feat(pipeline): refactor into its own project

AGENTS.md

@@ -244,113 +244,6 @@ 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

flake.lock

@@ -18,6 +18,24 @@
         "type": "github"
       }
     },
+    "flake-utils_2": {
+      "inputs": {
+        "systems": "systems_2"
+      },
+      "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,
@@ -34,10 +52,42 @@
         "type": "github"
       }
     },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1771369470,
+        "narHash": "sha256-0NBlEBKkN3lufyvFegY4TYv5mCNHbi5OmBDrzihbBMQ=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "0182a361324364ae3f436a63005877674cf45efb",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "pipeline": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nixpkgs": "nixpkgs_2"
+      },
+      "locked": {
+        "path": "./pipeline",
+        "type": "path"
+      },
+      "original": {
+        "path": "./pipeline",
+        "type": "path"
+      },
+      "parent": []
+    },
     "root": {
       "inputs": {
         "flake-utils": "flake-utils",
-        "nixpkgs": "nixpkgs"
+        "nixpkgs": "nixpkgs",
+        "pipeline": "pipeline"
       }
     },
     "systems": {
@@ -54,6 +104,21 @@
         "repo": "default",
         "type": "github"
       }
+    },
+    "systems_2": {
+      "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",

flake.nix

@@ -4,22 +4,30 @@
   inputs = {
     nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
     flake-utils.url = "github:numtide/flake-utils";
+    pipeline.url = "path:./pipeline";
   };
 
-  outputs = { self, nixpkgs, flake-utils }:
+  outputs = { self, nixpkgs, flake-utils, pipeline }:
     flake-utils.lib.eachDefaultSystem (system:
       let
         pkgs = import nixpkgs { inherit system; };
+        fs = pkgs.lib.fileset;
 
-        # Emacs with ox-hugo — shared between devShell and buildApp
+        pipelineApp = pipeline.packages.${system}.default;
-        emacsWithOxHugo = (pkgs.emacsPackagesFor pkgs.emacs-nox).emacsWithPackages
-          (epkgs: [ epkgs.ox-hugo ]);
 
-        # Pre-fetched npm dependency tree (node_modules)
+        # Pre-fetched npm dependency tree (node_modules).
+        # src is filtered to only package.json + package-lock.json so that
+        # edits to Quartz source files do not invalidate this derivation.
         quartzDeps = pkgs.buildNpmPackage {
           pname = "quartz-deps";
           version = "4.5.2";
-          src = ./.;
+          src = fs.toSource {
+            root = ./.;
+            fileset = fs.unions [
+              ./package.json
+              ./package-lock.json
+            ];
+          };
           npmDepsHash = "sha256-7u+VlIx44B3/ivM9vLMIOn+e4TL4eS6B682vhS+Ikb4=";
           dontBuild = true;
           installPhase = ''
@@ -28,18 +36,10 @@
           '';
         };
 
-        # 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 ];
+          runtimeInputs = [ pkgs.nodejs_22 ];
           text = ''
             NOTES_DIR="''${1:?Usage: build <path-to-notes-dir>}"
             NOTES_DIR=$(realpath "$NOTES_DIR")
@@ -54,15 +54,10 @@
             # 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
+            # Run the pre-compiled pipeline escript (org → md, citations transform)
-            cp -r ${pipelineMixDeps} "$WORK/repo/scripts/pipeline/deps"
+            ${pipelineApp}/bin/pipeline "$NOTES_DIR" \
-            chmod -R u+w "$WORK/repo/scripts/pipeline/deps"
+              --output "$WORK/repo" \
-
+              --content-dir "$WORK/repo/content"
-            # ox-hugo requires static/ to exist before it can copy image assets
-            mkdir -p "$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.
@@ -79,19 +74,18 @@
           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;
+        packages.pipeline = pipelineApp;
 
         apps.default = { type = "app"; program = "${buildApp}/bin/build"; };
         apps.build = { type = "app"; program = "${buildApp}/bin/build"; };

notes/example-citation.org

@@ -7,7 +7,7 @@ The methodology described in [cite:@podlovics2021journalArticle] provides a
 useful framework for analysis.
 
