docrev - npm Package Compare versions

Comparing version 0.9.17 to 0.9.18

issues.md

+# docrev — Open Issues
+
+Three issues identified during real-world use on the ADAPT proposal build. Working through one by one.
+
+Status legend: `[ ]` planned · `[~]` in progress · `[x]` shipped
+
+---
+
+## Issue 1 — Allow custom pandoc filters / args through `rev build`  `[x]`
+
+### Problem
+
+Source markdown with custom raw-LaTeX commands needs a pandoc filter to convert them for docx (e.g. `\tofill{X}` → bold `[X]`). `rev build docx` has no escape hatch:
+
+- `rev build --help` exposes no `--filter` / `--lua-filter` / `--pandoc-arg`.
+- `rev.yaml` exposes `docx.reference` and `docx.keepComments` but no generic pandoc passthrough.
+
+Working around it requires letting `rev build` produce `paper.md` as a side effect, then calling pandoc manually — which defeats the point of `rev build`.
+
+### Design (agreed)
+
+**rev.yaml**: top-level `pandoc-args` (applied to every format) plus per-format `<format>.pandoc-args` (concatenated *after* the top-level list so format-specific can override):
+
+```yaml
+pandoc-args:
+  - --lua-filter=tofill_filter.lua
+docx:
+  pandoc-args:
+    - --lua-filter=docx_only.lua
+pdf:
+  pandoc-args:
+    - --variable=papersize:a4
+```
+
+**CLI**: repeatable `--pandoc-arg <arg>` on `rev build`, appended *after* config args so CLI wins:
+
+```bash
+rev build docx --pandoc-arg=--lua-filter=tofill.lua --pandoc-arg=--shift-heading-level-by=1
+```
+
+**Verbose mode**: `rev build --verbose` already exists but doesn't echo the pandoc invocation. Print the full `pandoc <args>` command (one line per format) so users can copy-paste to replicate manually.
+
+### Touch points
+
+- `lib/build.ts` — `BuildConfig` + `DEFAULT_CONFIG` (add `pandocArgs: string[]`; add `pandocArgs` to each format config), `buildPandocArgs()` (append top-level then format-specific), `runPandoc()` (echo command under verbose), `loadConfig()` (read hyphenated `pandoc-args` key and map to camelCase `pandocArgs`).
+- `lib/commands/build.ts` — add `--pandoc-arg <arg>` (repeatable via custom collector), forward through `BuildOptions`, ensure CLI args are appended last.
+- `lib/schema.ts` — declare `pandoc-args` (array of strings) at top level and inside each format object.
+- `skill/SKILL.md` + `skill/REFERENCE.md` — document new field and flag with a `--lua-filter=` example.
+- `test/build.test.js` — cover (a) top-level only, (b) format-specific only, (c) both concatenated in order, (d) CLI overrides config.
+
+### Open questions
+
+None. Hyphenated YAML key + camelCase TS field is consistent with how the rest of the schema is read (we're already free-form on the JS side, just need a small key transform in `loadConfig`).
+
+---
+
+## Issue 2 — Output filename is auto-truncated mid-word and not configurable  `[x]`
+
+### Problem
+
+Default output landed at `output/adapt-alien-dark-diversity-across-plant-communitie.docx` — title slugified and hard-truncated at 50 chars (`communitie` missing the trailing `s`). No `-o` flag, no `output:` field in `rev.yaml`.
+
+Root cause: `lib/build.ts:1055-1056` (`runPandoc`) and `lib/commands/build.ts:591-592` (`--show-changes` path):
+
+```ts
+const baseName = config.title
+  ? config.title.toLowerCase().replace(/[^a-z0-9]+/g, '-').slice(0, 50)
+  : 'paper';
+```
+
+`.slice(0, 50)` is a blind cut.
+
+### Design (agreed)
+
+**rev.yaml**: per-format `output:` map. Extensions optional — added if missing.
+
+```yaml
+output:
+  docx: ADAPT_proposal_draft.docx
+  pdf: ADAPT_proposal_draft.pdf
+```
+
+**CLI**: `-o, --output <path>` on `rev build`. When multiple formats are built, applies as basename to all (extension swapped per format); for single-format builds, used verbatim.
+
+**Truncation fix**: when no `output:` is configured, slug at last `-` boundary at-or-before 50 chars instead of mid-word. Also bump the cap to 80 — 50 is conservative.
+
+**Doc fix**: surface the default `output/` directory in `rev build --help` and SKILL.md "Project Structure" tree (already mentioned in passing — make it explicit).
+
+### Touch points
+
+- `lib/build.ts` — `BuildConfig` (`output?: Record<string, string>`), `DEFAULT_CONFIG`, `runPandoc()` (resolve filename: `config.output[format]` → CLI `-o` → slug). Helper: `resolveOutputName(config, format, cliOverride)`.
+- `lib/commands/build.ts` — add `-o, --output <path>` flag, wire into `BuildOptions`; same fix applied to the `--show-changes` branch's `baseName` construction.
+- `lib/schema.ts` — declare `output` as object mapping format → string.
+- `skill/SKILL.md` — "Project Structure" tree explicitly notes `output/`; new `output:` example under config.
+- `test/build.test.js` — cover (a) `output:` per-format honored, (b) `-o` CLI override, (c) word-boundary truncation when title >50 chars.
+
+### Resolved
+
+- `-o` relative paths resolve under `outputDir`; absolute paths bypass it. Same rule applies to values in `output:`.
+- Cap raised from 50 → 80 chars; fallback truncates at the last `-` boundary at-or-before the cap so words stay whole (the ADAPT title now slugs cleanly without losing the trailing "s" on "communities").
+- `--show-changes` and `--dual` derived filenames (`-changes.docx`, `_comments.docx`, `_comments.pdf`) follow the chosen base name.
+- Fixed an unrelated misleading example in SKILL.md that showed `output: { docx: { reference-doc: ... } }` — the real config key is `docx.reference` (top-level), not nested under `output:`.
+
+---
+
+## Issue 3 — Raw LaTeX figure blocks silently disappear in docx builds  `[x]`
+
+### Problem
+
+Source markdown with `\begin{figure}[H]\includegraphics{...}\end{figure}` blocks renders correctly in the PDF target but produces a docx where all figures are silently missing. Pandoc strips the raw LaTeX because docx has no LaTeX rendering pipeline. No warning is emitted.
+
+This catches you only on careful inspection — a less careful user would ship a docx with no figures and not notice until a reviewer asks.
+
+### Design (agreed)
+
+Three layers, combined:
+
+**1. Warn during build (always on).** In `applyFormatTransforms()` for docx, scan for raw LaTeX figure environments (`\begin{figure}` … `\end{figure}` containing `\includegraphics`). Emit:
+
+```
+Warning: 3 raw LaTeX figure block(s) won't render in docx.
+  intro.md:42  \begin{figure}[H] ... \includegraphics{figures/map.pdf} ...
+  methods.md:118
+  results.md:201
+  Hint: use ![caption](path){#fig:label width=80%} for format-portable figures, or
+        pass --pandoc-arg=--lua-filter=<your.lua> to translate them yourself.
+```
+
+Counted by file/line so the user can jump to fix.
+
+**2. Auto-translate the common shape (opt-out via `docx.translateRawFigures: false`).** Convert
+
+```latex
+\begin{figure}[H]
+\centering
+\includegraphics[width=0.8\textwidth]{figures/map.pdf}
+\caption{Map of study sites.}
+\label{fig:map}
+\end{figure}
+```
+
+→
+
+```markdown
+![Map of study sites.](figures/map.pdf){#fig:map width=80%}
+```
+
+Cover the 80% case. If the block has anything more exotic (`\subfloat`, `\rotatebox`, multi-`\includegraphics`), skip auto-translate, warn loudly, and leave the block as-is.
+
+Width conversion: `0.8\textwidth` → `80%`; bare `8cm` → `8cm`; missing → omit.
+
+**3. Document.** SKILL.md "Cross-References" section currently mentions `@fig:label` and `{#fig:label}` but doesn't show how to *insert* a figure. Add:
+
+```markdown
+![Caption text.](figures/foo.pdf){#fig:foo width=80%}
+```
+
+Note this is the format-portable form. Also mention that raw `\begin{figure}` blocks are PDF-only.
+
+### Touch points
+
+- `lib/build.ts` — new helper `detectRawLatexFigures(content): {file?, line, block}[]` and `translateRawLatexFigures(content): {translated, untranslatedCount}`. Wire into `applyFormatTransforms()` for docx (after `convertDynamicRefsToDisplay`).
+- `lib/build.ts` — propagate warnings up via the existing `warnings: string[]` returned by `build()`. `rev build` already prints from there.
+- `lib/commands/build.ts` — surface warnings in normal output (not just verbose).
+- `lib/schema.ts` — declare `docx.translateRawFigures: boolean` (default true).
+- `skill/SKILL.md` — figure-insertion example under "Cross-References".
+- `test/build.test.js` — cover (a) detection counts blocks correctly, (b) auto-translate of `\includegraphics{path}`, (c) auto-translate of `\includegraphics[width=0.8\textwidth]{path}` → `width=80%`, (d) exotic block → not translated, warned, left alone, (e) opt-out via `translateRawFigures: false`.
+
+### Open questions
+
+- Should auto-translate also handle bare `\includegraphics{...}` outside a `figure` env? Lean no — keep scope to figure environments. If a user writes raw `\includegraphics` without wrapping, that's a deliberate choice we shouldn't second-guess.
+- Width unit handling: `0.8\textwidth` → `80%` is unambiguous. `\linewidth` → `100%`? Yes. Other relative units → leave raw and warn.
+
+---
+
+## Working order
+
+1. **Issue 1** first — unblocks immediate workflow needs and provides the manual escape hatch for issue 3 even before auto-translate ships.
+2. **Issue 2** next — small, low-risk, quality-of-life win.
+3. **Issue 3** last — biggest behavior change; benefits from the verbose pandoc echo (Issue 1) for debugging the lua-filter fallback path.

