info =
+      with :error <- try_zotero(key, state),
+           :error <- try_bibtex(key, state) do
+        handle_unresolved(key, state)
+      else
+        {:ok, citation_info} -> citation_info
+      end
+
+    format_result(info)
+  end
+
+  defp try_zotero(_key, %{zotero_available: false}), do: :error
+
+  defp try_zotero(key, %{zotero_url: url}) do
+    Zotero.resolve(key, url)
+  end
+
+  defp try_bibtex(_key, %{bibtex_entries: entries}) when map_size(entries) == 0, do: :error
+
+  defp try_bibtex(key, %{bibtex_entries: entries}) do
+    BibTeX.resolve(key, entries)
+  end
+
+  defp handle_unresolved(key, %{citation_mode: mode}) do
+    case mode do
+      :strict ->
+        raise "Citations: could not resolve citation key '#{key}' and mode is :strict"
+
+      :warn ->
+        Logger.warning("Citations: unresolved citation key '#{key}' — using bare-key fallback")
+        {:ok, result} = DOI.resolve(key)
+        result
+
+      :silent ->
+        {:ok, result} = DOI.resolve(key)
+        result
+    end
+  end
+
+  defp format_result(%{label: label, url: nil}), do: "[#{label}]"
+  defp format_result(%{label: label, url: url}), do: "[#{label}](#{url})"
+
+  # ------------------------------------------------------------------
+  # Init helpers
+  # ------------------------------------------------------------------
+
+  defp load_bibtex(opts) do
+    path = Map.get(opts, :bibtex_file) || System.get_env("BIBTEX_FILE")
+
+    cond do
+      is_nil(path) ->
+        Logger.debug("Citations: BIBTEX_FILE not set — BibTeX resolver disabled")
+        %{}
+
+      not File.exists?(path) ->
+        Logger.warning("Citations: BIBTEX_FILE=#{path} does not exist — BibTeX resolver disabled")
+        %{}
+
+      true ->
+        case BibTeX.load(path) do
+          {:ok, entries} -> entries
+          {:error, reason} ->
+            Logger.warning("Citations: failed to load BibTeX file #{path}: #{inspect(reason)}")
+            %{}
+        end
+    end
+  end
+
+  defp probe_zotero(opts) do
+    url = Map.get(opts, :zotero_url, "http://localhost:23119")
+
+    # Use a no-op JSON-RPC call to probe availability.
+    # /better-bibtex/cayw is intentionally avoided — it blocks waiting for
+    # user interaction and never returns without a pick.
+    payload =
+      Jason.encode!(%{
+        jsonrpc: "2.0",
+        method: "item.search",
+        params: [[[]]],
+        id: 0
+      })
+
+    result =
+      try do
+        Req.post(url <> "/better-bibtex/json-rpc",
+          body: payload,
+          headers: [{"content-type", "application/json"}],
+          receive_timeout: 3_000,
+          finch: Pipeline.Finch
+        )
+      rescue
+        e -> {:error, e}
+      end
+
+    case result do
+      {:ok, %{status: 200}} ->
+        Logger.info("Citations: Zotero Better BibTeX is available at #{url}")
+        true
+
+      {:ok, %{status: status}} ->
+        Logger.warning(
+          "Citations: Zotero responded HTTP #{status} at #{url} — " <>
+            "is Better BibTeX installed?"
+        )
+        false
+
+      _ ->
+        Logger.warning(
+          "Citations: Zotero not reachable at #{url} — " <>
+            "start Zotero with Better BibTeX or set BIBTEX_FILE as fallback"
+        )
+        false
+    end
+  end
+end

scripts/pipeline/mix.exs

@@ -0,0 +1,27 @@
+defmodule Pipeline.MixProject do
+  use Mix.Project
+
+  def project do
+    [
+      app: :pipeline,
+      version: "0.1.0",
+      elixir: "~> 1.15",
+      start_permanent: Mix.env() == :prod,
+      deps: deps()
+    ]
+  end
+
+  def application do
+    [
+      extra_applications: [:logger, :inets, :ssl],
+      mod: {Pipeline.Application, []}
+    ]
+  end
+
+  defp deps do
+    [
+      {:req, "~> 0.5"},
+      {:jason, "~> 1.4"}
+    ]
+  end
+end

