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

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/`
-and generates a fallback `index.md` if your notes don't include one.
+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