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+              <path d="M6 .278a.768.768 0 0 1 .08.858 7.208 7.208 0 0 0-.878 3.46c0 4.021 3.278 7.277 7.318 7.277.527 0 1.04-.055 1.533-.16a.787.787 0 0 1 .81.316.733.733 0 0 1-.031.893A8.349 8.349 0 0 1 8.344 16C3.734 16 0 12.286 0 7.71 0 4.266 2.114 1.312 5.124.06A.752.752 0 0 1 6 .278"/>
+            </svg>
+          </button>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link" href="https://github.com/gcol33/docrev" aria-label="GitHub">
+            <svg xmlns="http://www.w3.org/2000/svg" width="18" height="18" fill="currentColor" viewBox="0 0 16 16">
+              <path d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.012 8.012 0 0 0 16 8c0-4.42-3.58-8-8-8"/>
+            </svg>
+          </a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link" href="https://www.npmjs.com/package/docrev" aria-label="npm">
+            <svg xmlns="http://www.w3.org/2000/svg" width="20" height="20" fill="currentColor" viewBox="0 0 16 16">
+              <path d="M0 0v16h16V0zm5.333 13.333H2.667V5.333h2.666v5.334H8V5.333h2.667v8H5.333z"/>
+            </svg>
+          </a>
+        </li>
+      </ul>
+    </div>
+  </div>
+</nav>
+
+<div class="container template-article">
+  <div class="row">
+    <main id="main" class="col-md-9">
+      <h1 id="command-reference">Command Reference</h1>
+      <p>Complete list of <code>rev</code> commands.</p>
+      <h2 id="build-create">Build &amp; Create</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev build [formats...]</code></td>
+      <td>Build PDF/DOCX/TEX from sections</td>
+      </tr>
+      <tr>
+      <td><code>rev build pdf</code></td>
+      <td>Build PDF only</td>
+      </tr>
+      <tr>
+      <td><code>rev build docx</code></td>
+      <td>Build DOCX only</td>
+      </tr>
+      <tr>
+      <td><code>rev build tex</code></td>
+      <td>Build LaTeX only</td>
+      </tr>
+      <tr>
+      <td><code>rev build all</code></td>
+      <td>Build PDF + DOCX + TEX</td>
+      </tr>
+      <tr>
+      <td><code>rev build --toc</code></td>
+      <td>Include table of contents</td>
+      </tr>
+      <tr>
+      <td><code>rev build --dual</code></td>
+      <td>Output clean + comments DOCX (with threaded comments)</td>
+      </tr>
+      <tr>
+      <td><code>rev build --show-changes</code></td>
+      <td>Export DOCX with visible track changes</td>
+      </tr>
+      <tr>
+      <td><code>rev new &lt;name&gt;</code></td>
+      <td>Create new project (prompts for sections)</td>
+      </tr>
+      <tr>
+      <td><code>rev new &lt;name&gt; -s intro,methods,results</code></td>
+      <td>Create with specified sections</td>
+      </tr>
+      <tr>
+      <td><code>rev new --list</code></td>
+      <td>List available templates</td>
+      </tr>
+      <tr>
+      <td><code>rev install</code></td>
+      <td>Check/install dependencies (pandoc-crossref)</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="import-export">Import &amp; Export</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev import &lt;docx&gt;</code></td>
+      <td>Bootstrap project from Word (creates sections + rev.yaml)</td>
+      </tr>
+      <tr>
+      <td><code>rev import &lt;docx&gt; &lt;md&gt;</code></td>
+      <td>Import changes by diffing Word against your MD</td>
+      </tr>
+      <tr>
+      <td><code>rev sync [docx] [sections...]</code></td>
+      <td>Sync feedback from Word to section files</td>
+      </tr>
+      <tr>
+      <td><code>rev sync</code></td>
+      <td>Auto-detect most recent .docx</td>
+      </tr>
+      <tr>
+      <td><code>rev sync reviewed.docx methods</code></td>
+      <td>Sync only methods section</td>
+      </tr>
+      <tr>
+      <td><code>rev sync annotated.pdf</code></td>
+      <td>Extract comments from PDF into markdown</td>
+      </tr>
+      <tr>
+      <td><code>rev extract &lt;docx&gt;</code></td>
+      <td>Extract plain text from Word</td>
+      </tr>
+      <tr>
+      <td><code>rev archive</code></td>
+      <td>Move reviewer .docx files to archive folder</td>
+      </tr>
+      <tr>
+      <td><code>rev archive --by Smith</code></td>
+      <td>Specify reviewer name</td>
+      </tr>
+      <tr>
+      <td><code>rev archive --dry-run</code></td>
+      <td>Preview without moving</td>
+      </tr>
+      </tbody>
+      </table>
+      <p><strong>Word Import Features:</strong> - Extracts text
+      preserving structure - Extracts comments with author and anchor
+      text - Converts OMML equations to LaTeX - Extracts embedded images
+      to <code>media/</code> directory</p>
+      <h2 id="pdf-comments">PDF Comments</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev pdf-comments &lt;pdf&gt;</code></td>
+      <td>Extract and display comments from annotated PDF</td>
+      </tr>
+      <tr>
+      <td><code>rev pdf-comments &lt;pdf&gt; --with-text</code></td>
+      <td>Also extract the highlighted text content</td>
+      </tr>
+      <tr>
+      <td><code>rev pdf-comments &lt;pdf&gt; --append &lt;file.md&gt;</code></td>
+      <td>Append extracted comments to markdown file</td>
+      </tr>
+      <tr>
+      <td><code>rev pdf-comments &lt;pdf&gt; --json</code></td>
+      <td>Output comments as JSON</td>
+      </tr>
+      <tr>
+      <td><code>rev pdf-comments &lt;pdf&gt; --by-page</code></td>
+      <td>Group comments by page (default)</td>
+      </tr>
+      <tr>
+      <td><code>rev pdf-comments &lt;pdf&gt; --by-author</code></td>
+      <td>Group comments by author</td>
+      </tr>
+      <tr>
+      <td><code>rev build pdf --dual</code></td>
+      <td>Build clean PDF + annotated PDF with margin notes</td>
+      </tr>
+      </tbody>
+      </table>
+      <p><strong>Supported PDF Annotations:</strong> - Sticky notes
+      (Text annotations) - Text boxes (FreeText) - Highlights with
+      comments (text extraction supported) - Underlines with comments
+      (text extraction supported) - Strikethrough/deletion suggestions
+      (text extraction supported) - Squiggly underlines (text extraction
+      supported)</p>
+      <p><strong>Text Extraction:</strong> Use <code>--with-text</code>
+      to extract the actual text that was highlighted, underlined, or
+      struck through. This is slower but shows exactly what the reviewer
+      marked.</p>
+      <p><strong>PDF Dual Export:</strong> When building with
+      <code>--dual</code>, produces: - <code>paper.pdf</code> — clean
+      version for submission - <code>paper_comments.pdf</code> —
+      CriticMarkup comments rendered as LaTeX margin notes</p>
+      <h2 id="review-edit">Review &amp; Edit</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev review &lt;file&gt;</code></td>
+      <td>Interactive accept/reject TUI for track changes</td>
+      </tr>
+      <tr>
+      <td><code>rev status</code></td>
+      <td>Show project overview (words, comments, changes)</td>
+      </tr>
+      <tr>
+      <td><code>rev status &lt;file&gt;</code></td>
+      <td>Show annotation counts for specific file</td>
+      </tr>
+      <tr>
+      <td><code>rev comments &lt;file&gt;</code></td>
+      <td>List all comments with context</td>
+      </tr>
+      <tr>
+      <td><code>rev comments &lt;file&gt; --export comments.csv</code></td>
+      <td>Export comments to CSV</td>
+      </tr>
+      <tr>
+      <td><code>rev resolve &lt;file&gt; -n 1</code></td>
+      <td>Mark comment #1 as resolved</td>
+      </tr>
+      <tr>
+      <td><code>rev strip &lt;file&gt;</code></td>
+      <td>Output clean Markdown (annotations applied)</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="comment-navigation">Comment Navigation</h2>
+      <table>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev next</code></td>
+      <td>Show next pending comment</td>
+      </tr>
+      <tr>
+      <td><code>rev next -n 3</code></td>
+      <td>Show 3rd pending comment</td>
+      </tr>
+      <tr>
+      <td><code>rev prev</code></td>
+      <td>Show last pending comment</td>
+      </tr>
+      <tr>
+      <td><code>rev prev -n 2</code></td>
+      <td>Show 2nd from last pending</td>
+      </tr>
+      <tr>
+      <td><code>rev first</code></td>
+      <td>Show first comment (all, not just pending)</td>
+      </tr>
+      <tr>
+      <td><code>rev first methods</code></td>
+      <td>First comment in methods section</td>
+      </tr>
+      <tr>
+      <td><code>rev last</code></td>
+      <td>Show last comment</td>
+      </tr>
+      <tr>
+      <td><code>rev todo</code></td>
+      <td>List all pending comments as checklist</td>
+      </tr>
+      <tr>
+      <td><code>rev todo --by-author</code></td>
+      <td>Group pending comments by author</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="track-changes">Track Changes</h2>
+      <table>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev accept &lt;file&gt;</code></td>
+      <td>List track changes</td>
+      </tr>
+      <tr>
+      <td><code>rev accept &lt;file&gt; -n 1</code></td>
+      <td>Accept change #1</td>
+      </tr>
+      <tr>
+      <td><code>rev accept &lt;file&gt; -a</code></td>
+      <td>Accept all changes</td>
+      </tr>
+      <tr>
+      <td><code>rev reject &lt;file&gt; -n 1</code></td>
+      <td>Reject change #1</td>
+      </tr>
+      <tr>
+      <td><code>rev reject &lt;file&gt; -a</code></td>
+      <td>Reject all changes</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="cross-references">Cross-References</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev refs [file]</code></td>
+      <td>Show figure/table registry and reference status</td>
+      </tr>
+      <tr>
+      <td><code>rev migrate &lt;file&gt;</code></td>
+      <td>Convert hardcoded refs (Fig. 1) to dynamic (<span
+      class="citation" data-cites="fig:label">@fig:label</span>)</td>
+      </tr>
+      </tbody>
+      </table>
+      <p><strong>Supported patterns:</strong> - <code>Figure 1</code> →
+      <code>@fig:label</code> - <code>Fig. 2a</code> →
+      <code>@fig:label</code> - <code>Figs. 1-3</code> →
+      <code>@fig:one; @fig:two; @fig:three</code> -
+      <code>Figures 1, 2, and 3</code> → multiple refs -
+      <code>Fig. 1a-c</code> → expands letter suffixes</p>
+      <h2 id="comments-replies">Comments &amp; Replies</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev config user "Name"</code></td>
+      <td>Set your name for replies</td>
+      </tr>
+      <tr>
+      <td><code>rev config sections "a,b,c"</code></td>
+      <td>Set default sections for new projects</td>
+      </tr>
+      <tr>
+      <td><code>rev reply &lt;file&gt;</code></td>
+      <td>Interactive reply to reviewer comments</td>
+      </tr>
+      <tr>
+      <td><code>rev reply &lt;file&gt; -n 1 -m "text"</code></td>
+      <td>Reply to specific comment (non-interactive)</td>
+      </tr>
+      </tbody>
+      </table>
+      <p><strong>Comment Threading:</strong> Adjacent comments from
+      different authors become threaded replies in Word:</p>
+      <div class="sourceCode" id="cb1"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>{&gt;&gt;Guy Colling: Question?&lt;&lt;} {&gt;&gt;Gilles Colling: Answer.&lt;&lt;}</span></code></pre></div>
+      <h2 id="bibliography-dois">Bibliography &amp; DOIs</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev doi check [file.bib]</code></td>
+      <td>Validate DOIs in bibliography (Crossref + DataCite)</td>
+      </tr>
+      <tr>
+      <td><code>rev doi lookup [file.bib]</code></td>
+      <td>Search for missing DOIs by title/author/year</td>
+      </tr>
+      <tr>
+      <td><code>rev doi fetch &lt;doi&gt;</code></td>
+      <td>Fetch BibTeX entry from DOI</td>
+      </tr>
+      <tr>
+      <td><code>rev doi add &lt;doi&gt;</code></td>
+      <td>Fetch and add DOI entry to bibliography</td>
+      </tr>
+      </tbody>
+      </table>
+      <p><strong>Options:</strong> -
+      <code>--confidence low|medium|high</code> - Filter lookup results
+      - <code>--strict</code> - Fail if articles are missing DOIs - Skip
+      entries: add <code>nodoi = {true}</code> or <code>% no-doi</code>
+      comment</p>
+      <h2 id="validation-analysis">Validation &amp; Analysis</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev citations [file.bib]</code></td>
+      <td>Validate citations against bibliography</td>
+      </tr>
+      <tr>
+      <td><code>rev figures [file]</code></td>
+      <td>List figures/tables with reference counts</td>
+      </tr>
+      <tr>
+      <td><code>rev equations list</code></td>
+      <td>List all equations in section files</td>
+      </tr>
+      <tr>
+      <td><code>rev equations from-word &lt;docx&gt;</code></td>
+      <td>Extract equations from Word to LaTeX</td>
+      </tr>
+      <tr>
+      <td><code>rev response [files]</code></td>
+      <td>Generate response letter from comments</td>
+      </tr>
+      <tr>
+      <td><code>rev anonymize &lt;file&gt;</code></td>
+      <td>Prepare document for blind review</td>
+      </tr>
+      <tr>
+      <td><code>rev validate --journal &lt;name&gt;</code></td>
+      <td>Check manuscript against journal requirements</td>
+      </tr>
+      <tr>
+      <td><code>rev validate --list</code></td>
+      <td>List 21 available journal profiles</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="multi-reviewer-git">Multi-Reviewer &amp; Git</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev merge &lt;md&gt; &lt;docx...&gt;</code></td>
+      <td>Merge feedback from multiple Word documents</td>
+      </tr>
+      <tr>
+      <td><code>rev diff [ref]</code></td>
+      <td>Compare sections against git history</td>
+      </tr>
+      <tr>
+      <td><code>rev history [file]</code></td>
+      <td>Show revision history for sections</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="convenience-commands">Convenience Commands</h2>
+      <table>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev word-count</code></td>
+      <td>Show word counts per section</td>
+      </tr>
+      <tr>
+      <td><code>rev word-count --limit 5000</code></td>
+      <td>Warn if over limit</td>
+      </tr>
+      <tr>
+      <td><code>rev word-count -j &lt;journal&gt;</code></td>
+      <td>Use journal word limit</td>
+      </tr>
+      <tr>
+      <td><code>rev stats</code></td>
+      <td>Project dashboard (words, figures, citations)</td>
+      </tr>
+      <tr>
+      <td><code>rev search &lt;query&gt;</code></td>
+      <td>Search across all section files</td>
+      </tr>
+      <tr>
+      <td><code>rev search -i &lt;query&gt;</code></td>
+      <td>Case-insensitive search</td>
+      </tr>
+      <tr>
+      <td><code>rev backup</code></td>
+      <td>Create timestamped backup zip</td>
+      </tr>
+      <tr>
+      <td><code>rev backup --name v1</code></td>
+      <td>Custom backup name</td>
+      </tr>
+      <tr>
+      <td><code>rev export</code></td>
+      <td>Export project as distributable zip</td>
+      </tr>
+      <tr>
+      <td><code>rev preview &lt;format&gt;</code></td>
+      <td>Build and open document</td>
+      </tr>
+      <tr>
+      <td><code>rev watch [format]</code></td>
+      <td>Auto-rebuild on file changes</td>
+      </tr>
+      <tr>
+      <td><code>rev lint</code></td>
+      <td>Check for broken refs, missing citations</td>
+      </tr>
+      <tr>
+      <td><code>rev clean</code></td>
+      <td>Remove generated files</td>
+      </tr>
+      <tr>
+      <td><code>rev clean --all</code></td>
+      <td>Also remove backups and exports</td>
+      </tr>
+      <tr>
+      <td><code>rev check</code></td>
+      <td>Pre-submission check (lint + grammar + citations)</td>
+      </tr>
+      <tr>
+      <td><code>rev open</code></td>
+      <td>Open project folder</td>
+      </tr>
+      <tr>
+      <td><code>rev open paper.pdf</code></td>
+      <td>Open specific file</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="grammar-spelling">Grammar &amp; Spelling</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev grammar</code></td>
+      <td>Check grammar/style issues</td>
+      </tr>
+      <tr>
+      <td><code>rev grammar --rules</code></td>
+      <td>List available grammar rules</td>
+      </tr>
+      <tr>
+      <td><code>rev grammar --learn &lt;word&gt;</code></td>
+      <td>Add word to custom dictionary</td>
+      </tr>
+      <tr>
+      <td><code>rev grammar --list</code></td>
+      <td>Show custom dictionary</td>
+      </tr>
+      <tr>
+      <td><code>rev spelling</code></td>
+      <td>Check spelling in all sections</td>
+      </tr>
+      <tr>
+      <td><code>rev spelling --british</code></td>
+      <td>Use British English dictionary</td>
+      </tr>
+      <tr>
+      <td><code>rev spelling --learn &lt;word&gt;</code></td>
+      <td>Add word to global dictionary</td>
+      </tr>
+      <tr>
+      <td><code>rev spelling --learn-project &lt;word&gt;</code></td>
+      <td>Add word to project dictionary</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="direct-docx-editing">Direct DOCX Editing</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 59%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev annotate &lt;docx&gt; -m "Comment" -s "text"</code></td>
+      <td>Add comment to Word doc</td>
+      </tr>
+      <tr>
+      <td><code>rev apply &lt;md&gt; &lt;docx&gt;</code></td>
+      <td>Apply annotations as track changes</td>
+      </tr>
+      <tr>
+      <td><code>rev comment &lt;docx&gt;</code></td>
+      <td>Interactive comment mode</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="shell-completions">Shell Completions</h2>
+      <div class="sourceCode" id="cb2"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Bash - add to ~/.bashrc</span></span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="bu">eval</span> <span class="st">&quot;</span><span class="va">$(</span><span class="fu">rev</span> completions bash<span class="va">)</span><span class="st">&quot;</span></span>
+<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co"># Zsh - add to ~/.zshrc</span></span>
+<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="bu">eval</span> <span class="st">&quot;</span><span class="va">$(</span><span class="fu">rev</span> completions zsh<span class="va">)</span><span class="st">&quot;</span></span>
+<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="co"># PowerShell - add to $PROFILE</span></span>
+<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a><span class="ex">Invoke-Expression</span> <span class="er">(</span><span class="fu">rev</span> completions powershell <span class="kw">|</span> <span class="ex">Out-String</span><span class="kw">)</span></span></code></pre></div>
+      <h2 id="collaboration-git">Collaboration &amp; Git</h2>
+      <table>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev contributors</code></td>
+      <td>Show author contributions across all sections</td>
+      </tr>
+      <tr>
+      <td><code>rev contributors &lt;file&gt;</code></td>
+      <td>Show who wrote what in a specific file</td>
+      </tr>
+      <tr>
+      <td><code>rev contributors &lt;file&gt; --blame</code></td>
+      <td>Line-by-line blame output</td>
+      </tr>
+      <tr>
+      <td><code>rev history</code></td>
+      <td>Show revision history</td>
+      </tr>
+      <tr>
+      <td><code>rev diff</code></td>
+      <td>Compare sections against git history</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="orcid-integration">ORCID Integration</h2>
+      <table>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev orcid &lt;id&gt;</code></td>
+      <td>Fetch author info from ORCID</td>
+      </tr>
+      <tr>
+      <td><code>rev orcid &lt;id&gt; --yaml</code></td>
+      <td>Output as YAML for rev.yaml authors</td>
+      </tr>
+      <tr>
+      <td><code>rev orcid &lt;id&gt; --badge</code></td>
+      <td>Generate markdown badge</td>
+      </tr>
+      </tbody>
+      </table>
+      <h2 id="self-update">Self-Update</h2>
+      <table>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev upgrade</code></td>
+      <td>Update docrev to latest version</td>
+      </tr>
+      <tr>
+      <td><code>rev upgrade --check</code></td>
+      <td>Check for updates without installing</td>
+      </tr>
+      </tbody>
+      </table>
+    </main>
+    <aside class="col-md-3 d-none d-md-block">
+      <nav id="toc" data-toggle="toc" aria-label="On this page">
+        <h2 class="h6">On this page</h2>
+        <div class="toc"><ul>
+<li><a href="#command-reference" id="toc-command-reference">Command
+Reference</a>
+<ul>
+<li><a href="#build-create" id="toc-build-create">Build &amp;
+Create</a></li>
+<li><a href="#import-export" id="toc-import-export">Import &amp;
+Export</a></li>
+<li><a href="#pdf-comments" id="toc-pdf-comments">PDF Comments</a></li>
+<li><a href="#review-edit" id="toc-review-edit">Review &amp;
+Edit</a></li>
+<li><a href="#comment-navigation" id="toc-comment-navigation">Comment
+Navigation</a></li>
+<li><a href="#track-changes" id="toc-track-changes">Track
+Changes</a></li>
+<li><a href="#cross-references"
+id="toc-cross-references">Cross-References</a></li>
+<li><a href="#comments-replies" id="toc-comments-replies">Comments &amp;
+Replies</a></li>
+<li><a href="#bibliography-dois" id="toc-bibliography-dois">Bibliography
+&amp; DOIs</a></li>
+<li><a href="#validation-analysis"
+id="toc-validation-analysis">Validation &amp; Analysis</a></li>
+<li><a href="#multi-reviewer-git"
+id="toc-multi-reviewer-git">Multi-Reviewer &amp; Git</a></li>
+<li><a href="#convenience-commands"
+id="toc-convenience-commands">Convenience Commands</a></li>
+<li><a href="#grammar-spelling" id="toc-grammar-spelling">Grammar &amp;
+Spelling</a></li>
+<li><a href="#direct-docx-editing" id="toc-direct-docx-editing">Direct
+DOCX Editing</a></li>
+<li><a href="#shell-completions" id="toc-shell-completions">Shell
+Completions</a></li>
+<li><a href="#collaboration-git"
+id="toc-collaboration-git">Collaboration &amp; Git</a></li>
+<li><a href="#orcid-integration" id="toc-orcid-integration">ORCID
+Integration</a></li>
+<li><a href="#self-update" id="toc-self-update">Self-Update</a></li>
+</ul></li>
+</ul></div>
+      </nav>
+    </aside>
+  </div>
+</div>
+
+<footer class="border-top py-3 mt-auto">
+  <div class="container d-flex justify-content-between align-items-center text-muted" style="font-size:.85rem">
+    <span>docrev 0.9.15</span>
+    <span>Built with <a href="https://pandoc.org" class="text-muted">pandoc</a></span>
+  </div>
+</footer>
+
+<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
+<script>
+(function () {
+  var html  = document.documentElement;
+  var sun   = document.getElementById('icon-sun');
+  var moon  = document.getElementById('icon-moon');
+  function apply(t) {
+    html.setAttribute('data-bs-theme', t);
+    sun.style.display  = t === 'dark' ? 'none' : '';
+    moon.style.display = t === 'dark' ? ''     : 'none';
+  }
+  apply(localStorage.getItem('docrev-theme') || 'light');
+  document.getElementById('theme-toggle').addEventListener('click', function () {
+    var next = html.getAttribute('data-bs-theme') === 'dark' ? 'light' : 'dark';
+    localStorage.setItem('docrev-theme', next);
+    apply(next);
+  });
+})();
+</script>
+
+</body>
+</html>

