diff --git a/.agent-shell/transcripts/2026-02-21-14-47-23.md b/.agent-shell/transcripts/2026-02-21-14-47-23.md
index 8c822ac..2921329 100644
--- a/.agent-shell/transcripts/2026-02-21-14-47-23.md
+++ b/.agent-shell/transcripts/2026-02-21-14-47-23.md
@@ -10171,4 +10171,582 @@ Generated org_garden app
```
## Agent (2026-02-21 21:50:09)
-Now let's commit and push:
\ No newline at end of file
+Now let's commit and push:
+
+### Tool Call [completed]: git add -A && git commit -m "Fix Quartz port not being passed correctly
+
+When CLI options --port/--ws-port were not provided, nil values were
+being explicitly passed to Server.start_link, which caused Keyword.get
+to return nil instead of the default. Now we only include port options
+in the keyword list if they have actual values."
+
+**Tool:** execute
+**Timestamp:** 2026-02-21 21:50:13
+
+```
+[main 11ab833] Fix Quartz port not being passed correctly
+ 2 files changed, 1147 insertions(+), 7 deletions(-)
+```
+
+
+### Tool Call [completed]: git push
+
+**Tool:** execute
+**Timestamp:** 2026-02-21 21:50:17
+
+```
+remote: . Processing 1 references
+remote: Processed 1 references in total
+To gitea.bueso.eu:ignacio.ballesteros/org-garden.git
+ 87fd311..11ab833 main -> main
+```
+## Agent (2026-02-21 21:50:19)
+
+Fixed. The issue was that when CLI options `--port` and `--ws-port` weren't provided, the code was passing `port: nil` and `ws_port: nil` explicitly. `Keyword.get(opts, :port, default)` returns `nil` (not the default) when the key exists with a `nil` value.
+
+Now only non-nil port values are included in the options passed to `Server.start_link`.
+
+## User (2026-02-22 11:44:42)
+
+Now index.md is missing, review the pipeline and transformations
+
+➜ org-garden git:(main) ✗
+
+## Agent (2026-02-22 11:44:46)
+
+Let me investigate the index generation issue by reviewing the pipeline flow:
+
+### Tool Call [completed]: read
+
+**Tool:** read
+**Timestamp:** 2026-02-22 11:44:47
+
+```
+/home/ignaciobll/code/org-garden/lib/org_garden/index.ex
+file
+1: defmodule OrgGarden.Index do
+2: @moduledoc """
+3: Generates a fallback `index.md` in the content directory if none was
+4: exported from an `.org` file.
+5:
+6: The generated index lists all markdown pages alphabetically with links.
+7: """
+8:
+9: @doc """
+10: Generate `content_dir/index.md` if it does not already exist.
+11:
+12: If an `index.md` was already created by ox-hugo (from an `index.org`),
+13: it is left untouched.
+14: """
+15: @spec generate(String.t()) :: :ok
+16: def generate(content_dir) do
+17: index_path = Path.join(content_dir, "index.md")
+18:
+19: unless File.exists?(index_path) do
+20: IO.puts(" generating default index.md")
+21:
+22: pages =
+23: Path.join(content_dir, "**/*.md")
+24: |> Path.wildcard()
+25: |> Enum.map(fn path ->
+26: slug = Path.relative_to(path, content_dir) |> Path.rootname()
+27:
+28: title =
+29: path
+30: |> File.read!()
+31: |> then(fn content ->
+32: case Regex.run(~r/^title\s*=\s*"(.+)"/m, content) do
+33: [_, t] -> t
+34: _ -> slug
+35: end
+36: end)
+37:
+38: {slug, title}
+39: end)
+40: |> Enum.sort_by(fn {_, title} -> title end)
+41: |> Enum.map(fn {slug, title} -> "- [#{title}](#{slug})" end)
+42: |> Enum.join("\n")
+43:
+44: File.write!(index_path, """
+45: ---
+46: title: Index
+47: ---
+48:
+49: #{pages}
+50: """)
+51: end
+52:
+53: :ok
+54: end
+55:
+56: @doc """
+57: Regenerate the index by removing any previously generated one first.
+58:
+59: Only removes the index if it was generated by us (contains `title: Index`).
