docs: update AGENTS.md and README with pipeline and citation details

AGENTS.md

@@ -246,21 +246,22 @@ git branch -d feature/my-feature
 
 ## Org-Roam Workflow
 
-Notes live in a **separate directory** outside this repo. The export script
+Notes live in a **separate directory** outside this repo. The export pipeline
-converts them to Markdown via ox-hugo, then Quartz builds the site.
+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
+- `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)
+# Export only (wipes content/, exports all .org files, runs pipeline)
 NOTES_DIR=/path/to/notes npm run export
 
 # Export then build the site
@@ -270,9 +271,85 @@ NOTES_DIR=/path/to/notes npm run build:notes
 elixir scripts/export.exs /path/to/notes
 ```
 
-The export script (`scripts/export.exs`) runs Emacs in batch mode, calling
+Optional env vars for the pipeline:
-`org-hugo-export-to-md` per file (per-file mode, not per-subtree). It uses
+
-YAML frontmatter (ox-hugo default). `content/` is wiped before each export.
+| 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
 
@@ -280,3 +357,5 @@ YAML frontmatter (ox-hugo default). `content/` is wiped before each export.
 - **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

@@ -41,8 +41,33 @@ NOTES_DIR=/path/to/notes npm run serve:notes
 NOTES_DIR=/path/to/notes npm run export
 ```
 
-The export script mirrors the subdirectory structure of your notes into `content/`
+The export pipeline runs in four phases:
-and generates a fallback `index.md` if your notes don't include one.
+
+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