site/configuration.html

+<!DOCTYPE html>
+<html lang="en" data-bs-theme="light">
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <title>Configuration — docrev</title>
+  <meta name="description" content="CLI for writing documents in Markdown while collaborating with Word users.">
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootswatch@5.3.3/dist/sandstone/bootstrap.min.css">
+  <style>
+html { -webkit-text-size-adjust: 100%; }
+pre > code.sourceCode { white-space: pre; position: relative; }
+pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span:empty { height: 1.2em; }
+.sourceCode { overflow: visible; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+div.sourceCode { margin: 1em 0; }
+pre.sourceCode { margin: 0; }
+@media screen {
+div.sourceCode { overflow: auto; }
+}
+@media print {
+pre > code.sourceCode { white-space: pre-wrap; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+}
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; display: inline-block;
+    -webkit-touch-callout: none; -webkit-user-select: none;
+    -khtml-user-select: none; -moz-user-select: none;
+    -ms-user-select: none; user-select: none;
+    padding: 0 4px; width: 4em;
+    color: #aaaaaa;
+  }
+pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
+code span.al { color: #ff0000; font-weight: bold; } /* Alert */
+code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
+code span.at { color: #7d9029; } /* Attribute */
+code span.bn { color: #40a070; } /* BaseN */
+code span.bu { color: #008000; } /* BuiltIn */
+code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
+code span.ch { color: #4070a0; } /* Char */
+code span.cn { color: #880000; } /* Constant */
+code span.co { color: #60a0b0; font-style: italic; } /* Comment */
+code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
+code span.do { color: #ba2121; font-style: italic; } /* Documentation */
+code span.dt { color: #902000; } /* DataType */
+code span.dv { color: #40a070; } /* DecVal */
+code span.er { color: #ff0000; font-weight: bold; } /* Error */
+code span.ex { } /* Extension */
+code span.fl { color: #40a070; } /* Float */
+code span.fu { color: #06287e; } /* Function */
+code span.im { color: #008000; font-weight: bold; } /* Import */
+code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
+code span.kw { color: #007020; font-weight: bold; } /* Keyword */
+code span.op { color: #666666; } /* Operator */
+code span.ot { color: #007020; } /* Other */
+code span.pp { color: #bc7a00; } /* Preprocessor */
+code span.sc { color: #4070a0; } /* SpecialChar */
+code span.ss { color: #bb6688; } /* SpecialString */
+code span.st { color: #4070a0; } /* String */
+code span.va { color: #19177c; } /* Variable */
+code span.vs { color: #4070a0; } /* VerbatimString */
+code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
+  </style>
+  <link rel="stylesheet" href="assets/extra.css">
+</head>
+<body>
+
+<nav class="navbar navbar-expand-lg fixed-top" aria-label="Site navigation">
+  <div class="container">
+    <a class="navbar-brand me-2" href="index.html">docrev</a>
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar-main" aria-controls="navbar-main" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+    <div class="collapse navbar-collapse" id="navbar-main">
+      <ul class="navbar-nav me-auto">
+        <li class="nav-item">
+          <a class="nav-link"  href="index.html">Home</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="workflow.html">Get Started</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="commands.html">Commands</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link active" aria-current="page" href="configuration.html">Configuration</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="troubleshooting.html">Troubleshooting</a>
+        </li>
+      </ul>
+      <ul class="navbar-nav">
+        <li class="nav-item">
+          <button id="theme-toggle" class="btn btn-link nav-link border-0" aria-label="Toggle dark mode">
+            <svg id="icon-sun" xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" viewBox="0 0 16 16">
+              <path d="M8 11a3 3 0 1 1 0-6 3 3 0 0 1 0 6m0 1a4 4 0 1 0 0-8 4 4 0 0 0 0 8M8 0a.5.5 0 0 1 .5.5v2a.5.5 0 0 1-1 0v-2A.5.5 0 0 1 8 0m0 13a.5.5 0 0 1 .5.5v2a.5.5 0 0 1-1 0v-2A.5.5 0 0 1 8 13m8-5a.5.5 0 0 1-.5.5h-2a.5.5 0 0 1 0-1h2a.5.5 0 0 1 .5.5M3 8a.5.5 0 0 1-.5.5h-2a.5.5 0 0 1 0-1h2A.5.5 0 0 1 3 8m10.657-5.657a.5.5 0 0 1 0 .707l-1.414 1.415a.5.5 0 1 1-.707-.708l1.414-1.414a.5.5 0 0 1 .707 0m-9.193 9.193a.5.5 0 0 1 0 .707L3.05 13.657a.5.5 0 0 1-.707-.707l1.414-1.414a.5.5 0 0 1 .707 0m9.193 2.121a.5.5 0 0 1-.707 0l-1.414-1.414a.5.5 0 0 1 .707-.707l1.414 1.414a.5.5 0 0 1 0 .707M4.464 4.465a.5.5 0 0 1-.707 0L2.343 3.05a.5.5 0 1 1 .707-.707l1.414 1.414a.5.5 0 0 1 0 .707"/>
+            </svg>
+            <svg id="icon-moon" xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" viewBox="0 0 16 16" style="display:none">
+              <path d="M6 .278a.768.768 0 0 1 .08.858 7.208 7.208 0 0 0-.878 3.46c0 4.021 3.278 7.277 7.318 7.277.527 0 1.04-.055 1.533-.16a.787.787 0 0 1 .81.316.733.733 0 0 1-.031.893A8.349 8.349 0 0 1 8.344 16C3.734 16 0 12.286 0 7.71 0 4.266 2.114 1.312 5.124.06A.752.752 0 0 1 6 .278"/>
+            </svg>
+          </button>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link" href="https://github.com/gcol33/docrev" aria-label="GitHub">
+            <svg xmlns="http://www.w3.org/2000/svg" width="18" height="18" fill="currentColor" viewBox="0 0 16 16">
+              <path d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.012 8.012 0 0 0 16 8c0-4.42-3.58-8-8-8"/>
+            </svg>
+          </a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link" href="https://www.npmjs.com/package/docrev" aria-label="npm">
+            <svg xmlns="http://www.w3.org/2000/svg" width="20" height="20" fill="currentColor" viewBox="0 0 16 16">
+              <path d="M0 0v16h16V0zm5.333 13.333H2.667V5.333h2.666v5.334H8V5.333h2.667v8H5.333z"/>
+            </svg>
+          </a>
+        </li>
+      </ul>
+    </div>
+  </div>
+</nav>
+
+<div class="container template-article">
+  <div class="row">
+    <main id="main" class="col-md-9">
+      <h1 id="configuration">Configuration</h1>
+      <h2 id="rev.yaml">rev.yaml</h2>
+      <p>The project configuration file.</p>
+      <div class="sourceCode" id="cb1"><pre
+      class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">title</span><span class="kw">:</span><span class="at"> </span><span class="st">&quot;Your Paper Title&quot;</span></span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">version</span><span class="kw">:</span><span class="at"> </span><span class="st">&quot;1.0&quot;</span></span>
+<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">authors</span><span class="kw">:</span></span>
+<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> </span><span class="fu">name</span><span class="kw">:</span><span class="at"> First Author</span></span>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">affiliation</span><span class="kw">:</span><span class="at"> Institution</span></span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">email</span><span class="kw">:</span><span class="at"> [e-mail]</span></span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> </span><span class="fu">name</span><span class="kw">:</span><span class="at"> Second Author</span></span>
+<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">affiliation</span><span class="kw">:</span><span class="at"> Another Institution</span></span>
+<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="fu">sections</span><span class="kw">:</span></span>
+<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> introduction.md</span></span>
+<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> methods.md</span></span>
+<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> results.md</span></span>
+<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> discussion.md</span></span>
+<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="fu">bibliography</span><span class="kw">:</span><span class="at"> references.bib</span></span>
+<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="fu">csl</span><span class="kw">:</span><span class="at"> nature.csl</span><span class="co">           # Citation style (optional)</span></span>
+<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a><span class="co"># Cross-reference settings (pandoc-crossref)</span></span>
+<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="fu">crossref</span><span class="kw">:</span></span>
+<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">figureTitle</span><span class="kw">:</span><span class="at"> Figure</span></span>
+<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">tableTitle</span><span class="kw">:</span><span class="at"> Table</span></span>
+<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">figPrefix</span><span class="kw">:</span><span class="at"> </span><span class="kw">[</span><span class="at">Fig.</span><span class="kw">,</span><span class="at"> Figs.</span><span class="kw">]</span></span>
+<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">tblPrefix</span><span class="kw">:</span><span class="at"> </span><span class="kw">[</span><span class="at">Table</span><span class="kw">,</span><span class="at"> Tables</span><span class="kw">]</span></span>
+<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">eqnPrefix</span><span class="kw">:</span><span class="at"> </span><span class="kw">[</span><span class="at">Eq.</span><span class="kw">,</span><span class="at"> Eqs.</span><span class="kw">]</span></span>
+<span id="cb1-27"><a href="#cb1-27" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">secPrefix</span><span class="kw">:</span><span class="at"> </span><span class="kw">[</span><span class="at">Section</span><span class="kw">,</span><span class="at"> Sections</span><span class="kw">]</span></span>
+<span id="cb1-28"><a href="#cb1-28" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb1-29"><a href="#cb1-29" aria-hidden="true" tabindex="-1"></a><span class="co"># PDF output settings</span></span>
+<span id="cb1-30"><a href="#cb1-30" aria-hidden="true" tabindex="-1"></a><span class="fu">pdf</span><span class="kw">:</span></span>
+<span id="cb1-31"><a href="#cb1-31" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">documentclass</span><span class="kw">:</span><span class="at"> article</span></span>
+<span id="cb1-32"><a href="#cb1-32" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">fontsize</span><span class="kw">:</span><span class="at"> 12pt</span></span>
+<span id="cb1-33"><a href="#cb1-33" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">geometry</span><span class="kw">:</span><span class="at"> margin=1in</span></span>
+<span id="cb1-34"><a href="#cb1-34" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">linestretch</span><span class="kw">:</span><span class="at"> </span><span class="fl">1.5</span></span>
+<span id="cb1-35"><a href="#cb1-35" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">toc</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
+<span id="cb1-36"><a href="#cb1-36" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">numbersections</span><span class="kw">:</span><span class="at"> </span><span class="ch">true</span></span>
+<span id="cb1-37"><a href="#cb1-37" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb1-38"><a href="#cb1-38" aria-hidden="true" tabindex="-1"></a><span class="co"># Word output settings</span></span>
+<span id="cb1-39"><a href="#cb1-39" aria-hidden="true" tabindex="-1"></a><span class="fu">docx</span><span class="kw">:</span></span>
+<span id="cb1-40"><a href="#cb1-40" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">reference</span><span class="kw">:</span><span class="at"> template.docx</span><span class="co">   # Optional reference doc for styling</span></span>
+<span id="cb1-41"><a href="#cb1-41" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">keepComments</span><span class="kw">:</span><span class="at"> </span><span class="ch">true</span><span class="co">         # Preserve CriticMarkup comments</span></span>
+<span id="cb1-42"><a href="#cb1-42" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">toc</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span></code></pre></div>
+      <h2 id="template-variables">Template Variables</h2>
+      <p>Use in section files (processed during build):</p>
+      <table>
+      <thead>
+      <tr>
+      <th>Variable</th>
+      <th>Description</th>
+      <th>Example Output</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>{{date}}</code></td>
+      <td>Current date</td>
+      <td>2025-12-30</td>
+      </tr>
+      <tr>
+      <td><code>{{date:MMMM D, YYYY}}</code></td>
+      <td>Custom format</td>
+      <td>December 30, 2025</td>
+      </tr>
+      <tr>
+      <td><code>{{year}}</code></td>
+      <td>Current year</td>
+      <td>2025</td>
+      </tr>
+      <tr>
+      <td><code>{{version}}</code></td>
+      <td>From rev.yaml</td>
+      <td>1.0</td>
+      </tr>
+      <tr>
+      <td><code>{{title}}</code></td>
+      <td>Document title</td>
+      <td>Your Paper Title</td>
+      </tr>
+      <tr>
+      <td><code>{{author}}</code></td>
+      <td>First author</td>
+      <td>First Author</td>
+      </tr>
+      <tr>
+      <td><code>{{authors}}</code></td>
+      <td>All authors</td>
+      <td>First Author, Second Author</td>
+      </tr>
+      <tr>
+      <td><code>{{word_count}}</code></td>
+      <td>Total words</td>
+      <td>5,432</td>
+      </tr>
+      </tbody>
+      </table>
+      <p><strong>Example usage:</strong></p>
+      <div class="sourceCode" id="cb2"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu"># Methods</span></span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>Last updated: {{date:MMMM D, YYYY}}</span>
+<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>Word count: {{word_count}}</span></code></pre></div>
+      <h2 id="user-configuration">User Configuration</h2>
+      <p>Set your name for comment replies:</p>
+      <div class="sourceCode" id="cb3"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> config user <span class="st">&quot;Your Name&quot;</span></span></code></pre></div>
+      <p>Set default sections for new projects:</p>
+      <div class="sourceCode" id="cb4"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> config sections <span class="st">&quot;intro,methods,results,discussion&quot;</span></span></code></pre></div>
+      <p>This creates <code>~/.revrc</code>:</p>
+      <div class="sourceCode" id="cb5"><pre
+      class="sourceCode json"><code class="sourceCode json"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">{</span></span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>  <span class="dt">&quot;userName&quot;</span><span class="fu">:</span> <span class="st">&quot;Your Name&quot;</span><span class="fu">,</span></span>
+<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>  <span class="dt">&quot;defaultSections&quot;</span><span class="fu">:</span> <span class="ot">[</span><span class="st">&quot;intro&quot;</span><span class="ot">,</span> <span class="st">&quot;methods&quot;</span><span class="ot">,</span> <span class="st">&quot;results&quot;</span><span class="ot">,</span> <span class="st">&quot;discussion&quot;</span><span class="ot">]</span></span>
+<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="fu">}</span></span></code></pre></div>
+      <p>When <code>defaultSections</code> is set, <code>rev new</code>
+      uses these sections automatically. When not set,
+      <code>rev new</code> prompts for sections interactively.</p>
+      <h2 id="dictionaries">Dictionaries</h2>
+      <p><strong>Global dictionary</strong>
+      (<code>~/.rev-dictionary</code>):</p>
+      <div class="sourceCode" id="cb6"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> spelling <span class="at">--learn</span> myword      <span class="co"># Add word</span></span>
+<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> spelling <span class="at">--forget</span> myword     <span class="co"># Remove word</span></span>
+<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> spelling <span class="at">--list</span>              <span class="co"># Show dictionary</span></span></code></pre></div>
+      <p><strong>Project dictionary</strong>
+      (<code>.rev-dictionary</code> in project root):</p>
+      <div class="sourceCode" id="cb7"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> spelling <span class="at">--learn-project</span> myterm</span></code></pre></div>
+      <p><strong>Grammar dictionary</strong> (same locations):</p>
+      <div class="sourceCode" id="cb8"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> grammar <span class="at">--learn</span> acronym</span>
+<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> grammar <span class="at">--forget</span> acronym</span></code></pre></div>
+      <h2 id="journal-profiles">Journal Profiles</h2>
+      <p>21 built-in journal profiles for validation. Six also provide
+      <strong>build formatting defaults</strong> (CSL citation style,
+      PDF settings):</p>
+      <div class="sourceCode" id="cb9"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> validate <span class="at">--list</span>              <span class="co"># List all profiles ([formatting] = build support)</span></span>
+<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> validate <span class="at">-j</span> nature           <span class="co"># Check against Nature requirements</span></span>
+<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> word-count <span class="at">-j</span> ecology-letters  <span class="co"># Use journal word limit</span></span></code></pre></div>
+      <p>Profiles include: nature, science, pnas, elife, cell, plos-one,
+      ecology-letters, global-change-biology, etc.</p>
+      <h3 id="setting-a-journal">Setting a Journal</h3>
+      <p>In <code>rev.yaml</code>:</p>
+      <div class="sourceCode" id="cb10"><pre
+      class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="fu">journal</span><span class="kw">:</span><span class="at"> nature</span></span></code></pre></div>
+      <p>Or via CLI flag (overrides rev.yaml):</p>
+      <div class="sourceCode" id="cb11"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build pdf docx <span class="at">-j</span> nature</span></code></pre></div>
+      <h3 id="config-cascade">Config Cascade</h3>
+      <p>When a journal with formatting is set, settings are applied in
+      three layers:</p>
+      <ol type="1">
+      <li><strong>Defaults</strong> — docrev built-in defaults (12pt,
+      margin=1in, linestretch=1.5, etc.)</li>
+      <li><strong>Journal formatting</strong> — from the journal profile
+      (e.g., Nature uses 11pt, 2.5cm margins, double spacing)</li>
+      <li><strong>Your rev.yaml</strong> — explicit settings always
+      win</li>
+      </ol>
+      <p>This means you can set <code>journal: nature</code> and still
+      override individual settings:</p>
+      <div class="sourceCode" id="cb12"><pre
+      class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="fu">journal</span><span class="kw">:</span><span class="at"> nature</span></span>
+<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a><span class="fu">pdf</span><span class="kw">:</span></span>
+<span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">linestretch</span><span class="kw">:</span><span class="at"> </span><span class="fl">1.5</span><span class="co">    # override Nature&#39;s double spacing</span></span></code></pre></div>
+      <h3 id="csl-citation-styles">CSL Citation Styles</h3>
+      <p>Journal profiles specify a CSL style name. docrev resolves CSL
+      files in this order:</p>
+      <ol type="1">
+      <li>File path in project directory (e.g.,
+      <code>nature.csl</code>)</li>
+      <li>Cached file in <code>~/.rev/csl/</code></li>
+      <li>Bare name passed to pandoc –citeproc (works for some built-in
+      styles)</li>
+      </ol>
+      <p>Download and cache a style:</p>
+      <div class="sourceCode" id="cb13"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> profiles <span class="at">--fetch-csl</span> nature    <span class="co"># downloads to ~/.rev/csl/nature.csl</span></span>
+<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> profiles <span class="at">--fetch-csl</span> apa       <span class="co"># works with short names</span></span>
+<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> profiles <span class="at">--list-csl</span>            <span class="co"># list cached files</span></span></code></pre></div>
+      <p>Known short names: apa, chicago, vancouver, ieee, nature,
+      science, cell, pnas, plos, elife, ecology-letters, ama, acs,
+      harvard, mla, elsevier, springer, biomed-central.</p>
+      <h3 id="custom-profiles-with-formatting">Custom Profiles with
+      Formatting</h3>
+      <p>Custom profiles (YAML files in <code>~/.rev/profiles/</code> or
+      <code>.rev/profiles/</code>) can include a <code>formatting</code>
+      section:</p>
+      <div class="sourceCode" id="cb14"><pre
+      class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a><span class="fu">id</span><span class="kw">:</span><span class="at"> my-journal</span></span>
+<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a><span class="fu">name</span><span class="kw">:</span><span class="at"> </span><span class="st">&quot;My Journal&quot;</span></span>
+<span id="cb14-3"><a href="#cb14-3" aria-hidden="true" tabindex="-1"></a><span class="fu">url</span><span class="kw">:</span><span class="at"> </span><span class="st">&quot;https://journal.example.com/guidelines&quot;</span></span>
+<span id="cb14-4"><a href="#cb14-4" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb14-5"><a href="#cb14-5" aria-hidden="true" tabindex="-1"></a><span class="co"># Validation requirements</span></span>
+<span id="cb14-6"><a href="#cb14-6" aria-hidden="true" tabindex="-1"></a><span class="fu">wordLimit</span><span class="kw">:</span></span>
+<span id="cb14-7"><a href="#cb14-7" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">main</span><span class="kw">:</span><span class="at"> </span><span class="dv">6000</span></span>
+<span id="cb14-8"><a href="#cb14-8" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">abstract</span><span class="kw">:</span><span class="at"> </span><span class="dv">250</span></span>
+<span id="cb14-9"><a href="#cb14-9" aria-hidden="true" tabindex="-1"></a><span class="fu">references</span><span class="kw">:</span></span>
+<span id="cb14-10"><a href="#cb14-10" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">max</span><span class="kw">:</span><span class="at"> </span><span class="dv">50</span></span>
+<span id="cb14-11"><a href="#cb14-11" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">doiRequired</span><span class="kw">:</span><span class="at"> </span><span class="ch">true</span></span>
+<span id="cb14-12"><a href="#cb14-12" aria-hidden="true" tabindex="-1"></a><span class="fu">sections</span><span class="kw">:</span></span>
+<span id="cb14-13"><a href="#cb14-13" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">required</span><span class="kw">:</span></span>
+<span id="cb14-14"><a href="#cb14-14" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="kw">-</span><span class="at"> Abstract</span></span>
+<span id="cb14-15"><a href="#cb14-15" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="kw">-</span><span class="at"> Introduction</span></span>
+<span id="cb14-16"><a href="#cb14-16" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="kw">-</span><span class="at"> Methods</span></span>
+<span id="cb14-17"><a href="#cb14-17" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="kw">-</span><span class="at"> Results</span></span>
+<span id="cb14-18"><a href="#cb14-18" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="kw">-</span><span class="at"> Discussion</span></span>
+<span id="cb14-19"><a href="#cb14-19" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb14-20"><a href="#cb14-20" aria-hidden="true" tabindex="-1"></a><span class="co"># Build formatting defaults</span></span>
+<span id="cb14-21"><a href="#cb14-21" aria-hidden="true" tabindex="-1"></a><span class="fu">formatting</span><span class="kw">:</span></span>
+<span id="cb14-22"><a href="#cb14-22" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">csl</span><span class="kw">:</span><span class="at"> </span><span class="st">&quot;vancouver&quot;</span></span>
+<span id="cb14-23"><a href="#cb14-23" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">pdf</span><span class="kw">:</span></span>
+<span id="cb14-24"><a href="#cb14-24" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">fontsize</span><span class="kw">:</span><span class="at"> 11pt</span></span>
+<span id="cb14-25"><a href="#cb14-25" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">geometry</span><span class="kw">:</span><span class="at"> margin=2cm</span></span>
+<span id="cb14-26"><a href="#cb14-26" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">linestretch</span><span class="kw">:</span><span class="at"> </span><span class="dv">2</span></span>
+<span id="cb14-27"><a href="#cb14-27" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">numbersections</span><span class="kw">:</span><span class="at"> </span><span class="ch">false</span></span>
+<span id="cb14-28"><a href="#cb14-28" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">docx</span><span class="kw">:</span></span>
+<span id="cb14-29"><a href="#cb14-29" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">reference</span><span class="kw">:</span><span class="at"> </span><span class="ch">null</span></span>
+<span id="cb14-30"><a href="#cb14-30" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">crossref</span><span class="kw">:</span></span>
+<span id="cb14-31"><a href="#cb14-31" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">figPrefix</span><span class="kw">:</span><span class="at"> </span><span class="kw">[</span><span class="at">Fig.</span><span class="kw">,</span><span class="at"> Figs.</span><span class="kw">]</span></span>
+<span id="cb14-32"><a href="#cb14-32" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">tblPrefix</span><span class="kw">:</span><span class="at"> </span><span class="kw">[</span><span class="at">Table</span><span class="kw">,</span><span class="at"> Tables</span><span class="kw">]</span></span></code></pre></div>
+      <p>Create a new profile template (includes formatting
+      section):</p>
+      <div class="sourceCode" id="cb15"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> profiles <span class="at">--new</span> <span class="st">&quot;My Journal&quot;</span></span></code></pre></div>
+      <h3 id="cli-reference">CLI Reference</h3>
+      <table>
+      <thead>
+      <tr>
+      <th>Command</th>
+      <th>Description</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td><code>rev validate --list</code></td>
+      <td>List all profiles with formatting tags</td>
+      </tr>
+      <tr>
+      <td><code>rev validate -j nature</code></td>
+      <td>Validate against journal requirements</td>
+      </tr>
+      <tr>
+      <td><code>rev build -j nature</code></td>
+      <td>Build with journal formatting defaults</td>
+      </tr>
+      <tr>
+      <td><code>rev profiles --new "Name"</code></td>
+      <td>Create custom profile template</td>
+      </tr>
+      <tr>
+      <td><code>rev profiles --fetch-csl name</code></td>
+      <td>Download CSL style to cache</td>
+      </tr>
+      <tr>
+      <td><code>rev profiles --list-csl</code></td>
+      <td>List cached CSL styles</td>
+      </tr>
+      <tr>
+      <td><code>rev profiles --dirs</code></td>
+      <td>Show profile directory locations</td>
+      </tr>
+      </tbody>
+      </table>
+    </main>
+    <aside class="col-md-3 d-none d-md-block">
+      <nav id="toc" data-toggle="toc" aria-label="On this page">
+        <h2 class="h6">On this page</h2>
+        <div class="toc"><ul>
+<li><a href="#configuration" id="toc-configuration">Configuration</a>
+<ul>
+<li><a href="#rev.yaml" id="toc-rev.yaml">rev.yaml</a></li>
+<li><a href="#template-variables" id="toc-template-variables">Template
+Variables</a></li>
+<li><a href="#user-configuration" id="toc-user-configuration">User
+Configuration</a></li>
+<li><a href="#dictionaries" id="toc-dictionaries">Dictionaries</a></li>
+<li><a href="#journal-profiles" id="toc-journal-profiles">Journal
+Profiles</a>
+<ul>
+<li><a href="#setting-a-journal" id="toc-setting-a-journal">Setting a
+Journal</a></li>
+<li><a href="#config-cascade" id="toc-config-cascade">Config
+Cascade</a></li>
+<li><a href="#csl-citation-styles" id="toc-csl-citation-styles">CSL
+Citation Styles</a></li>
+<li><a href="#custom-profiles-with-formatting"
+id="toc-custom-profiles-with-formatting">Custom Profiles with
+Formatting</a></li>
+<li><a href="#cli-reference" id="toc-cli-reference">CLI
+Reference</a></li>
+</ul></li>
+</ul></li>
+</ul></div>
+      </nav>
+    </aside>
+  </div>
+</div>
+
+<footer class="border-top py-3 mt-auto">
+  <div class="container d-flex justify-content-between align-items-center text-muted" style="font-size:.85rem">
+    <span>docrev 0.9.15</span>
+    <span>Built with <a href="https://pandoc.org" class="text-muted">pandoc</a></span>
+  </div>
+</footer>
+
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+})();
+</script>
+
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+</html>