 Multiple citations can appear together:
-[cite:@podlovics2021journalArticle]
+[cite:@podlovics2021journalArticle;@petersen2022book]
 
 Older bare-cite style (org-roam v1 / older citar) also works:
-cite:podlovics2021journalArticle
+cite:@podlovics2021journalArticle

pipeline/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": 1771369470,
+        "narHash": "sha256-0NBlEBKkN3lufyvFegY4TYv5mCNHbi5OmBDrzihbBMQ=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "0182a361324364ae3f436a63005877674cf45efb",
+        "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
+}

pipeline/flake.nix

@@ -0,0 +1,69 @@
+{
+  description = "Org-roam export pipeline — Elixir escript";
+
+  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; };
+        fs = pkgs.lib.fileset;
+
+        # Emacs with ox-hugo — needed at runtime by the pipeline escript
+        # (export_org_files calls `emacs --batch` with ox-hugo).
+        emacsWithOxHugo = (pkgs.emacsPackagesFor pkgs.emacs-nox).emacsWithPackages
+          (epkgs: [ epkgs.ox-hugo ]);
+
+        # Pre-fetched Hex/Mix dependencies.
+        # src is filtered to mix.exs + mix.lock so source edits don't
+        # invalidate this derivation.
+        mixDeps = pkgs.beamPackages.fetchMixDeps {
+          pname = "pipeline-mix-deps";
+          version = "0.1.0";
+          src = fs.toSource {
+            root = ./.;
+            fileset = fs.unions [
+              ./mix.exs
+              ./mix.lock
+            ];
+          };
+          sha256 = "sha256-E79X+nUy86G1Jrwv3T7dXekoGv8Hd14ZgJSKWjvlmAw=";
+        };
+
+        # Compiled pipeline escript (without runtime wrappers).
+        pipelineEscript = pkgs.beamPackages.mixRelease {
+          pname = "pipeline";
+          version = "0.1.0";
+          src = ./.;
+
+          escriptBinName = "pipeline";
+          mixFodDeps = mixDeps;
+
+          stripDebug = true;
+        };
+
+        # Wrapped pipeline that puts emacs (with ox-hugo) on PATH so
+        # the escript's System.cmd("emacs", ...) calls succeed.
+        pipelineApp = pkgs.writeShellApplication {
+          name = "pipeline";
+          runtimeInputs = [ emacsWithOxHugo ];
+          text = ''
+            exec ${pipelineEscript}/bin/pipeline "$@"
+          '';
+        };
+      in
+      {
+        packages.default = pipelineApp;
+        packages.escript = pipelineEscript;
+
+        devShells.default = pkgs.mkShell {
+          buildInputs = [
+            pkgs.elixir
+            emacsWithOxHugo
+          ];
+        };
+      });
+}