+60: User-exported index files (from `index.org`) are left untouched.
+61: """
+62: @spec regenerate(String.t()) :: :ok
+63: def regenerate(content_dir) do
+64: index_path = Path.join(content_dir, "index.md")
+65:
+66: if File.exists?(index_path) do
+67: content = File.read!(index_path)
+68:
+69: if generated_index?(content) do
+70: File.rm!(index_path)
+71: end
+72: end
+73:
+74: generate(content_dir)
+75: end
+76:
+77: defp generated_index?(content) do
+78: # Our generated index uses "title: Index" in YAML frontmatter.
+79: # ox-hugo uses TOML frontmatter (title = "..."), so this won't
+80: # match user-exported files.
+81: String.contains?(content, "title: Index")
+82: end
+83: end
+84:
+
+(End of file - total 84 lines)
+
+```
+## Agent (2026-02-22 11:44:49)
+
+The index module looks fine. Let me check the server.ex to see how the pipeline is called:
+
+### Tool Call [completed]: read
+
+**Tool:** read
+**Timestamp:** 2026-02-22 11:44:51
+
+```
+/home/ignaciobll/code/org-garden/lib/org_garden/server.ex
+file
+136: defp run_initial_pipeline(state) do
+137: %{
+138: notes_dir: notes_dir,
+139: output_dir: output_dir,
+140: content_dir: content_dir,
+141: pipeline_opts: pipeline_opts
+142: } = state
+143:
+144: Logger.info("Running initial export pipeline...")
+145:
+146: # Wipe content directory
+147: wipe(content_dir)
+148:
+149: # Export all org files
+150: case OrgGarden.Export.export_all(notes_dir, output_dir) do
+151: {:ok, 0} ->
+152: Logger.warning("No .org files found in #{notes_dir}")
+153: :ok
+154:
+155: {:ok, count} ->
+156: Logger.info("Exported #{count} file(s)")
+157:
+158: # Run transforms
+159: {:ok, stats} = OrgGarden.run(content_dir, @transforms, pipeline_opts)
+160:
+161: Enum.each(stats, fn {mod, c} ->
+162: Logger.info("#{inspect(mod)}: #{c} file(s) modified")
+163: end)
+164:
+165: # Generate index
+166: OrgGarden.Index.generate(content_dir)
+167: :ok
+168:
+169: {:error, failures} ->
+170: Logger.error("Failed to export #{length(failures)} file(s)")
+171: {:error, {:export_failed, failures}}
+172: end
+173: end
+174:
+175: defp start_supervisor(state) do
+
+(File has more lines. Use 'offset' parameter to read beyond line 175)
+
+```
+## Agent (2026-02-22 11:44:53)
+
+I see the issue! When there are 0 org files (line 151-153), we return `:ok` early without generating an index. But more importantly, let me check what happens with the parallel export - maybe it's returning early on the `{:ok, 0}` case incorrectly.
+
+Let me also check the export.ex parallel code more carefully:
+
+### Tool Call [completed]: read
+
+**Tool:** read
+**Timestamp:** 2026-02-22 11:44:57
+
+```
+/home/ignaciobll/code/org-garden/lib/org_garden/export.ex
+file
+74: @default_max_concurrency 8
+75:
+76: @doc """
+77: Export all `.org` files found under `notes_dir`.
+78:
+79: Exports files in parallel for improved performance. The concurrency level
+80: can be configured via the `:export_concurrency` application config or
+81: the `EXPORT_CONCURRENCY` environment variable. Defaults to #{@default_max_concurrency}.
+82:
+83: Returns `{:ok, count}` where `count` is the number of successfully
+84: exported files, or `{:error, failures}` if any files failed.