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+<!DOCTYPE html>
+<html lang="en" data-bs-theme="light">
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <title>Home — docrev</title>
+  <meta name="description" content="CLI for writing documents in Markdown while collaborating with Word users.">
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootswatch@5.3.3/dist/sandstone/bootstrap.min.css">
+  <style>
+html { -webkit-text-size-adjust: 100%; }
+pre > code.sourceCode { white-space: pre; position: relative; }
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+  { position: relative; left: -4em; counter-increment: source-line; }
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+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
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+    -webkit-touch-callout: none; -webkit-user-select: none;
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+    -ms-user-select: none; user-select: none;
+    padding: 0 4px; width: 4em;
+    color: #aaaaaa;
+  }
+pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
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+code span.al { color: #ff0000; font-weight: bold; } /* Alert */
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+code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
+code span.do { color: #ba2121; font-style: italic; } /* Documentation */
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+code span.kw { color: #007020; font-weight: bold; } /* Keyword */
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+code span.ot { color: #007020; } /* Other */
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+code span.vs { color: #4070a0; } /* VerbatimString */
+code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
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+  <link rel="stylesheet" href="assets/extra.css">
+</head>
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+
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+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar-main" aria-controls="navbar-main" aria-expanded="false" aria-label="Toggle navigation">
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+          <a class="nav-link"  href="workflow.html">Get Started</a>
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+          <a class="nav-link"  href="commands.html">Commands</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="configuration.html">Configuration</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="troubleshooting.html">Troubleshooting</a>
+        </li>
+      </ul>
+      <ul class="navbar-nav">
+        <li class="nav-item">
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+            </svg>
+            <svg id="icon-moon" xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" viewBox="0 0 16 16" style="display:none">
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+            </svg>
+          </button>
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+        </li>
+      </ul>
+    </div>
+  </div>
+</nav>
+
+<div class="container template-home">
+  <div class="row">
+    <main id="main" class="col-12">
+      <h1 id="docrev">docrev</h1>
+      <div class="badge-row">
+      <p><a href="https://www.npmjs.com/package/docrev"><img
+      src="https://img.shields.io/npm/v/docrev" alt="npm" /></a> <a
+      href="https://www.npmjs.com/package/docrev"><img
+      src="https://img.shields.io/npm/dm/docrev"
+      alt="npm downloads" /></a> <a href="https://nodejs.org"><img
+      src="https://img.shields.io/node/v/docrev" alt="node" /></a> <a
+      href="https://opensource.org/licenses/MIT"><img
+      src="https://img.shields.io/badge/License-MIT-blue.svg"
+      alt="License: MIT" /></a> <a
+      href="https://github.com/gcol33/docrev/actions/workflows/ci.yml"><img
+      src="https://github.com/gcol33/docrev/actions/workflows/ci.yml/badge.svg"
+      alt="CI" /></a></p>
+      </div>
+      <p>A CLI for writing documents in Markdown while collaborating
+      with Word users.</p>
+      <p>Write in <code>.md</code> files under version control; build
+      Word or PDF when you need to share. When reviewers return their
+      annotated copy, <code>rev sync</code> pulls the feedback into your
+      markdown sections, where you reply to comments, accept or reject
+      changes, and rebuild. Equations, figures, citations, and
+      cross-references survive both directions.</p>
+      <h2 id="the-problem">The Problem</h2>
+      <p>After a few rounds of feedback, the project directory looks
+      like this:</p>
+      <pre><code>manuscript_v1.docx
+manuscript_v2_john_comments.docx
+manuscript_v2_jane_comments.docx
+manuscript_v3_merged_final.docx
+manuscript_v3_merged_final_REAL.docx
+manuscript_v3_merged_final_REAL_submitted.docx</code></pre>
+      <p>By the third filename, there’s no canonical version. Jane’s
+      comments are in one file, John’s track changes in another, your
+      reconciliation attempt in a third; whether you merged the right
+      sources depends on what you remember from last Tuesday.</p>
+      <p>docrev keeps the markdown as the canonical version, under git.
+      The DOCX is rebuilt each time you share; reviewer comments and
+      track changes come back into your section files when you sync,
+      where you reply to or accept them in the terminal.</p>
+      <h2 id="install">Install</h2>
+      <div class="sourceCode" id="cb2"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">npm</span> install <span class="at">-g</span> docrev</span></code></pre></div>
+      <p>Requires <a href="https://nodejs.org">Node.js</a> 18+. Building
+      DOCX or PDF needs <a href="https://pandoc.org">Pandoc</a>. For
+      complex PDFs (math, cross-references, journal styles), LaTeX is
+      also needed — see the <a
+      href="troubleshooting.html">Troubleshooting</a> page.</p>
+      <h2 id="quick-start">Quick Start</h2>
+      <p>Write in Markdown with citations and cross-references:</p>
+      <div class="sourceCode" id="cb3"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>Climate change poses significant challenges <span class="co">[</span><span class="ot">@IPCC2021</span><span class="co">]</span>. As shown in</span>
+<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>@fig:temperature, global temperatures have risen steadily.</span>
+<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="al">![Temperature anomalies](figures/temperature.png)</span>{#fig:temperature}</span></code></pre></div>
+      <p>Build and share:</p>
+      <div class="sourceCode" id="cb4"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build docx    <span class="co"># → output/paper.docx</span></span>
+<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build pdf     <span class="co"># → output/paper.pdf</span></span></code></pre></div>
+      <p>When collaborators return the Word doc with track changes:</p>
+      <div class="sourceCode" id="cb5"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> sync reviewed.docx    <span class="co"># their comments → your markdown</span></span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> todo                  <span class="co"># list all pending comments</span></span>
+<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> reply methods.md <span class="at">-n</span> 1 <span class="at">-m</span> <span class="st">&quot;Clarified in revised text.&quot;</span></span>
+<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build docx <span class="at">--dual</span>     <span class="co"># clean + annotated versions</span></span></code></pre></div>
+      <h2 id="documentation">Documentation</h2>
+      <div class="row g-3 mt-1">
+      <div class="col-sm-6">
+      <div class="doc-card position-relative">
+      <h5>
+      Get Started
+      </h5>
+      <p>
+      The full revision cycle: import, build, sync, reply, resolve,
+      rebuild, archive.
+      </p>
+      <p><a href="workflow.html" class="stretched-link text-decoration-none">Revision
+      Workflow →</a></p>
+      </div>
+      </div>
+      <div class="col-sm-6">
+      <div class="doc-card position-relative">
+      <h5>
+      Commands
+      </h5>
+      <p>
+      Complete reference for all <code>rev</code> commands, grouped by
+      task.
+      </p>
+      <p><a href="commands.html" class="stretched-link text-decoration-none">Command
+      Reference →</a></p>
+      </div>
+      </div>
+      <div class="col-sm-6">
+      <div class="doc-card position-relative">
+      <h5>
+      Configuration
+      </h5>
+      <p>
+      <code>rev.yaml</code> options, journal profiles, custom templates,
+      CSL styles.
+      </p>
+      <p><a href="configuration.html" class="stretched-link text-decoration-none">Configuration
+      →</a></p>
+      </div>
+      </div>
+      <div class="col-sm-6">
+      <div class="doc-card position-relative">
+      <h5>
+      Troubleshooting
+      </h5>
+      <p>
+      Common issues with installation, builds, imports, and
+      cross-references.
+      </p>
+      <p><a href="troubleshooting.html" class="stretched-link text-decoration-none">Troubleshooting
+      →</a></p>
+      </div>
+      </div>
+      </div>
+    </main>
+  </div>
+</div>
+
+<footer class="border-top py-3 mt-auto">
+  <div class="container d-flex justify-content-between align-items-center text-muted" style="font-size:.85rem">
+    <span>docrev 0.9.15</span>
+    <span>Built with <a href="https://pandoc.org" class="text-muted">pandoc</a></span>
+  </div>
+</footer>
+
+<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
+<script>
+(function () {
+  var html  = document.documentElement;
+  var sun   = document.getElementById('icon-sun');
+  var moon  = document.getElementById('icon-moon');
+  function apply(t) {
+    html.setAttribute('data-bs-theme', t);
+    sun.style.display  = t === 'dark' ? 'none' : '';
+    moon.style.display = t === 'dark' ? ''     : 'none';
+  }
+  apply(localStorage.getItem('docrev-theme') || 'light');
+  document.getElementById('theme-toggle').addEventListener('click', function () {
+    var next = html.getAttribute('data-bs-theme') === 'dark' ? 'light' : 'dark';
+    localStorage.setItem('docrev-theme', next);
+    apply(next);
+  });
+})();
+</script>
+
+</body>
+</html>