pipeline/lib/pipeline/cli.ex

@@ -0,0 +1,261 @@
+defmodule Pipeline.CLI do
+  @moduledoc """
+  Escript entry point for the org-roam export pipeline.
+
+  Runs four phases in sequence:
+
+    1. Wipe `content/` (preserving `.gitkeep`)
+    2. Export each `.org` file via `emacs --batch` + ox-hugo → `content/**/*.md`
+    3. Run Elixir transform modules over every `.md` file
+    4. Generate a fallback `content/index.md` if none was exported
+
+  ## Usage
+
+      pipeline <notes-dir> [--output <path>]
+
+  Arguments:
+    notes-dir          Path to the directory containing `.org` notes (required).
+                       Also accepts the `NOTES_DIR` env var.
+
+  Options:
+    --output <path>    Output root directory (used as ox-hugo base dir).
+                       Defaults to the `OUTPUT_DIR` env var, or the current
+                       working directory.
+    --content-dir <p>  Output directory for exported Markdown. Defaults to
+                       `<output>/content`.
+
+  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.
+  """
+
+  require Logger
+
+  def main(argv) do
+    Application.ensure_all_started(:pipeline)
+
+    {notes_dir, output_dir, content_dir} = parse_args(argv)
+
+    wipe(content_dir)
+    export_org_files(notes_dir, output_dir)
+    run_pipeline(content_dir)
+    generate_index(content_dir)
+
+    md_count =
+      content_dir
+      |> Path.join("**/*.md")
+      |> Path.wildcard()
+      |> length()
+
+    IO.puts("==> Done. #{md_count} markdown files in #{content_dir}")
+  end
+
+  # ---------------------------------------------------------------------------
+  # Argument parsing
+  # ---------------------------------------------------------------------------
+
+  defp parse_args(argv) do
+    {opts, positional, _invalid} =
+      OptionParser.parse(argv,
+        strict: [output: :string, content_dir: :string]
+      )
+
+    notes_dir =
+      case positional do
+        [dir | _] ->
+          dir
+
+        [] ->
+          System.get_env("NOTES_DIR") ||
+            abort("Usage: pipeline <notes-dir> [--output <path>]")
+      end
+
+    notes_dir = Path.expand(notes_dir)
+
+    unless File.dir?(notes_dir) do
+      abort("Error: notes directory does not exist: #{notes_dir}")
+    end
+
+    output_dir =
+      (opts[:output] || System.get_env("OUTPUT_DIR") || File.cwd!())
+      |> Path.expand()
+
+    content_dir =
+      (opts[:content_dir] || Path.join(output_dir, "content"))
+      |> Path.expand()
+
+    {notes_dir, output_dir, content_dir}
+  end
+
+  # ---------------------------------------------------------------------------
+  # Phase 1: Wipe content/
+  # ---------------------------------------------------------------------------
+
+  defp wipe(content_dir) do
+    IO.puts("==> Wiping #{content_dir}")
+    File.mkdir_p!(content_dir)
+
+    content_dir
+    |> File.ls!()
+    |> Enum.reject(&(&1 == ".gitkeep"))
+    |> Enum.each(fn entry ->
+      Path.join(content_dir, entry) |> File.rm_rf!()
+    end)
+  end
+
+  # ---------------------------------------------------------------------------
+  # Phase 2: Export org files via Emacs + ox-hugo
+  # ---------------------------------------------------------------------------
+
+  defp export_org_files(notes_dir, output_dir) do
+    IO.puts("==> Exporting org files from #{notes_dir}")
+
+    # ox-hugo requires static/ to exist for image asset copying
+    File.mkdir_p!(Path.join(output_dir, "static"))
+
+    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", """
+              (org-cite-register-processor 'passthrough
+                :export-citation
+                (lambda (citation _style _backend _info)
+                  (let ((keys (mapcar (lambda (ref)
+                                        (concat "@" (org-element-property :key ref)))
+                                      (org-cite-get-references citation))))
+                    (format "[cite:%s]" (string-join keys ";")))))
+              """,
+              "--eval", "(setq org-cite-export-processors '((t passthrough)))",
+              "--eval", ~s[(setq org-hugo-base-dir "#{output_dir}")],
+              "--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
+  end
+
+  # ---------------------------------------------------------------------------
+  # Phase 3: Markdown transformation pipeline
+  # ---------------------------------------------------------------------------
+
+  defp run_pipeline(content_dir) do
+    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
+  end
+
+  # ---------------------------------------------------------------------------
+  # Phase 4: Generate default index.md if none was exported
+  # ---------------------------------------------------------------------------
+
+  defp generate_index(content_dir) do
+    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
+  end
+
+  # ---------------------------------------------------------------------------
+  # Helpers
+  # ---------------------------------------------------------------------------
+
+  defp abort(message) do
+    IO.puts(:stderr, message)
+    System.halt(1)
+  end
+end

pipeline/lib/pipeline/transforms/citations.ex

@@ -48,8 +48,8 @@ defmodule Pipeline.Transforms.Citations do
   # 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)
+  # Match bare cite:key or cite:@key (older roam style, no brackets, optional @ prefix)
-  @cite_bare_regex ~r/(?<![(\[])cite:([a-zA-Z0-9_:-]+)/
+  @cite_bare_regex ~r/(?<![(\[])cite:@?([a-zA-Z0-9_:-]+)/
 
   # ------------------------------------------------------------------
   # Pipeline callbacks

pipeline/mix.exs

@@ -5,21 +5,27 @@ defmodule Pipeline.MixProject do
     [
       app: :pipeline,
       version: "0.1.0",
-      elixir: "~> 1.15",
+      elixir: "~> 1.17",
       start_permanent: Mix.env() == :prod,
-      deps: deps()
+      deps: deps(),
+      escript: escript()
     ]
   end
 
   def application do
     [
-      extra_applications: [:logger, :inets, :ssl],
+      extra_applications: [:logger],
       mod: {Pipeline.Application, []}
     ]
   end
 
+  defp escript do
+    [main_module: Pipeline.CLI]
+  end
+
   defp deps do
     [
+      {:finch, "~> 0.19"},
       {:req, "~> 0.5"},
       {:jason, "~> 1.4"}
     ]

scripts/export.exs

@@ -1,217 +0,0 @@
-#!/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}")