scripts/pipeline/mix.lock

@@ -0,0 +1,11 @@
+%{
+  "finch": {:hex, :finch, "0.21.0", "b1c3b2d48af02d0c66d2a9ebfb5622be5c5ecd62937cf79a88a7f98d48a8290c", [:mix], [{:mime, "~> 1.0 or ~> 2.0", [hex: :mime, repo: "hexpm", optional: false]}, {:mint, "~> 1.6.2 or ~> 1.7", [hex: :mint, repo: "hexpm", optional: false]}, {:nimble_options, "~> 0.4 or ~> 1.0", [hex: :nimble_options, repo: "hexpm", optional: false]}, {:nimble_pool, "~> 1.1", [hex: :nimble_pool, repo: "hexpm", optional: false]}, {:telemetry, "~> 0.4 or ~> 1.0", [hex: :telemetry, repo: "hexpm", optional: false]}], "hexpm", "87dc6e169794cb2570f75841a19da99cfde834249568f2a5b121b809588a4377"},
+  "hpax": {:hex, :hpax, "1.0.3", "ed67ef51ad4df91e75cc6a1494f851850c0bd98ebc0be6e81b026e765ee535aa", [:mix], [], "hexpm", "8eab6e1cfa8d5918c2ce4ba43588e894af35dbd8e91e6e55c817bca5847df34a"},
+  "jason": {:hex, :jason, "1.4.4", "b9226785a9aa77b6857ca22832cffa5d5011a667207eb2a0ad56adb5db443b8a", [:mix], [{:decimal, "~> 1.0 or ~> 2.0", [hex: :decimal, repo: "hexpm", optional: true]}], "hexpm", "c5eb0cab91f094599f94d55bc63409236a8ec69a21a67814529e8d5f6cc90b3b"},
+  "mime": {:hex, :mime, "2.0.7", "b8d739037be7cd402aee1ba0306edfdef982687ee7e9859bee6198c1e7e2f128", [:mix], [], "hexpm", "6171188e399ee16023ffc5b76ce445eb6d9672e2e241d2df6050f3c771e80ccd"},
+  "mint": {:hex, :mint, "1.7.1", "113fdb2b2f3b59e47c7955971854641c61f378549d73e829e1768de90fc1abf1", [:mix], [{:castore, "~> 0.1.0 or ~> 1.0", [hex: :castore, repo: "hexpm", optional: true]}, {:hpax, "~> 0.1.1 or ~> 0.2.0 or ~> 1.0", [hex: :hpax, repo: "hexpm", optional: false]}], "hexpm", "fceba0a4d0f24301ddee3024ae116df1c3f4bb7a563a731f45fdfeb9d39a231b"},
+  "nimble_options": {:hex, :nimble_options, "1.1.1", "e3a492d54d85fc3fd7c5baf411d9d2852922f66e69476317787a7b2bb000a61b", [:mix], [], "hexpm", "821b2470ca9442c4b6984882fe9bb0389371b8ddec4d45a9504f00a66f650b44"},
+  "nimble_pool": {:hex, :nimble_pool, "1.1.0", "bf9c29fbdcba3564a8b800d1eeb5a3c58f36e1e11d7b7fb2e084a643f645f06b", [:mix], [], "hexpm", "af2e4e6b34197db81f7aad230c1118eac993acc0dae6bc83bac0126d4ae0813a"},
+  "req": {:hex, :req, "0.5.17", "0096ddd5b0ed6f576a03dde4b158a0c727215b15d2795e59e0916c6971066ede", [:mix], [{:brotli, "~> 0.3.1", [hex: :brotli, repo: "hexpm", optional: true]}, {:ezstd, "~> 1.0", [hex: :ezstd, repo: "hexpm", optional: true]}, {:finch, "~> 0.17", [hex: :finch, repo: "hexpm", optional: false]}, {:jason, "~> 1.0", [hex: :jason, repo: "hexpm", optional: false]}, {:mime, "~> 2.0.6 or ~> 2.1", [hex: :mime, repo: "hexpm", optional: false]}, {:nimble_csv, "~> 1.0", [hex: :nimble_csv, repo: "hexpm", optional: true]}, {:plug, "~> 1.0", [hex: :plug, repo: "hexpm", optional: true]}], "hexpm", "0b8bc6ffdfebbc07968e59d3ff96d52f2202d0536f10fef4dc11dc02a2a43e39"},
+  "telemetry": {:hex, :telemetry, "1.3.0", "fedebbae410d715cf8e7062c96a1ef32ec22e764197f70cda73d82778d61e7a2", [:rebar3], [], "hexpm", "7015fc8919dbe63764f4b4b87a95b7c0996bd539e0d499be6ec9d7f3875b79e6"},
+}