site/troubleshooting.html

+<!DOCTYPE html>
+<html lang="en" data-bs-theme="light">
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <title>Troubleshooting — docrev</title>
+  <meta name="description" content="CLI for writing documents in Markdown while collaborating with Word users.">
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootswatch@5.3.3/dist/sandstone/bootstrap.min.css">
+  <style>
+html { -webkit-text-size-adjust: 100%; }
+pre > code.sourceCode { white-space: pre; position: relative; }
+pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span:empty { height: 1.2em; }
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+code.sourceCode > span { color: inherit; text-decoration: inherit; }
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+pre.sourceCode { margin: 0; }
+@media screen {
+div.sourceCode { overflow: auto; }
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+pre > code.sourceCode { white-space: pre-wrap; }
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+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
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+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; display: inline-block;
+    -webkit-touch-callout: none; -webkit-user-select: none;
+    -khtml-user-select: none; -moz-user-select: none;
+    -ms-user-select: none; user-select: none;
+    padding: 0 4px; width: 4em;
+    color: #aaaaaa;
+  }
+pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
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+  {   }
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+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
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+code span.fu { color: #06287e; } /* Function */
+code span.im { color: #008000; font-weight: bold; } /* Import */
+code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
+code span.kw { color: #007020; font-weight: bold; } /* Keyword */
+code span.op { color: #666666; } /* Operator */
+code span.ot { color: #007020; } /* Other */
+code span.pp { color: #bc7a00; } /* Preprocessor */
+code span.sc { color: #4070a0; } /* SpecialChar */
+code span.ss { color: #bb6688; } /* SpecialString */
+code span.st { color: #4070a0; } /* String */
+code span.va { color: #19177c; } /* Variable */
+code span.vs { color: #4070a0; } /* VerbatimString */
+code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
+  </style>
+  <link rel="stylesheet" href="assets/extra.css">
+</head>
+<body>
+
+<nav class="navbar navbar-expand-lg fixed-top" aria-label="Site navigation">
+  <div class="container">
+    <a class="navbar-brand me-2" href="index.html">docrev</a>
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar-main" aria-controls="navbar-main" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+    <div class="collapse navbar-collapse" id="navbar-main">
+      <ul class="navbar-nav me-auto">
+        <li class="nav-item">
+          <a class="nav-link"  href="index.html">Home</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="workflow.html">Get Started</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="commands.html">Commands</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="configuration.html">Configuration</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link active" aria-current="page" href="troubleshooting.html">Troubleshooting</a>
+        </li>
+      </ul>
+      <ul class="navbar-nav">
+        <li class="nav-item">
+          <button id="theme-toggle" class="btn btn-link nav-link border-0" aria-label="Toggle dark mode">
+            <svg id="icon-sun" xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" viewBox="0 0 16 16">
+              <path d="M8 11a3 3 0 1 1 0-6 3 3 0 0 1 0 6m0 1a4 4 0 1 0 0-8 4 4 0 0 0 0 8M8 0a.5.5 0 0 1 .5.5v2a.5.5 0 0 1-1 0v-2A.5.5 0 0 1 8 0m0 13a.5.5 0 0 1 .5.5v2a.5.5 0 0 1-1 0v-2A.5.5 0 0 1 8 13m8-5a.5.5 0 0 1-.5.5h-2a.5.5 0 0 1 0-1h2a.5.5 0 0 1 .5.5M3 8a.5.5 0 0 1-.5.5h-2a.5.5 0 0 1 0-1h2A.5.5 0 0 1 3 8m10.657-5.657a.5.5 0 0 1 0 .707l-1.414 1.415a.5.5 0 1 1-.707-.708l1.414-1.414a.5.5 0 0 1 .707 0m-9.193 9.193a.5.5 0 0 1 0 .707L3.05 13.657a.5.5 0 0 1-.707-.707l1.414-1.414a.5.5 0 0 1 .707 0m9.193 2.121a.5.5 0 0 1-.707 0l-1.414-1.414a.5.5 0 0 1 .707-.707l1.414 1.414a.5.5 0 0 1 0 .707M4.464 4.465a.5.5 0 0 1-.707 0L2.343 3.05a.5.5 0 1 1 .707-.707l1.414 1.414a.5.5 0 0 1 0 .707"/>
+            </svg>
+            <svg id="icon-moon" xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" viewBox="0 0 16 16" style="display:none">
+              <path d="M6 .278a.768.768 0 0 1 .08.858 7.208 7.208 0 0 0-.878 3.46c0 4.021 3.278 7.277 7.318 7.277.527 0 1.04-.055 1.533-.16a.787.787 0 0 1 .81.316.733.733 0 0 1-.031.893A8.349 8.349 0 0 1 8.344 16C3.734 16 0 12.286 0 7.71 0 4.266 2.114 1.312 5.124.06A.752.752 0 0 1 6 .278"/>
+            </svg>
+          </button>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link" href="https://github.com/gcol33/docrev" aria-label="GitHub">
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+              <path d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.012 8.012 0 0 0 16 8c0-4.42-3.58-8-8-8"/>
+            </svg>
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+          <a class="nav-link" href="https://www.npmjs.com/package/docrev" aria-label="npm">
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+          </a>
+        </li>
+      </ul>
+    </div>
+  </div>
+</nav>
+
+<div class="container template-article">
+  <div class="row">
+    <main id="main" class="col-md-9">
+      <h1 id="troubleshooting">Troubleshooting</h1>
+      <p>Common issues and solutions for docrev.</p>
+      <h2 id="installation-issues">Installation Issues</h2>
+      <h3 id="pandoc-command-not-found">“pandoc: command not found”</h3>
+      <p>Pandoc is required for building documents.</p>
+      <p><strong>macOS:</strong></p>
+      <div class="sourceCode" id="cb1"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">brew</span> install pandoc</span></code></pre></div>
+      <p><strong>Windows:</strong></p>
+      <div class="sourceCode" id="cb2"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">winget</span> install JohnMacFarlane.Pandoc</span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="co"># or download from https://pandoc.org/installing.html</span></span></code></pre></div>
+      <p><strong>Linux (Debian/Ubuntu):</strong></p>
+      <div class="sourceCode" id="cb3"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sudo</span> apt install pandoc</span></code></pre></div>
+      <p>Verify installation:</p>
+      <div class="sourceCode" id="cb4"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">pandoc</span> <span class="at">--version</span></span></code></pre></div>
+      <h3 id="pandoc-crossref-command-not-found">“pandoc-crossref:
+      command not found”</h3>
+      <p>pandoc-crossref is optional but required for figure/table
+      cross-references.</p>
+      <p><strong>macOS:</strong></p>
+      <div class="sourceCode" id="cb5"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="ex">brew</span> install pandoc-crossref</span></code></pre></div>
+      <p><strong>Windows:</strong> Download from
+      https://github.com/lierdakil/pandoc-crossref/releases</p>
+      <p><strong>Linux:</strong></p>
+      <div class="sourceCode" id="cb6"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Check your package manager or download from GitHub releases</span></span></code></pre></div>
+      <h3 id="latex-not-found-pdf-generation-fails">LaTeX not found (PDF
+      generation fails)</h3>
+      <p>PDF output requires a LaTeX distribution.</p>
+      <p><strong>macOS:</strong></p>
+      <div class="sourceCode" id="cb7"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="ex">brew</span> install <span class="at">--cask</span> mactex-no-gui</span>
+<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="co"># or smaller: brew install --cask basictex</span></span></code></pre></div>
+      <p><strong>Windows:</strong> Install MiKTeX from
+      https://miktex.org/download</p>
+      <p><strong>Linux:</strong></p>
+      <div class="sourceCode" id="cb8"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="fu">sudo</span> apt install texlive-latex-base texlive-fonts-recommended</span></code></pre></div>
+      <h2 id="build-errors">Build Errors</h2>
+      <h3 id="no-section-files-found">“No section files found”</h3>
+      <p><strong>Cause:</strong> No <code>.md</code> files in the
+      directory, or sections not specified in <code>rev.yaml</code>.</p>
+      <p><strong>Solutions:</strong> 1. Create section files:
+      <code>rev new</code> 2. Specify sections in <code>rev.yaml</code>:
+      <code>yaml    sections:      - introduction.md      - methods.md</code>
+      3. Check you’re in the correct directory</p>
+      <h3 id="failed-to-parse-rev.yaml">“Failed to parse rev.yaml”</h3>
+      <p><strong>Cause:</strong> Invalid YAML syntax.</p>
+      <p><strong>Common fixes:</strong> - Check indentation (use spaces,
+      not tabs) - Quote strings with special characters - Validate with:
+      <code>rev check</code></p>
+      <p><strong>Example of correct YAML:</strong></p>
+      <div class="sourceCode" id="cb9"><pre
+      class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">title</span><span class="kw">:</span><span class="at"> </span><span class="st">&quot;My Paper: A Study&quot;</span><span class="co">  # Quotes needed for colon</span></span>
+<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="fu">authors</span><span class="kw">:</span></span>
+<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="kw">-</span><span class="at"> </span><span class="fu">name</span><span class="kw">:</span><span class="at"> John Doe</span><span class="co">          # 2-space indent</span></span>
+<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a><span class="at">    </span><span class="fu">affiliation</span><span class="kw">:</span><span class="at"> University</span></span></code></pre></div>
+      <h3 id="build-produces-empty-pdf">Build produces empty PDF</h3>
+      <p><strong>Causes:</strong> 1. Section files are empty 2. Pandoc
+      filter errors (check terminal output) 3. LaTeX errors</p>
+      <p><strong>Debug:</strong></p>
+      <div class="sourceCode" id="cb10"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build <span class="at">--verbose</span></span>
+<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build tex  <span class="co"># Check the .tex file for errors</span></span></code></pre></div>
+      <h2 id="import-issues">Import Issues</h2>
+      <h3 id="comments-not-imported-from-word">Comments not imported
+      from Word</h3>
+      <p><strong>Causes:</strong> 1. Document uses older .doc format
+      (only .docx supported) 2. Comments are in review mode but not
+      finalized</p>
+      <p><strong>Solutions:</strong> 1. Save as .docx in Word 2.
+      Accept/reject track changes before importing if you want clean
+      text</p>
+      <h3 id="track-changes-garbled-or-missing">Track changes garbled or
+      missing</h3>
+      <p><strong>Cause:</strong> Complex nested changes or unsupported
+      Word features.</p>
+      <p><strong>Solution:</strong></p>
+      <div class="sourceCode" id="cb11"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> import document.docx <span class="at">--no-track-changes</span></span>
+<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a><span class="co"># Then manually review the Word file</span></span></code></pre></div>
+      <h3 id="cannot-read-file-errors">“Cannot read file” errors</h3>
+      <p><strong>Causes:</strong> 1. File is open in Word (Windows locks
+      open files) 2. File path contains special characters 3. Corrupted
+      .docx file</p>
+      <p><strong>Solutions:</strong> 1. Close the file in Word 2. Rename
+      file to remove special characters 3. Try opening in Word and
+      re-saving</p>
+      <h2 id="comment-issues">Comment Issues</h2>
+      <h3 id="comments-not-appearing-in-word-export">Comments not
+      appearing in Word export</h3>
+      <p><strong>Cause:</strong> Comments marked as resolved are hidden
+      by default.</p>
+      <p><strong>Solutions:</strong></p>
+      <div class="sourceCode" id="cb12"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> comments file.md <span class="at">--resolved</span>  <span class="co"># Check resolved comments</span></span>
+<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> resolve file.md <span class="at">-a</span> <span class="at">-u</span>        <span class="co"># Unresolve all comments</span></span></code></pre></div>
+      <h3 id="reply-threading-not-working">Reply threading not
+      working</h3>
+      <p>Comments must be adjacent (no text between them) to thread in
+      Word.</p>
+      <p><strong>Works:</strong></p>
+      <div class="sourceCode" id="cb13"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>text{&gt;&gt;Author1: comment&lt;&lt;}{&gt;&gt;Author2: reply&lt;&lt;}</span></code></pre></div>
+      <p><strong>Won’t thread:</strong></p>
+      <div class="sourceCode" id="cb14"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>text{&gt;&gt;Author1: comment&lt;&lt;} more text {&gt;&gt;Author2: reply&lt;&lt;}</span></code></pre></div>
+      <h3 id="author-name-not-set">Author name not set</h3>
+      <div class="sourceCode" id="cb15"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> config user <span class="st">&quot;Your Name&quot;</span></span>
+<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a><span class="co"># Or per-command:</span></span>
+<span id="cb15-3"><a href="#cb15-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> reply file.md <span class="at">--author</span> <span class="st">&quot;Your Name&quot;</span></span></code></pre></div>
+      <h2 id="cross-reference-issues">Cross-Reference Issues</h2>
+      <h3 id="figurestables-not-numbered">Figures/tables not
+      numbered</h3>
+      <p><strong>Causes:</strong> 1. pandoc-crossref not installed 2.
+      Labels not in correct format</p>
+      <p><strong>Correct format:</strong></p>
+      <div class="sourceCode" id="cb16"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="al">![Caption](image.png)</span>{#fig:label}</span>
+<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a><span class="pp">|</span> Col1 <span class="pp">|</span> Col2 <span class="pp">|</span></span>
+<span id="cb16-4"><a href="#cb16-4" aria-hidden="true" tabindex="-1"></a><span class="pp">|------|------|</span></span>
+<span id="cb16-5"><a href="#cb16-5" aria-hidden="true" tabindex="-1"></a><span class="pp">|</span> a    <span class="pp">|</span> b    <span class="pp">|</span></span>
+<span id="cb16-6"><a href="#cb16-6" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb16-7"><a href="#cb16-7" aria-hidden="true" tabindex="-1"></a>: Caption {#tbl:label}</span></code></pre></div>
+      <h3 id="references-show-instead-of-numbers">References show “??”
+      instead of numbers</h3>
+      <p><strong>Causes:</strong> 1. Label doesn’t exist 2. Typo in
+      reference 3. pandoc-crossref not running</p>
+      <p><strong>Debug:</strong></p>
+      <div class="sourceCode" id="cb17"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> refs           <span class="co"># List all labels</span></span>
+<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> refs <span class="at">--check</span>   <span class="co"># Find broken references</span></span></code></pre></div>
+      <h2 id="pdf-issues">PDF Issues</h2>
+      <h3 id="fonts-missing-or-wrong">Fonts missing or wrong</h3>
+      <p><strong>LaTeX errors about fonts:</strong></p>
+      <div class="sourceCode" id="cb18"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Install more fonts</span></span>
+<span id="cb18-2"><a href="#cb18-2" aria-hidden="true" tabindex="-1"></a><span class="fu">sudo</span> apt install texlive-fonts-extra  <span class="co"># Linux</span></span>
+<span id="cb18-3"><a href="#cb18-3" aria-hidden="true" tabindex="-1"></a><span class="co"># Or use standard fonts in rev.yaml:</span></span>
+<span id="cb18-4"><a href="#cb18-4" aria-hidden="true" tabindex="-1"></a><span class="ex">pdf:</span></span>
+<span id="cb18-5"><a href="#cb18-5" aria-hidden="true" tabindex="-1"></a>  <span class="ex">mainfont:</span> <span class="st">&quot;Times New Roman&quot;</span></span></code></pre></div>
+      <h3 id="images-not-appearing">Images not appearing</h3>
+      <p><strong>Causes:</strong> 1. Image path incorrect (relative to
+      project root) 2. Image format not supported by LaTeX</p>
+      <p><strong>Solutions:</strong> 1. Use relative paths:
+      <code>![](images/fig1.png)</code> 2. Convert to PNG/PDF: LaTeX
+      prefers PDF for vector graphics</p>
+      <h3 id="pdf-too-large">PDF too large</h3>
+      <div class="sourceCode" id="cb19"><pre
+      class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a><span class="co"># In rev.yaml</span></span>
+<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a><span class="fu">pdf</span><span class="kw">:</span></span>
+<span id="cb19-3"><a href="#cb19-3" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">geometry</span><span class="kw">:</span><span class="at"> </span><span class="st">&quot;margin=0.75in&quot;</span><span class="co">  # Smaller margins</span></span>
+<span id="cb19-4"><a href="#cb19-4" aria-hidden="true" tabindex="-1"></a><span class="at">  </span><span class="fu">fontsize</span><span class="kw">:</span><span class="at"> </span><span class="st">&quot;11pt&quot;</span><span class="co">           # Smaller font</span></span></code></pre></div>
+      <h2 id="performance-issues">Performance Issues</h2>
+      <h3 id="doi-lookup-slow">DOI lookup slow</h3>
+      <p>DOI validation queries external APIs. For large
+      bibliographies:</p>
+      <div class="sourceCode" id="cb20"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> doi check <span class="at">--no-lookup</span>  <span class="co"># Skip online validation</span></span></code></pre></div>
+      <h3 id="build-taking-too-long">Build taking too long</h3>
+      <div class="sourceCode" id="cb21"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Build only what you need</span></span>
+<span id="cb21-2"><a href="#cb21-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build docx        <span class="co"># Skip PDF</span></span>
+<span id="cb21-3"><a href="#cb21-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build <span class="at">--no-toc</span>    <span class="co"># Skip table of contents</span></span></code></pre></div>
+      <h2 id="encoding-issues">Encoding Issues</h2>
+      <h3 id="special-characters-corrupted">Special characters
+      corrupted</h3>
+      <p><strong>Cause:</strong> File encoding mismatch.</p>
+      <p><strong>Solutions:</strong> 1. Ensure files are UTF-8 encoded
+      2. In Word, save with “UTF-8” encoding option 3. Check your
+      editor’s encoding settings</p>
+      <h3 id="bibtex-entries-with-accents-fail">BibTeX entries with
+      accents fail</h3>
+      <p>Use LaTeX-style escapes or UTF-8:</p>
+      <div class="sourceCode" id="cb22"><pre
+      class="sourceCode bibtex"><code class="sourceCode bibtex"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="co">author = {M{\&quot;u}ller, Hans}</span></span>
+<span id="cb22-2"><a href="#cb22-2" aria-hidden="true" tabindex="-1"></a><span class="co"># or with UTF-8:</span></span>
+<span id="cb22-3"><a href="#cb22-3" aria-hidden="true" tabindex="-1"></a><span class="co">author = {Müller, Hans}</span></span></code></pre></div>
+      <h2 id="getting-help">Getting Help</h2>
+      <h3 id="debug-mode">Debug mode</h3>
+      <div class="sourceCode" id="cb23"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build <span class="at">--verbose</span> <span class="dv">2</span><span class="op">&gt;&amp;</span><span class="dv">1</span> <span class="kw">|</span> <span class="fu">tee</span> build.log</span></code></pre></div>
+      <h3 id="check-system-status">Check system status</h3>
+      <div class="sourceCode" id="cb24"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> doctor</span></code></pre></div>
+      <h3 id="report-issues">Report issues</h3>
+      <p>https://github.com/gcol33/docrev/issues</p>
+      <p>Include: - <code>rev --version</code> output -
+      <code>rev doctor</code> output - Minimal reproducible example</p>
+    </main>
+    <aside class="col-md-3 d-none d-md-block">
+      <nav id="toc" data-toggle="toc" aria-label="On this page">
+        <h2 class="h6">On this page</h2>
+        <div class="toc"><ul>
+<li><a href="#troubleshooting"
+id="toc-troubleshooting">Troubleshooting</a>
+<ul>
+<li><a href="#installation-issues"
+id="toc-installation-issues">Installation Issues</a>
+<ul>
+<li><a href="#pandoc-command-not-found"
+id="toc-pandoc-command-not-found">“pandoc: command not found”</a></li>
+<li><a href="#pandoc-crossref-command-not-found"
+id="toc-pandoc-crossref-command-not-found">“pandoc-crossref: command not
+found”</a></li>
+<li><a href="#latex-not-found-pdf-generation-fails"
+id="toc-latex-not-found-pdf-generation-fails">LaTeX not found (PDF
+generation fails)</a></li>
+</ul></li>
+<li><a href="#build-errors" id="toc-build-errors">Build Errors</a>
+<ul>
+<li><a href="#no-section-files-found"
+id="toc-no-section-files-found">“No section files found”</a></li>
+<li><a href="#failed-to-parse-rev.yaml"
+id="toc-failed-to-parse-rev.yaml">“Failed to parse rev.yaml”</a></li>
+<li><a href="#build-produces-empty-pdf"
+id="toc-build-produces-empty-pdf">Build produces empty PDF</a></li>
+</ul></li>
+<li><a href="#import-issues" id="toc-import-issues">Import Issues</a>
+<ul>
+<li><a href="#comments-not-imported-from-word"
+id="toc-comments-not-imported-from-word">Comments not imported from
+Word</a></li>
+<li><a href="#track-changes-garbled-or-missing"
+id="toc-track-changes-garbled-or-missing">Track changes garbled or
+missing</a></li>
+<li><a href="#cannot-read-file-errors"
+id="toc-cannot-read-file-errors">“Cannot read file” errors</a></li>
+</ul></li>
+<li><a href="#comment-issues" id="toc-comment-issues">Comment Issues</a>
+<ul>
+<li><a href="#comments-not-appearing-in-word-export"
+id="toc-comments-not-appearing-in-word-export">Comments not appearing in
+Word export</a></li>
+<li><a href="#reply-threading-not-working"
+id="toc-reply-threading-not-working">Reply threading not
+working</a></li>
+<li><a href="#author-name-not-set" id="toc-author-name-not-set">Author
+name not set</a></li>
+</ul></li>
+<li><a href="#cross-reference-issues"
+id="toc-cross-reference-issues">Cross-Reference Issues</a>
+<ul>
+<li><a href="#figurestables-not-numbered"
+id="toc-figurestables-not-numbered">Figures/tables not numbered</a></li>
+<li><a href="#references-show-instead-of-numbers"
+id="toc-references-show-instead-of-numbers">References show “??” instead
+of numbers</a></li>
+</ul></li>
+<li><a href="#pdf-issues" id="toc-pdf-issues">PDF Issues</a>
+<ul>
+<li><a href="#fonts-missing-or-wrong"
+id="toc-fonts-missing-or-wrong">Fonts missing or wrong</a></li>
+<li><a href="#images-not-appearing" id="toc-images-not-appearing">Images
+not appearing</a></li>
+<li><a href="#pdf-too-large" id="toc-pdf-too-large">PDF too
+large</a></li>
+</ul></li>
+<li><a href="#performance-issues"
+id="toc-performance-issues">Performance Issues</a>
+<ul>
+<li><a href="#doi-lookup-slow" id="toc-doi-lookup-slow">DOI lookup
+slow</a></li>
+<li><a href="#build-taking-too-long"
+id="toc-build-taking-too-long">Build taking too long</a></li>
+</ul></li>
+<li><a href="#encoding-issues" id="toc-encoding-issues">Encoding
+Issues</a>
+<ul>
+<li><a href="#special-characters-corrupted"
+id="toc-special-characters-corrupted">Special characters
+corrupted</a></li>
+<li><a href="#bibtex-entries-with-accents-fail"
+id="toc-bibtex-entries-with-accents-fail">BibTeX entries with accents
+fail</a></li>
+</ul></li>
+<li><a href="#getting-help" id="toc-getting-help">Getting Help</a>
+<ul>
+<li><a href="#debug-mode" id="toc-debug-mode">Debug mode</a></li>
+<li><a href="#check-system-status" id="toc-check-system-status">Check
+system status</a></li>
+<li><a href="#report-issues" id="toc-report-issues">Report
+issues</a></li>
+</ul></li>
+</ul></li>
+</ul></div>
+      </nav>
+    </aside>
+  </div>
+</div>
+
+<footer class="border-top py-3 mt-auto">
+  <div class="container d-flex justify-content-between align-items-center text-muted" style="font-size:.85rem">
+    <span>docrev 0.9.15</span>
+    <span>Built with <a href="https://pandoc.org" class="text-muted">pandoc</a></span>
+  </div>
+</footer>
+
+<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
+<script>
+(function () {
+  var html  = document.documentElement;
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+    html.setAttribute('data-bs-theme', t);
+    sun.style.display  = t === 'dark' ? 'none' : '';
+    moon.style.display = t === 'dark' ? ''     : 'none';
+  }
+  apply(localStorage.getItem('docrev-theme') || 'light');
+  document.getElementById('theme-toggle').addEventListener('click', function () {
+    var next = html.getAttribute('data-bs-theme') === 'dark' ? 'light' : 'dark';
+    localStorage.setItem('docrev-theme', next);
+    apply(next);
+  });
+})();
+</script>
+
+</body>
+</html>