+85: """
+86: @spec export_all(String.t(), String.t()) :: {:ok, non_neg_integer()} | {:error, list()}
+87: def export_all(notes_dir, output_dir) do
+88: org_files =
+89: Path.join(notes_dir, "**/*.org")
+90: |> Path.wildcard()
+91:
+92: if org_files == [] do
+93: Logger.warning("No .org files found in #{notes_dir}")
+94: {:ok, 0}
+95: else
+96: max_concurrency = get_concurrency()
+97: Logger.info("Exporting #{length(org_files)} org file(s) from #{notes_dir} (concurrency: #{max_concurrency})")
+98:
+99: results =
+100: org_files
+101: |> Task.async_stream(
+102: fn orgfile ->
+103: Logger.info(" exporting: #{orgfile}")
+104: {orgfile, export_file(orgfile, notes_dir, output_dir)}
+105: end,
+106: max_concurrency: max_concurrency,
+107: timeout: :infinity,
+108: ordered: false
+109: )
+110: |> Enum.map(fn {:ok, result} -> result end)
+111:
+112: failures =
+113: Enum.filter(results, fn
+114: {_, {:ok, _}} -> false
+115: {_, {:error, _}} -> true
+116: end)
+117:
+118: if failures == [] do
+119: {:ok, length(results)}
+120: else
+121: {:error, failures}
+122: end
+123: end
+124: end
+125:
+126: defp get_concurrency do
+127: Application.get_env(:org_garden, :export_concurrency, @default_max_concurrency)
+128: end
+129:
+130: @doc """
+131: Compute the expected `.md` path for a given `.org` file.
+132:
+133: Uses the same section-mapping logic as ox-hugo: the relative directory
+
+(File has more lines. Use 'offset' parameter to read beyond line 133)
+
+```
+## Agent (2026-02-22 11:45:00)
+
+The export looks fine. Let me run the actual build to see what's happening. First let me check what the actual content_dir is and if index.md exists there:
+
+### Tool Call [completed]: ls -la content/ 2>/dev/null || echo "content/ doesn't exist"
+
+**Tool:** execute
+**Timestamp:** 2026-02-22 11:45:02
+
+```
+total 8
+drwxr-xr-x 2 ignaciobll users 4096 Feb 21 21:48 .
+drwxr-xr-x 15 ignaciobll users 4096 Feb 21 21:48 ..
+```
+## Agent (2026-02-22 11:45:06)
+
+Content directory is empty. Let me check what notes are available:
+
+### Tool Call [completed]: ls -la notes/ 2>/dev/null || echo "notes/ doesn't exist"
+
+**Tool:** execute
+**Timestamp:** 2026-02-22 11:45:07
+
+```
+total 20
+drwxr-xr-x 5 ignaciobll users 4096 Feb 21 00:35 .
+drwxr-xr-x 15 ignaciobll users 4096 Feb 21 21:48 ..
+drwxr-xr-x 2 ignaciobll users 4096 Feb 21 00:35 bus
+drwxr-xr-x 2 ignaciobll users 4096 Feb 21 00:35 metro
+drwxr-xr-x 2 ignaciobll users 4096 Feb 21 00:35 roads
+```
+
+
+### Tool Call [completed]: find notes/ -name "*.org" 2>/dev/null
+
+**Tool:** execute
+**Timestamp:** 2026-02-22 11:45:10
+
+```
+
+```
+## Agent (2026-02-22 11:45:12)
+
+There are no `.org` files in `notes/`. Let me check if there are any org files elsewhere, or if the content was previously in a different form:
+
+### Tool Call [completed]: find . -name "*.org" -not -path "./.git/*" 2>/dev/null | head -20
+
+**Tool:** execute
+**Timestamp:** 2026-02-22 11:45:13
+
+```
+./README.org
+```
+## Agent (2026-02-22 11:45:15)
+
+There's only the README.org. So the actual issue is that when there are no org files to export, the index.md isn't being generated. Let me trace through the pipeline:
+
+1. In `server.ex:run_initial_pipeline`, when `export_all` returns `{:ok, 0}`, we just return `:ok` without calling `OrgGarden.Index.generate`
+
+Let me also check the CLI flow since you might be running the CLI directly:
+
+### Tool Call [completed]: read
+
+**Tool:** read
+**Timestamp:** 2026-02-22 11:45:19
+
+```
+/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex
+file
+300: # ---------------------------------------------------------------------------
+301: # Phase 2: Export org files via Emacs + ox-hugo
+302: # ---------------------------------------------------------------------------
+303:
+304: defp export_all(notes_dir, output_dir) do
+305: IO.puts("==> Exporting org files from #{notes_dir}")
+306:
+307: case OrgGarden.Export.export_all(notes_dir, output_dir) do
+308: {:ok, 0} ->
+309: IO.puts("No .org files found in #{notes_dir}")
+310: System.halt(0)
+311:
+312: {:ok, count} ->
+313: IO.puts(" exported #{count} file(s)")
+314:
+315: {:error, failures} ->
+316: IO.puts(:stderr, "\nFailed to export #{length(failures)} file(s):")
+317:
+318: Enum.each(failures, fn {f, {:error, reason}} ->
+319: IO.puts(:stderr, " #{f}: #{inspect(reason)}")
+320: end)
+321:
+322: System.halt(1)
+323: end
+324: end
+325:
+326: # ---------------------------------------------------------------------------
+327: # Phase 3: Markdown transformation pipeline
+328: # ---------------------------------------------------------------------------
+329:
+
+(File has more lines. Use 'offset' parameter to read beyond line 329)
+
+```
+## Agent (2026-02-22 11:45:22)
+
+I see the problem! In the CLI's `export_all` function (line 308-310), when there are 0 org files, it calls `System.halt(0)` immediately - it doesn't even get to run transforms or generate the index!
