Add Elixir markdown pipeline with org-citar citation resolution

Introduces scripts/pipeline/, a Mix project that runs as a post-export
transformation pass over content/*.md before Quartz builds the site.

Pipeline (scripts/export.exs phase 3):
- Compiles and loads the Mix project at export time (cached after first run)
- Applies a list of Transform modules sequentially over all .md files
- Only rewrites files that were actually changed

Citations transform (Pipeline.Transforms.Citations):
- Resolves [cite:@key] and bare cite:key syntax produced by ox-hugo/citar
- Resolution chain: Zotero BBT JSON-RPC → BibTeX file → DOI/bare-key fallback
- Zotero probe uses a no-op JSON-RPC call (cayw endpoint blocks indefinitely)
- Zotero resolver fetches PDF attachments via item.attachments, producing
  zotero://open-pdf/... links; falls back to zotero://select/library/items/...
- BibTeX resolver parses .bib files with a simple regex parser (no deps)
- DOI resolver is the always-succeeding last resort

Configuration via env vars:
  BIBTEX_FILE   — path to .bib file for fallback resolution
  ZOTERO_URL    — Zotero base URL (default: http://localhost:23119)
  CITATION_MODE — silent | warn (default) | strict

Adding future transforms requires only implementing Pipeline.Transform
behaviour and appending the module to the transforms list in export.exs.

.gitignore

@@ -13,3 +13,10 @@ erl_crash.dump
 # content/ is generated by the export script; only keep the placeholder
 content/*
 !content/.gitkeep
+# 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

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

scripts/export.exs

@@ -1,22 +1,71 @@
 #!/usr/bin/env elixir
-# Export org-roam notes (per-file) to content/ via ox-hugo.
+# 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))
+        (IO.puts(:stderr, "Usage: NOTES_DIR=/path/to/notes elixir scripts/export.exs")
+         System.halt(1))
   end
 
 notes_dir = Path.expand(notes_dir)
-repo_root = __DIR__ |> Path.join("..") |> Path.expand()
 content_dir = Path.join(repo_root, "content")
 
 unless File.dir?(notes_dir) do
@@ -24,7 +73,9 @@ unless File.dir?(notes_dir) do
   System.halt(1)
 end
 
-# Wipe content/, preserving .gitkeep
+# ---------------------------------------------------------------------------
+# Phase 1: Wipe content/
+# ---------------------------------------------------------------------------
 IO.puts("==> Wiping #{content_dir}")
 
 content_dir
@@ -34,7 +85,9 @@ content_dir
   Path.join(content_dir, entry) |> File.rm_rf!()
 end)
 
-# Collect all .org files
+# ---------------------------------------------------------------------------
+# Phase 2: Export org files via Emacs + ox-hugo
+# ---------------------------------------------------------------------------
 IO.puts("==> Exporting org files from #{notes_dir}")
 
 org_files =
@@ -46,12 +99,10 @@ if org_files == [] do
   System.halt(0)
 end
 
-# Export each file via emacs --batch
 results =
   Enum.map(org_files, fn orgfile ->
     IO.puts("  exporting: #{orgfile}")
 
-    # Mirror the notes subdirectory structure under content/
     section =
       orgfile
       |> Path.dirname()
@@ -71,7 +122,6 @@ results =
         stderr_to_stdout: true
       )
 
-    # Filter noisy emacs startup lines, same as the shell script
     filtered =
       output
       |> String.split("\n")
@@ -91,12 +141,43 @@ if failures != [] do
   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()
 
-# Generate a default index.md if none was exported
 index_path = Path.join(content_dir, "index.md")
 
 unless File.exists?(index_path) do

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"},
+}