site/workflow.html

+<!DOCTYPE html>
+<html lang="en" data-bs-theme="light">
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <title>Get Started — docrev</title>
+  <meta name="description" content="CLI for writing documents in Markdown while collaborating with Word users.">
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootswatch@5.3.3/dist/sandstone/bootstrap.min.css">
+  <style>
+html { -webkit-text-size-adjust: 100%; }
+pre > code.sourceCode { white-space: pre; position: relative; }
+pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span:empty { height: 1.2em; }
+.sourceCode { overflow: visible; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+div.sourceCode { margin: 1em 0; }
+pre.sourceCode { margin: 0; }
+@media screen {
+div.sourceCode { overflow: auto; }
+}
+@media print {
+pre > code.sourceCode { white-space: pre-wrap; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+}
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; display: inline-block;
+    -webkit-touch-callout: none; -webkit-user-select: none;
+    -khtml-user-select: none; -moz-user-select: none;
+    -ms-user-select: none; user-select: none;
+    padding: 0 4px; width: 4em;
+    color: #aaaaaa;
+  }
+pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
+code span.al { color: #ff0000; font-weight: bold; } /* Alert */
+code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
+code span.at { color: #7d9029; } /* Attribute */
+code span.bn { color: #40a070; } /* BaseN */
+code span.bu { color: #008000; } /* BuiltIn */
+code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
+code span.ch { color: #4070a0; } /* Char */
+code span.cn { color: #880000; } /* Constant */
+code span.co { color: #60a0b0; font-style: italic; } /* Comment */
+code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
+code span.do { color: #ba2121; font-style: italic; } /* Documentation */
+code span.dt { color: #902000; } /* DataType */
+code span.dv { color: #40a070; } /* DecVal */
+code span.er { color: #ff0000; font-weight: bold; } /* Error */
+code span.ex { } /* Extension */
+code span.fl { color: #40a070; } /* Float */
+code span.fu { color: #06287e; } /* Function */
+code span.im { color: #008000; font-weight: bold; } /* Import */
+code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
+code span.kw { color: #007020; font-weight: bold; } /* Keyword */
+code span.op { color: #666666; } /* Operator */
+code span.ot { color: #007020; } /* Other */
+code span.pp { color: #bc7a00; } /* Preprocessor */
+code span.sc { color: #4070a0; } /* SpecialChar */
+code span.ss { color: #bb6688; } /* SpecialString */
+code span.st { color: #4070a0; } /* String */
+code span.va { color: #19177c; } /* Variable */
+code span.vs { color: #4070a0; } /* VerbatimString */
+code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
+  </style>
+  <link rel="stylesheet" href="assets/extra.css">
+</head>
+<body>
+
+<nav class="navbar navbar-expand-lg fixed-top" aria-label="Site navigation">
+  <div class="container">
+    <a class="navbar-brand me-2" href="index.html">docrev</a>
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar-main" aria-controls="navbar-main" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+    <div class="collapse navbar-collapse" id="navbar-main">
+      <ul class="navbar-nav me-auto">
+        <li class="nav-item">
+          <a class="nav-link"  href="index.html">Home</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link active" aria-current="page" href="workflow.html">Get Started</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="commands.html">Commands</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="configuration.html">Configuration</a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link"  href="troubleshooting.html">Troubleshooting</a>
+        </li>
+      </ul>
+      <ul class="navbar-nav">
+        <li class="nav-item">
+          <button id="theme-toggle" class="btn btn-link nav-link border-0" aria-label="Toggle dark mode">
+            <svg id="icon-sun" xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" viewBox="0 0 16 16">
+              <path d="M8 11a3 3 0 1 1 0-6 3 3 0 0 1 0 6m0 1a4 4 0 1 0 0-8 4 4 0 0 0 0 8M8 0a.5.5 0 0 1 .5.5v2a.5.5 0 0 1-1 0v-2A.5.5 0 0 1 8 0m0 13a.5.5 0 0 1 .5.5v2a.5.5 0 0 1-1 0v-2A.5.5 0 0 1 8 13m8-5a.5.5 0 0 1-.5.5h-2a.5.5 0 0 1 0-1h2a.5.5 0 0 1 .5.5M3 8a.5.5 0 0 1-.5.5h-2a.5.5 0 0 1 0-1h2A.5.5 0 0 1 3 8m10.657-5.657a.5.5 0 0 1 0 .707l-1.414 1.415a.5.5 0 1 1-.707-.708l1.414-1.414a.5.5 0 0 1 .707 0m-9.193 9.193a.5.5 0 0 1 0 .707L3.05 13.657a.5.5 0 0 1-.707-.707l1.414-1.414a.5.5 0 0 1 .707 0m9.193 2.121a.5.5 0 0 1-.707 0l-1.414-1.414a.5.5 0 0 1 .707-.707l1.414 1.414a.5.5 0 0 1 0 .707M4.464 4.465a.5.5 0 0 1-.707 0L2.343 3.05a.5.5 0 1 1 .707-.707l1.414 1.414a.5.5 0 0 1 0 .707"/>
+            </svg>
+            <svg id="icon-moon" xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" viewBox="0 0 16 16" style="display:none">
+              <path d="M6 .278a.768.768 0 0 1 .08.858 7.208 7.208 0 0 0-.878 3.46c0 4.021 3.278 7.277 7.318 7.277.527 0 1.04-.055 1.533-.16a.787.787 0 0 1 .81.316.733.733 0 0 1-.031.893A8.349 8.349 0 0 1 8.344 16C3.734 16 0 12.286 0 7.71 0 4.266 2.114 1.312 5.124.06A.752.752 0 0 1 6 .278"/>
+            </svg>
+          </button>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link" href="https://github.com/gcol33/docrev" aria-label="GitHub">
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+              <path d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.012 8.012 0 0 0 16 8c0-4.42-3.58-8-8-8"/>
+            </svg>
+          </a>
+        </li>
+        <li class="nav-item">
+          <a class="nav-link" href="https://www.npmjs.com/package/docrev" aria-label="npm">
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+              <path d="M0 0v16h16V0zm5.333 13.333H2.667V5.333h2.666v5.334H8V5.333h2.667v8H5.333z"/>
+            </svg>
+          </a>
+        </li>
+      </ul>
+    </div>
+  </div>
+</nav>
+
+<div class="container template-article">
+  <div class="row">
+    <main id="main" class="col-md-9">
+      <h1 id="revision-workflow">Revision Workflow</h1>
+      <p>The canonical version lives in your markdown files. Word is the
+      exchange format — you build it when you need to share, and sync it
+      when feedback comes back.</p>
+      <p>A revision cycle in brief:</p>
+      <ol type="1">
+      <li>Build a Word document and send it to reviewers.</li>
+      <li>They return it with track changes and comments.</li>
+      <li><code>rev sync</code> pulls the feedback into your markdown
+      sections.</li>
+      <li>Navigate comments with <code>rev next</code> and
+      <code>rev todo</code>, reply with <code>rev reply</code>, accept
+      or reject changes with <code>rev accept</code>.</li>
+      <li>Rebuild with <code>rev build docx --dual</code> — a clean
+      document and an annotated one with your replies threaded into the
+      original Word comments.</li>
+      <li>Archive the reviewer’s file. Repeat.</li>
+      </ol>
+      <hr />
+      <h2 id="starting-a-project">Starting a Project</h2>
+      <p>From an existing Word document:</p>
+      <div class="sourceCode" id="cb1"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> import manuscript.docx</span></code></pre></div>
+      <p>docrev splits the document at top-level headings and creates
+      one <code>.md</code> file per section. Images land in
+      <code>figures/</code>, equations convert from OMML to LaTeX, and
+      any existing comments or track changes are preserved as
+      CriticMarkup annotations.</p>
+      <p>From scratch:</p>
+      <div class="sourceCode" id="cb2"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> new my-paper <span class="at">-s</span> intro,methods,results,discussion</span>
+<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> my-paper</span></code></pre></div>
+      <p>The <code>-s</code> flag sets section names and skips the
+      interactive prompt. Set your preferred sections once and future
+      <code>rev new</code> calls use them automatically:</p>
+      <div class="sourceCode" id="cb3"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> config sections <span class="st">&quot;intro,methods,results,discussion&quot;</span></span></code></pre></div>
+      <p>Either way, the project has this shape:</p>
+      <pre><code>my-paper/
+├── rev.yaml          ← config: title, authors, section order, journal profile
+├── intro.md          ← section files — edit these
+├── methods.md
+├── results.md
+├── discussion.md
+├── references.bib    ← BibTeX bibliography
+├── figures/          ← images referenced from sections
+├── paper.md          ← auto-combined on each build, not hand-edited
+└── output/
+    ├── my-paper.docx
+    └── my-paper.pdf</code></pre>
+      <p><code>paper.md</code> is regenerated from the section files in
+      the order set by <code>rev.yaml</code>; output files go to
+      <code>output/</code> by default. Set <code>outputDir: null</code>
+      in <code>rev.yaml</code> if you prefer them alongside
+      <code>paper.md</code>.</p>
+      <hr />
+      <h2 id="writing-in-markdown">Writing in Markdown</h2>
+      <p>Citations use pandoc-citeproc syntax — <code>[@key]</code> for
+      one source, <code>[@key1; @key2]</code> for multiple:</p>
+      <div class="sourceCode" id="cb5"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>Global temperatures have risen by 1.1°C since pre-industrial levels <span class="co">[</span><span class="ot">@IPCC2021</span><span class="co">]</span>.</span></code></pre></div>
+      <p>Figures get a label so they can be referenced by number:</p>
+      <div class="sourceCode" id="cb6"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="al">![Temperature anomalies since 1880](figures/temperature.png)</span>{#fig:temperature}</span>
+<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>As shown in @fig:temperature, the trend has accelerated since 1970.</span></code></pre></div>
+      <p>Equations use standard LaTeX — inline with <code>$...$</code>,
+      display with <code>$$...$$</code>:</p>
+      <div class="sourceCode" id="cb7"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>The forcing relationship follows $\Delta T = \lambda \cdot \Delta F$, where</span>
+<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>$\lambda$ is the climate sensitivity parameter.</span>
+<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a>$$</span>
+<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a>\bar{x} = \frac{1}{n}\sum_{i=1}^{n} x_i</span>
+<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a>$$ {#eq:mean}</span>
+<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb7-8"><a href="#cb7-8" aria-hidden="true" tabindex="-1"></a>Reference with @eq:mean → &quot;Equation 1&quot;</span></code></pre></div>
+      <p>Simple tables take pipe syntax:</p>
+      <div class="sourceCode" id="cb8"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="pp">|</span> Site <span class="pp">|</span> Lat  <span class="pp">|</span> Long   <span class="pp">|</span> n  <span class="pp">|</span></span>
+<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="pp">|------|------|--------|----|</span></span>
+<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="pp">|</span> A    <span class="pp">|</span> 45.2 <span class="pp">|</span> -120.5 <span class="pp">|</span> 48 <span class="pp">|</span></span>
+<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a><span class="pp">|</span> B    <span class="pp">|</span> 52.1 <span class="pp">|</span> -105.3 <span class="pp">|</span> 61 <span class="pp">|</span></span>
+<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb8-6"><a href="#cb8-6" aria-hidden="true" tabindex="-1"></a>: Study sites {#tbl:sites}</span></code></pre></div>
+      <p>For merged cells or multi-line cell content, use grid table
+      syntax:</p>
+      <div class="sourceCode" id="cb9"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>+----------+----------+----------+</span>
+<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="pp">|</span> Results                        <span class="pp">|</span></span>
+<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a>+========<span class="al">==+==========+==</span>========+</span>
+<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a><span class="pp">|</span> Site     <span class="pp">|</span> 2023     <span class="pp">|</span> 2024     <span class="pp">|</span></span>
+<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a>+----------+----------+----------+</span>
+<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a><span class="pp">|</span> A        <span class="pp">|</span> 100      <span class="pp">|</span> 150      <span class="pp">|</span></span>
+<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a>+----------+----------+----------+</span>
+<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a>: Annual measurements {#tbl:results}</span></code></pre></div>
+      <p>Cross-references resolve automatically at build time —
+      <code>@fig:label</code>, <code>@tbl:label</code>,
+      <code>@eq:label</code>, <code>@sec:label</code> become “Figure 1”,
+      “Table 2”, “Equation 3”, “Section 4”. Use <code>rev migrate</code>
+      to convert hardcoded references (Fig. 1, Table 2) to dynamic ones
+      if you’re importing an existing document.</p>
+      <hr />
+      <h2 id="building-and-sharing">Building and Sharing</h2>
+      <div class="sourceCode" id="cb10"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build docx        <span class="co"># → output/my-paper.docx</span></span>
+<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build pdf         <span class="co"># → output/my-paper.pdf</span></span>
+<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build docx pdf    <span class="co"># both at once</span></span></code></pre></div>
+      <p>Set a journal profile to get the right citation style and PDF
+      formatting automatically:</p>
+      <div class="sourceCode" id="cb11"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build pdf <span class="at">-j</span> nature</span></code></pre></div>
+      <p>Six profiles include formatting defaults — <code>nature</code>,
+      <code>science</code>, <code>cell</code>, <code>pnas</code>,
+      <code>plos-one</code>, <code>elife</code>. All 21 support
+      validation. To see the full list:</p>
+      <div class="sourceCode" id="cb12"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> validate <span class="at">--list</span></span></code></pre></div>
+      <p>For a live preview while you write:</p>
+      <div class="sourceCode" id="cb13"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> watch docx    <span class="co"># rebuilds on every save</span></span></code></pre></div>
+      <hr />
+      <h2 id="syncing-reviewer-feedback">Syncing Reviewer Feedback</h2>
+      <p>When a reviewer returns a Word document with track changes and
+      comments:</p>
+      <div class="sourceCode" id="cb14"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> sync reviewed.docx</span></code></pre></div>
+      <p>Track changes become CriticMarkup annotations inline in your
+      section files:</p>
+      <div class="sourceCode" id="cb15"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a>The sample size was {--100--}{++150++} participants.</span>