+
+But wait, you said index.md is missing. Let me check if there ARE org files being exported but the index isn't being generated. Let me trace the full serve flow:
+
+### Tool Call [completed]: read
+
+**Tool:** read
+**Timestamp:** 2026-02-22 11:45:25
+
+```
+/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex
+file
+118: ]
+119: )
+120:
+121: notes_dir = extract_notes_dir(positional, "serve")
+122: output_dir = extract_output_dir(opts)
+123: content_dir = extract_content_dir(opts, output_dir)
+124:
+125: {notes_dir, output_dir, content_dir, opts}
+126: end
+127:
+128: # ---------------------------------------------------------------------------
+129: # Command: build
+130: # ---------------------------------------------------------------------------
+131:
+132: def handle_build(argv) do
+133: quartz_path = require_quartz_env()
+134: {notes_dir, output_dir, content_dir, _opts} = parse_build_args(argv)
+135: pipeline_opts = Config.pipeline_opts()
+136:
+137: # Full batch export
+138: wipe(content_dir)
+139: export_all(notes_dir, output_dir)
+140: run_pipeline(content_dir, pipeline_opts)
+141: generate_index(content_dir)
+142:
+143: node_path = Config.get(:node_path, "node")
+144:
+145: IO.puts("==> Building static site with Quartz...")
+146:
+147: {output, status} =
+148: System.cmd(
+149: node_path,
+150: [
+151: Path.join(quartz_path, "quartz/bootstrap-cli.mjs"),
+152: "build",
+153: "--directory",
+154: content_dir,
+155: "--output",
+156: Path.join(output_dir, "public")
+157: ],
+158: cd: quartz_path,
+159: stderr_to_stdout: true
+160: )
+161:
+162: IO.puts(output)
+163:
+164: if status != 0 do
+165: abort("Quartz build failed with status #{status}")
+166: end
+167:
+
+(File has more lines. Use 'offset' parameter to read beyond line 167)
+
+```
+## Agent (2026-02-22 11:45:27)
+
+I see - for `build` command, `generate_index` is called (line 141), but the problem is `export_all` on line 139 might call `System.halt(0)` before we get there if no org files exist.
+
+Let me look at where serve mode handles this:
+
+### Tool Call [completed]: read
+
+**Tool:** read
+**Timestamp:** 2026-02-22 11:45:29
+
+```
+/home/ignaciobll/code/org-garden/lib/org_garden/cli.ex
+file
+68: # ---------------------------------------------------------------------------
+69: # Command: serve
+70: # ---------------------------------------------------------------------------
+71:
+72: def handle_serve(argv) do
+73: require_quartz_env()
+74: {notes_dir, output_dir, content_dir, opts} = parse_serve_args(argv)
+75:
+76: IO.puts("==> Starting development server...")