+<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a>Data was collected {~~monthly~&gt;weekly~~}.</span></code></pre></div>
+      <p>Comments land with the reviewer’s name:</p>
+      <div class="sourceCode" id="cb16"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>{&gt;&gt;Reviewer 2: The confidence intervals here seem too narrow. Please clarify.&lt;&lt;}</span></code></pre></div>
+      <p>If your markdown has changed since you sent the document out —
+      new edits, reordered sections — run
+      <code>rev verify-anchors</code> first to see which comments will
+      land cleanly against the updated prose, then use
+      <code>--comments-only</code> to import only comments (not track
+      changes, which would overwrite your newer edits):</p>
+      <div class="sourceCode" id="cb17"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> verify-anchors reviewed.docx</span>
+<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> sync reviewed.docx <span class="at">--comments-only</span></span></code></pre></div>
+      <p>For reviewers who annotate PDFs rather than Word files:</p>
+      <div class="sourceCode" id="cb18"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> sync annotated.pdf</span></code></pre></div>
+      <p>Supported annotation types: sticky notes, text boxes,
+      highlights, underlines, strikethrough, squiggly underlines. Use
+      <code>rev pdf-comments annotated.pdf --with-text</code> to extract
+      the text that was highlighted or struck through.</p>
+      <hr />
+      <h2 id="track-changes">Track Changes</h2>
+      <p>List what’s pending:</p>
+      <div class="sourceCode" id="cb19"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> accept methods.md</span></code></pre></div>
+      <p>Accept or reject individually, or all at once:</p>
+      <div class="sourceCode" id="cb20"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> accept methods.md <span class="at">-n</span> 1    <span class="co"># accept change #1</span></span>
+<span id="cb20-2"><a href="#cb20-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> reject methods.md <span class="at">-n</span> 2    <span class="co"># reject change #2</span></span>
+<span id="cb20-3"><a href="#cb20-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> accept methods.md <span class="at">-a</span>      <span class="co"># accept all</span></span></code></pre></div>
+      <p>For an interactive review with keyboard shortcuts
+      (a/r/s/q):</p>
+      <div class="sourceCode" id="cb21"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> review methods.md</span></code></pre></div>
+      <hr />
+      <h2 id="comments">Comments</h2>
+      <p>Navigate pending comments:</p>
+      <div class="sourceCode" id="cb22"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> todo                         <span class="co"># list all pending as a checklist</span></span>
+<span id="cb22-2"><a href="#cb22-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> next                         <span class="co"># show the next one</span></span>
+<span id="cb22-3"><a href="#cb22-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> next <span class="at">-n</span> 3                    <span class="co"># skip to the 3rd</span></span>
+<span id="cb22-4"><a href="#cb22-4" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> comments methods.md          <span class="co"># all comments in one section, with context</span></span>
+<span id="cb22-5"><a href="#cb22-5" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> comments methods.md <span class="at">--author</span> <span class="st">&quot;Reviewer 2&quot;</span></span></code></pre></div>
+      <p>Reply with your name set once in config:</p>
+      <div class="sourceCode" id="cb23"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> config user <span class="st">&quot;Your Name&quot;</span></span>
+<span id="cb23-2"><a href="#cb23-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> reply methods.md <span class="at">-n</span> 1 <span class="at">-m</span> <span class="st">&quot;Added clarification in the revised text.&quot;</span></span></code></pre></div>
+      <p>The reply appears adjacent to the original:</p>
+      <div class="sourceCode" id="cb24"><pre
+      class="sourceCode markdown"><code class="sourceCode markdown"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a>{&gt;&gt;Reviewer 2: The confidence intervals seem too narrow.&lt;&lt;} {&gt;&gt;Your Name: Clarified; the intervals are bootstrap CIs at 95%.&lt;&lt;}</span></code></pre></div>
+      <p>Adjacent comments from different authors thread in Word
+      automatically. Comments must be adjacent — no text between them —
+      for threading to work.</p>
+      <p>Mark addressed:</p>
+      <div class="sourceCode" id="cb25"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> resolve methods.md <span class="at">-n</span> 1</span></code></pre></div>
+      <hr />
+      <h2 id="multiple-reviewers">Multiple Reviewers</h2>
+      <p>When several reviewers return separate files,
+      <code>rev merge</code> reconciles them against a shared
+      baseline:</p>
+      <div class="sourceCode" id="cb26"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> merge reviewer_A.docx reviewer_B.docx</span></code></pre></div>
+      <p>docrev compares each file against <code>.rev/base.docx</code>
+      (saved automatically on every build) to isolate each reviewer’s
+      changes. Conflicts on the same passage are flagged for interactive
+      resolution.</p>
+      <hr />
+      <h2 id="rebuilding-and-responding">Rebuilding and Responding</h2>
+      <p>Once you’ve handled the feedback, rebuild:</p>
+      <div class="sourceCode" id="cb27"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build docx <span class="at">--dual</span></span></code></pre></div>
+      <p>This produces two files — <code>my-paper.docx</code> (clean,
+      for submission or the next round) and
+      <code>my-paper_comments.docx</code> (with your replies threaded
+      under the original Word comments). The same flag works for PDF,
+      rendering comments as LaTeX margin notes:</p>
+      <div class="sourceCode" id="cb28"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> build pdf <span class="at">--dual</span></span></code></pre></div>
+      <p>Generate a point-by-point response letter from the resolved
+      comments:</p>
+      <div class="sourceCode" id="cb29"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb29-1"><a href="#cb29-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> response <span class="op">&gt;</span> response-letter.md</span></code></pre></div>
+      <hr />
+      <h2 id="archiving-and-repeating">Archiving and Repeating</h2>
+      <p>Move reviewer files out of the project folder:</p>
+      <div class="sourceCode" id="cb30"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb30-1"><a href="#cb30-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> archive                    <span class="co"># → archive/20241215_143022_reviewed.docx</span></span>
+<span id="cb30-2"><a href="#cb30-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> archive <span class="at">--by</span> Smith         <span class="co"># → archive/20241215_143022_Smith_my-paper.docx</span></span>
+<span id="cb30-3"><a href="#cb30-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> archive <span class="at">--dry-run</span>          <span class="co"># preview without moving</span></span></code></pre></div>
+      <p>Take a snapshot before a major revision round:</p>
+      <div class="sourceCode" id="cb31"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb31-1"><a href="#cb31-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> backup <span class="at">--name</span> <span class="st">&quot;before-round-2&quot;</span></span></code></pre></div>
+      <p>The cycle continues: receive feedback, sync, handle changes and
+      comments, rebuild, archive.</p>
+      <hr />
+      <h2 id="pre-submission-checks">Pre-Submission Checks</h2>
+      <div class="sourceCode" id="cb32"><pre
+      class="sourceCode bash"><code class="sourceCode bash"><span id="cb32-1"><a href="#cb32-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> check                       <span class="co"># full check: lint, citations, grammar</span></span>
+<span id="cb32-2"><a href="#cb32-2" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> doi check references.bib    <span class="co"># validate all DOIs</span></span>
+<span id="cb32-3"><a href="#cb32-3" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> validate <span class="at">-j</span> nature          <span class="co"># journal-specific requirements</span></span>
+<span id="cb32-4"><a href="#cb32-4" aria-hidden="true" tabindex="-1"></a><span class="fu">rev</span> word-count <span class="at">-j</span> nature        <span class="co"># check against word limit</span></span></code></pre></div>
+      <p>For journals with strict requirements, running
+      <code>rev validate --list</code> shows which profiles are
+      available and which include formatting support
+      (<code>[formatting]</code> tag).</p>
+      <hr />
+      <h2 id="quick-reference">Quick Reference</h2>
+      <table>
+      <colgroup>
+      <col style="width: 40%" />
+      <col style="width: 60%" />
+      </colgroup>
+      <thead>
+      <tr>
+      <th>Task</th>
+      <th>Command</th>
+      </tr>
+      </thead>
+      <tbody>
+      <tr>
+      <td>Start from Word</td>
+      <td><code>rev import manuscript.docx</code></td>
+      </tr>
+      <tr>
+      <td>Start fresh</td>
+      <td><code>rev new my-paper</code></td>
+      </tr>
+      <tr>
+      <td>Build DOCX</td>
+      <td><code>rev build docx</code></td>
+      </tr>
+      <tr>
+      <td>Build clean + annotated</td>
+      <td><code>rev build docx --dual</code></td>
+      </tr>
+      <tr>
+      <td>Build PDF</td>
+      <td><code>rev build pdf</code></td>
+      </tr>
+      <tr>
+      <td>Sync feedback</td>
+      <td><code>rev sync reviewed.docx</code></td>
+      </tr>
+      <tr>
+      <td>Sync comments only (prose changed)</td>
+      <td><code>rev sync reviewed.docx --comments-only</code></td>
+      </tr>
+      <tr>
+      <td>Check anchor drift</td>
+      <td><code>rev verify-anchors reviewed.docx</code></td>
+      </tr>
+      <tr>
+      <td>Project status</td>
+      <td><code>rev status</code></td>
+      </tr>
+      <tr>
+      <td>List pending</td>
+      <td><code>rev todo</code></td>
+      </tr>
+      <tr>
+      <td>Next comment</td>
+      <td><code>rev next</code></td>
+      </tr>
+      <tr>
+      <td>Accept all changes</td>
+      <td><code>rev accept file.md -a</code></td>
+      </tr>
+      <tr>
+      <td>Reply to comment</td>
+      <td><code>rev reply file.md -n 1 -m "..."</code></td>
+      </tr>
+      <tr>
+      <td>Archive reviewer files</td>
+      <td><code>rev archive</code></td>
+      </tr>
+      <tr>
+      <td>Response letter</td>
+      <td><code>rev response</code></td>
+      </tr>
+      <tr>
+      <td>Pre-submit check</td>
+      <td><code>rev check</code></td>
+      </tr>
+      </tbody>
+      </table>
+    </main>
+    <aside class="col-md-3 d-none d-md-block">
+      <nav id="toc" data-toggle="toc" aria-label="On this page">
+        <h2 class="h6">On this page</h2>
+        <div class="toc"><ul>
+<li><a href="#revision-workflow" id="toc-revision-workflow">Revision
+Workflow</a>
+<ul>
+<li><a href="#starting-a-project" id="toc-starting-a-project">Starting a
+Project</a></li>
+<li><a href="#writing-in-markdown" id="toc-writing-in-markdown">Writing
+in Markdown</a></li>
+<li><a href="#building-and-sharing"
+id="toc-building-and-sharing">Building and Sharing</a></li>
+<li><a href="#syncing-reviewer-feedback"
+id="toc-syncing-reviewer-feedback">Syncing Reviewer Feedback</a></li>
+<li><a href="#track-changes" id="toc-track-changes">Track
+Changes</a></li>
+<li><a href="#comments" id="toc-comments">Comments</a></li>
+<li><a href="#multiple-reviewers" id="toc-multiple-reviewers">Multiple
+Reviewers</a></li>
+<li><a href="#rebuilding-and-responding"
+id="toc-rebuilding-and-responding">Rebuilding and Responding</a></li>
+<li><a href="#archiving-and-repeating"
+id="toc-archiving-and-repeating">Archiving and Repeating</a></li>
+<li><a href="#pre-submission-checks"
+id="toc-pre-submission-checks">Pre-Submission Checks</a></li>
+<li><a href="#quick-reference" id="toc-quick-reference">Quick
+Reference</a></li>
+</ul></li>
+</ul></div>
+      </nav>
+    </aside>
+  </div>
+</div>
+
+<footer class="border-top py-3 mt-auto">
+  <div class="container d-flex justify-content-between align-items-center text-muted" style="font-size:.85rem">
+    <span>docrev 0.9.15</span>
+    <span>Built with <a href="https://pandoc.org" class="text-muted">pandoc</a></span>
+  </div>
+</footer>
+
+<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
+<script>
+(function () {
+  var html  = document.documentElement;
+  var sun   = document.getElementById('icon-sun');
+  var moon  = document.getElementById('icon-moon');
+  function apply(t) {
+    html.setAttribute('data-bs-theme', t);
+    sun.style.display  = t === 'dark' ? 'none' : '';
+    moon.style.display = t === 'dark' ? ''     : 'none';
+  }
+  apply(localStorage.getItem('docrev-theme') || 'light');
+  document.getElementById('theme-toggle').addEventListener('click', function () {
+    var next = html.getAttribute('data-bs-theme') === 'dark' ? 'light' : 'dark';
+    localStorage.setItem('docrev-theme', next);
+    apply(next);
+  });
+})();
+</script>
+
+</body>
+</html>

dist/lib/anchor-match.d.ts

@@ -7,3 +7,3 @@ /**
  */
-export type AnchorStrategy = 'direct' | 'normalized' | 'stripped' | 'partial-start' | 'partial-start-stripped' | 'partial-window' | 'partial-window-stripped' | 'context-both' | 'context-before' | 'context-after' | 'split-match' | 'empty-anchor' | 'failed';
+export type AnchorStrategy = 'direct' | 'normalized' | 'stripped' | 'partial-start' | 'partial-start-stripped' | 'context-both' | 'context-before' | 'context-after' | 'split-match' | 'empty-anchor' | 'failed';
 export interface AnchorSearchResult {
@@ -10,0 +10,0 @@ occurrences: number[];

dist/lib/anchor-match.d.ts.map

@@ -1,1 +0,1 @@
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+{"version":3,"file":"anchor-match.d.ts","sourceRoot":"","sources":["../../lib/anchor-match.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,MAAM,MAAM,cAAc,GACtB,QAAQ,GACR,YAAY,GACZ,UAAU,GACV,eAAe,GACf,wBAAwB,GACxB,cAAc,GACd,gBAAgB,GAChB,eAAe,GACf,aAAa,GACb,cAAc,GACd,QAAQ,CAAC;AAEb,MAAM,WAAW,kBAAkB;IACjC,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,QAAQ,EAAE,cAAc,CAAC;IACzB,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAOtD;AAED;;;;GAIG;AACH;;;;;;;;GAQG;AACH,wBAAgB,cAAc,CAC5B,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM,GAChB,MAAM,CAqBR;AAED,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,EAAE,CAS7E;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAC9B,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,MAAM,EACZ,MAAM,GAAE,MAAW,EACnB,KAAK,GAAE,MAAW,GACjB,kBAAkB,CA2IpB;AAED;;;GAGG;AACH,MAAM,MAAM,kBAAkB,GAAG,OAAO,GAAG,OAAO,GAAG,cAAc,GAAG,WAAW,CAAC;AAElF,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,cAAc,EAAE,WAAW,EAAE,MAAM,GAAG,kBAAkB,CAoBlG"}