+77:
+78: server_opts =
+79: [
+80: notes_dir: notes_dir,
+81: output_dir: output_dir,
+82: content_dir: content_dir
+83: ]
+84: |> maybe_put(:port, opts[:port])
+85: |> maybe_put(:ws_port, opts[:ws_port])
+86:
+87: case OrgGarden.Server.start_link(server_opts) do
+88: {:ok, pid} ->
+89: IO.puts("==> Server running at http://localhost:#{opts[:port] || Config.get(:http_port, 8080)}")
+90: IO.puts("==> Watching #{notes_dir} for changes (Ctrl+C to stop)")
+91:
+92: # Wait for server to exit
+93: ref = Process.monitor(pid)
+94:
+95: receive do
+96: {:DOWN, ^ref, :process, ^pid, reason} ->
+97: case reason do
+98: :normal -> :ok
+99: :shutdown -> :ok
+100: {:shutdown, _} -> :ok
+101: _ -> abort("Server crashed: #{inspect(reason)}")
+102: end
+
+(File has more lines. Use 'offset' parameter to read beyond line 102)
+
+```
+## Agent (2026-02-22 11:45:32)
+
+For `serve`, it delegates to `OrgGarden.Server` which calls `run_initial_pipeline`. The problem there is that when `{:ok, 0}` is returned, index is not generated.
+
+Let me fix both issues:
+
+1. In `server.ex`: Generate index even when there are 0 org files
+2. In `cli.ex`: Don't halt immediately when 0 org files - let the pipeline continue
+
+### Tool Call [completed]: edit
+
+**Tool:** edit
+**Timestamp:** 2026-02-22 11:45:39
+
+```
+Edit applied successfully.
+
+
+
+
+
+╭─────────╮
+│ changes │
+╰─────────╯
+
+@@ -2,6 +2,8 @@
+ case OrgGarden.Export.export_all(notes_dir, output_dir) do
+ {:ok, 0} ->
+ Logger.warning("No .org files found in #{notes_dir}")
++ # Still generate index (will be empty or have default content)
++ OrgGarden.Index.generate(content_dir)
+ :ok
+
+ {:ok, count} ->
+```
+## Agent (2026-02-22 11:45:41)
+
+Now let me fix the CLI as well - it shouldn't halt immediately when there are no files. That's overly aggressive. The pipeline should still complete (even if empty):
+
+### Tool Call [completed]: edit
+
+**Tool:** edit
+**Timestamp:** 2026-02-22 11:45:46
+
+```
+Edit applied successfully.
+
+
+
+
+
+╭─────────╮
+│ changes │
+╰─────────╯
+
+@@ -3,8 +3,7 @@
+
+ case OrgGarden.Export.export_all(notes_dir, output_dir) do
+ {:ok, 0} ->
+- IO.puts("No .org files found in #{notes_dir}")
+- System.halt(0)
++ IO.puts(" no .org files found")
+
+ {:ok, count} ->
+ IO.puts(" exported #{count} file(s)")
+```
+## Agent (2026-02-22 11:45:49)
+
+Now let's verify compilation:
+
+### Tool Call [completed]: nix develop --command mix compile --warnings-as-errors
+
+**Tool:** execute
+**Timestamp:** 2026-02-22 11:45:52
+
+```
+warning: Git tree '/home/ignaciobll/code/org-garden' is dirty
+Compiling 2 files (.ex)
+Generated org_garden app
+```
diff --git a/lib/org_garden/cli.ex b/lib/org_garden/cli.ex
index 977d1ca..a5c98c2 100644
--- a/lib/org_garden/cli.ex
+++ b/lib/org_garden/cli.ex
@@ -306,8 +306,7 @@ defmodule OrgGarden.CLI do
case OrgGarden.Export.export_all(notes_dir, output_dir) do
{:ok, 0} ->
- IO.puts("No .org files found in #{notes_dir}")
- System.halt(0)
+ IO.puts(" no .org files found")
{:ok, count} ->
IO.puts(" exported #{count} file(s)")
diff --git a/lib/org_garden/server.ex b/lib/org_garden/server.ex
index 2ca854b..0157528 100644
--- a/lib/org_garden/server.ex
+++ b/lib/org_garden/server.ex
@@ -150,6 +150,8 @@ defmodule OrgGarden.Server do
case OrgGarden.Export.export_all(notes_dir, output_dir) do
{:ok, 0} ->
Logger.warning("No .org files found in #{notes_dir}")
+ # Still generate index (will be empty or have default content)
+ OrgGarden.Index.generate(content_dir)
:ok
{:ok, count} ->