dist/lib/anchor-match.js

@@ -136,25 +136,20 @@ /**
     }
-    // Strategy 4: word window from anchor (prefix or interior).
-    // Sliding the window across the anchor catches the case where the
-    // anchor's prefix has been edited but a chunk in the middle/end
-    // survived intact (e.g. "Sensitivity analyses were performed by
-    // perturbing the prior variance" → drifted "Sensitivity analyses
-    // perturbed the prior variance" still contains "the prior variance").
+    // Strategy 4: first N words of anchor (long anchors)
     const words = anchor.split(/\s+/);
     if (words.length > 3) {
         for (let n = Math.min(6, words.length); n >= 3; n--) {
-            for (let start = 0; start + n <= words.length; start++) {
-                const window = words.slice(start, start + n).join(' ');
-                const windowLower = window.toLowerCase();
-                if (windowLower.length < 15)
-                    continue;
-                let occ = findAllOccurrences(textLower, windowLower);
-                if (occ.length > 0) {
-                    const strategy = start === 0 ? 'partial-start' : 'partial-window';
-                    return { occurrences: occ, matchedAnchor: window, strategy };
+            const partialAnchor = words.slice(0, n).join(' ').toLowerCase();
+            if (partialAnchor.length >= 15) {
+                occurrences = findAllOccurrences(textLower, partialAnchor);
+                if (occurrences.length > 0) {
+                    return { occurrences, matchedAnchor: words.slice(0, n).join(' '), strategy: 'partial-start' };
                 }
-                occ = findAllOccurrences(strippedLower, windowLower);
-                if (occ.length > 0) {
-                    const strategy = start === 0 ? 'partial-start-stripped' : 'partial-window-stripped';
-                    return { occurrences: occ, matchedAnchor: window, strategy, stripped: true };
+                occurrences = findAllOccurrences(strippedLower, partialAnchor);
+                if (occurrences.length > 0) {
+                    return {
+                        occurrences,
+                        matchedAnchor: words.slice(0, n).join(' '),
+                        strategy: 'partial-start-stripped',
+                        stripped: true,
+                    };
                 }
@@ -164,16 +159,6 @@ }
     }
-    // Strategy 5: context (before/after) only.
-    //
-    // For a non-empty anchor that already failed every text-based strategy
-    // above, we treat context as a degraded placement: classify it
-    // 'context-only' so callers can warn the user. We also reject
-    // implausible brackets — if both contexts match but the gap between
-    // them is far too small to contain the anchor (e.g. the anchored
-    // sentence was deleted), do not silently land the comment between
-    // the surviving sentences. Return 'failed' so the user is told to
-    // place it manually.
+    // Strategy 5: context (before/after) only
     if (before || after) {
         const beforeLower = before.toLowerCase();
         const afterLower = after.toLowerCase();
-        const anchorLen = anchor.length;
         if (before && after) {
@@ -184,17 +169,4 @@ const beforeIdx = textLower.indexOf(beforeLower.slice(-50));
                 const afterIdx = textLower.indexOf(afterLower.slice(0, 50), searchStart);
-                if (afterIdx !== -1) {
-                    const gap = afterIdx - searchStart;
-                    // Require the bracket to plausibly contain a remnant of the anchor.
-                    // Below 30% of anchor length: anchor was deleted — refuse to place.
-                    // Above 2× anchor length + slack: brackets are too far apart, the
-                    // matcher has latched onto unrelated repeats of common context.
-                    const minGap = Math.floor(anchorLen * 0.3);
-                    const maxGap = Math.min(500, anchorLen * 2 + 50);
-                    if (gap >= minGap && gap <= maxGap) {
-                        return { occurrences: [searchStart], matchedAnchor: null, strategy: 'context-both' };
-                    }
-                    // Both brackets found but gap implausible: anchor likely deleted.
-                    // Don't fall back to single-side context — that would silently
-                    // place the comment in the wrong location.
-                    return { occurrences: [], matchedAnchor: null, strategy: 'failed' };
+                if (afterIdx !== -1 && afterIdx - searchStart < 500) {
+                    return { occurrences: [searchStart], matchedAnchor: null, strategy: 'context-both' };
                 }
@@ -246,4 +218,2 @@ }
         case 'partial-start-stripped':
-        case 'partial-window':
-        case 'partial-window-stripped':
         case 'split-match':
@@ -250,0 +220,0 @@ return 'drift';

dist/lib/anchor-match.js.map

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dist/lib/build.d.ts

@@ -40,2 +40,4 @@ /**
     monofont?: string;
+    /** Extra pandoc args appended for this format (after top-level pandocArgs). */
+    pandocArgs?: string[];
 }
@@ -47,5 +49,14 @@ export interface DocxConfig {
     toc?: boolean;
+    pandocArgs?: string[];
+    /**
+     * Auto-translate the common-shape raw `\begin{figure}...\end{figure}` block
+     * to portable `![caption](path){#fig:label width=N%}` markdown so figures
+     * survive the docx build (pandoc otherwise drops raw LaTeX silently).
+     * Default true. Set false to opt out — blocks then warn and are left alone.
+     */
+    translateRawFigures?: boolean;
 }
 export interface TexConfig {
     standalone?: boolean;
+    pandocArgs?: string[];
 }
@@ -61,2 +72,3 @@ export interface BeamerConfig {
     fit_images?: boolean;
+    pandocArgs?: string[];
 }
@@ -76,2 +88,3 @@ export interface PptxConfig {
     };
+    pandocArgs?: string[];
 }
@@ -111,2 +124,15 @@ export interface TablesConfig {
     outputDir?: string | null;
+    /**
+     * Per-format output filenames. Keys are format names (pdf/docx/tex/beamer/
+     * pptx); values are paths. Relative paths resolve under outputDir; absolute
+     * paths are honored as-is. Extension is added if missing. CLI `-o` wins
+     * over this map.
+     */
+    output?: Record<string, string>;
+    /**
+     * Extra pandoc args applied to every format. Format-specific args
+     * (e.g. docx.pandocArgs) are appended *after* these, and CLI --pandoc-arg
+     * values are appended last.
+     */
+    pandocArgs?: string[];
     _configPath?: string | null;
@@ -123,4 +149,16 @@ }
     config?: BuildConfig;
+    /**
+     * Internal: forces the exact output path. Used by dual-mode/temp builds that
+     * route to specific temp files. Bypasses the `output:` resolver.
+     */
     outputPath?: string;
+    /**
+     * CLI override (`-o, --output <path>`). Beats `config.output[format]` but
+     * loses to `options.outputPath`. Relative paths resolve under outputDir;
+     * absolute paths bypass outputDir.
+     */
+    output?: string;
     crossref?: boolean;
+    /** Extra pandoc args from CLI (--pandoc-arg). Appended after config args. */
+    pandocArgs?: string[];
     _refsAutoInjected?: boolean;
@@ -213,6 +251,51 @@ _forwardRefsResolved?: number;
 /**
- * Build pandoc arguments for format
+ * A raw LaTeX `\begin{figure}...\end{figure}` block found in source markdown.
+ * `exotic` blocks contain features we don't auto-translate (multiple
+ * `\includegraphics`, `\subfloat`, `\rotatebox`, unrecognised width units);
+ * pandoc strips raw LaTeX silently in docx output, so users get warned about
+ * anything that won't be translated.
  */
+export interface RawLatexFigure {
+    file?: string;
+    line: number;
+    block: string;
+    exotic: boolean;
+}
+/**
+ * Find raw LaTeX figure blocks containing `\includegraphics` in markdown.
+ * `file`, if given, is attached to each result. `line` is 1-based within the
+ * supplied content (the line where `\begin{figure}` sits).
+ */
+export declare function detectRawLatexFigures(content: string, file?: string): RawLatexFigure[];
+/**
+ * Translate the 80% case: single `\includegraphics` figure with optional
+ * `\caption{...}` and `\label{...}`, wrapped in `\begin{figure}...\end{figure}`,
+ * to portable `![caption](path){#fig:label width=N%}` markdown. Exotic blocks
+ * (see `isExoticFigureBlock`) are left untouched.
+ */
+export declare function translateRawLatexFigures(content: string): {
+    translated: string;
+    translatedCount: number;
+};
+/**
+ * Walk section files and gather a warning for any raw LaTeX figure blocks that
+ * won't survive the docx build. Returns null when there's nothing to warn about.
+ */
+export declare function collectRawLatexFigureWarning(directory: string, config: BuildConfig): string | null;
+/**
+ * Build pandoc arguments for format.
+ *
+ * Returns only the built-in args derived from config. Passthrough args
+ * (config.pandocArgs, config[format].pandocArgs, CLI --pandoc-arg) are
+ * appended later in runPandoc so they win against pptx/crossref defaults
+ * added there.
+ */
 export declare function buildPandocArgs(format: string, config: BuildConfig, outputPath: string): string[];
 /**
+ * Collect passthrough pandoc args for a format in the canonical order:
+ * top-level config → format-specific config → CLI extras. Later wins for
+ * repeated flags.
+ */
+export declare function collectPandocPassthroughArgs(format: string, config: BuildConfig, extraArgs?: string[]): string[];
+/**
  * Resolve the absolute directory where final outputs should land.
@@ -222,3 +305,30 @@ * Honors config.outputDir; falls back to the project directory when null/empty.
 export declare function resolveOutputDir(directory: string, config: BuildConfig): string;
+/** Get file extension for a format, defaulting to `.pdf`. */
+export declare function getFormatExtension(format: string): string;
 /**
+ * Slugify a title for use as a default output filename. Lowercases, replaces
+ * non-alphanumeric runs with `-`, and truncates at the last `-` boundary
+ * at-or-before MAX_TITLE_FILENAME_LENGTH so words stay whole (the old blind
+ * `.slice` cut mid-word).
+ */
+export declare function slugifyTitle(title: string): string;
+/**
+ * Resolve the final output path for a build.
+ *
+ * Priority: `options.outputPath` (internal force) > `cliOverride` (-o flag) >
+ * `config.output[format]` > slugified title fallback.
+ *
+ * Relative paths from `cliOverride`/`config.output` resolve under outputDir;
+ * absolute paths bypass outputDir. The fallback path always lives under
+ * outputDir.
+ *
+ * @param suffix - Appended before the extension (e.g. "-changes", "-slides").
+ *                 Suppressed when user supplied an explicit name via CLI or
+ *                 config — they pick their own suffix.
+ */
+export declare function resolveOutputPath(directory: string, config: BuildConfig, format: string, options?: {
+    cliOverride?: string;
+    suffix?: string;
+}): string;
+/**
  * Run pandoc build
@@ -225,0 +335,0 @@ */

dist/lib/build.d.ts.map

@@ -1,1 +0,1 @@
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dist/lib/build.js

@@ -30,5 +30,10 @@ /**
 const SUPPORTED_FORMATS = ['pdf', 'docx', 'tex', 'beamer', 'pptx'];
-/** Maximum title length for output filename */
-const MAX_TITLE_FILENAME_LENGTH = 50;
 /**
+ * Maximum length for slugified-title output filenames. Only used when no
+ * explicit `output:` filename is configured. Long titles are truncated at the
+ * last `-` boundary at-or-before this length so words stay intact (the old
+ * blind `.slice(0, 50)` cut mid-word).
+ */
+const MAX_TITLE_FILENAME_LENGTH = 80;
+/**
  * Default rev.yaml configuration
@@ -65,2 +70,3 @@ */
         toc: false,
+        translateRawFigures: true,
     },
@@ -164,2 +170,17 @@ tex: {
 /**
+ * In-place: copy `pandoc-args` → `pandocArgs` on an object (if not already set).
+ * Idempotent. Coerces a single string into a one-element array.
+ */
+function normalizePandocArgsKey(obj) {
+    if (!obj || typeof obj !== 'object')
+        return;
+    const hy = obj['pandoc-args'];
+    if (hy === undefined)
+        return;
+    if (obj.pandocArgs === undefined) {
+        obj.pandocArgs = Array.isArray(hy) ? hy : [hy];
+    }
+    delete obj['pandoc-args'];
+}
+/**
  * Load rev.yaml config from directory
@@ -182,2 +203,11 @@ * @param directory - Project directory path
         const userConfig = YAML.parse(content) || {};
+        // Accept hyphenated `pandoc-args` (the form pandoc itself uses) in addition
+        // to camelCase `pandocArgs`. Hyphenated is what we document; camelCase is
+        // accepted for users who already prefer that convention.
+        normalizePandocArgsKey(userConfig);
+        for (const fmt of ['pdf', 'docx', 'tex', 'beamer', 'pptx']) {
+            if (userConfig[fmt] && typeof userConfig[fmt] === 'object') {
+                normalizePandocArgsKey(userConfig[fmt]);
+            }
+        }
         // Deep merge with defaults
@@ -583,2 +613,9 @@ let config = {
         content = convertDynamicRefsToDisplay(content, registry);
+        // Pandoc strips raw LaTeX in docx output. Translate the common
+        // `\begin{figure}...\end{figure}` shape to portable markdown so figures
+        // actually appear; exotic blocks are left alone (warned about in build()).
+        if (config.docx?.translateRawFigures !== false) {
+            const { translated } = translateRawLatexFigures(content);
+            content = translated;
+        }
         if (hasNumberedAffiliations(config)) {
@@ -637,5 +674,199 @@ const mdBlock = generateMarkdownAuthorBlock(config);
 }
+/** Match `\begin{figure}` / `\begin{figure*}` … `\end{figure}` blocks. */
+function makeRawFigureRegex() {
+    return /\\begin\{figure\*?\}(?:\[[^\]]*\])?[\s\S]*?\\end\{figure\*?\}/g;
+}
 /**
- * Build pandoc arguments for format
+ * Convert a LaTeX width spec to a markdown image attribute value.
+ * - `0.8\textwidth` → `80%`
+ * - `\linewidth` → `100%`
+ * - `8cm`, `2in`, `12pt` → kept verbatim
+ * Returns null for anything we don't translate (block stays "exotic").
  */
+function convertLatexWidth(raw) {
+    const trimmed = raw.trim();
+    // Coefficient × relative length
+    const rel = trimmed.match(/^([\d.]+)\s*\\(textwidth|linewidth|columnwidth)$/);
+    if (rel) {
+        const pct = Math.round(parseFloat(rel[1]) * 100);
+        if (!isFinite(pct) || pct <= 0)
+            return null;
+        return `${pct}%`;
+    }
+    // Bare relative length
+    if (/^\\(textwidth|linewidth|columnwidth)$/.test(trimmed))
+        return '100%';
+    // Absolute units
+    if (/^[\d.]+\s*(cm|mm|in|pt|px|em|ex)$/.test(trimmed))
+        return trimmed.replace(/\s+/g, '');
+    return null;
+}
+/** Extract a balanced `{...}` argument that follows `command` in `text`. */
+function extractBracedArg(text, command) {
+    const idx = text.indexOf(command);
+    if (idx === -1)
+        return null;
+    let i = idx + command.length;
+    while (i < text.length && /\s/.test(text[i]))
+        i++;
+    if (text[i] !== '{')
+        return null;
+    i++;
+    const start = i;
+    let depth = 1;
+    while (i < text.length) {
+        const ch = text[i];
+        if (ch === '\\' && i + 1 < text.length) {
+            i += 2;
+            continue;
+        }
+        if (ch === '{')
+            depth++;
+        else if (ch === '}') {
+            depth--;
+            if (depth === 0)
+                return text.slice(start, i);
+        }
+        i++;
+    }
+    return null;
+}
+/** True if a `\begin{figure}` block contains features we don't auto-translate. */
+function isExoticFigureBlock(block) {
+    if (/\\subfloat\b/.test(block))
+        return true;
+    if (/\\rotatebox\b/.test(block))
+        return true;
+    const includes = (block.match(/\\includegraphics\b/g) || []).length;
+    if (includes !== 1)
+        return true;
+    const m = block.match(/\\includegraphics\s*(?:\[([^\]]*)\])?\s*\{([^}]+)\}/);
+    if (!m)
+        return true;
+    const opts = m[1] || '';
+    const widthMatch = opts.match(/(?:^|,)\s*width\s*=\s*([^,]+)/);
+    if (widthMatch && !convertLatexWidth(widthMatch[1]))
+        return true;
+    return false;
+}
+/**
+ * Find raw LaTeX figure blocks containing `\includegraphics` in markdown.
+ * `file`, if given, is attached to each result. `line` is 1-based within the
+ * supplied content (the line where `\begin{figure}` sits).
+ */
+export function detectRawLatexFigures(content, file) {
+    const figures = [];
+    const re = makeRawFigureRegex();
+    let m;
+    while ((m = re.exec(content)) !== null) {
+        const block = m[0];
+        if (!block.includes('\\includegraphics'))
+            continue;
+        const line = content.slice(0, m.index).split(/\r?\n/).length;
+        figures.push({ file, line, block, exotic: isExoticFigureBlock(block) });
+    }
+    return figures;
+}
+/**
+ * Translate the 80% case: single `\includegraphics` figure with optional
+ * `\caption{...}` and `\label{...}`, wrapped in `\begin{figure}...\end{figure}`,
+ * to portable `![caption](path){#fig:label width=N%}` markdown. Exotic blocks
+ * (see `isExoticFigureBlock`) are left untouched.
+ */
+export function translateRawLatexFigures(content) {
+    let translatedCount = 0;
+    const re = makeRawFigureRegex();
+    const translated = content.replace(re, (block) => {
+        if (!block.includes('\\includegraphics'))
+            return block;
+        if (isExoticFigureBlock(block))
+            return block;
+        const inc = block.match(/\\includegraphics\s*(?:\[([^\]]*)\])?\s*\{([^}]+)\}/);
+        if (!inc)
+            return block;
+        const optsStr = inc[1] || '';
+        const imgPath = inc[2].trim();
+        let width;
+        const widthMatch = optsStr.match(/(?:^|,)\s*width\s*=\s*([^,]+)/);
+        if (widthMatch) {
+            const w = convertLatexWidth(widthMatch[1]);
+            if (!w)
+                return block; // already filtered by isExoticFigureBlock, defensive
+            width = w;
+        }
+        const caption = (extractBracedArg(block, '\\caption') ?? '').trim();
+        const labelRaw = extractBracedArg(block, '\\label');
+        const attrs = [];
+        if (labelRaw) {
+            const label = labelRaw.trim();
+            const labelWithPrefix = /^[a-z]+:/i.test(label) ? label : `fig:${label}`;
+            attrs.push(`#${labelWithPrefix}`);
+        }
+        if (width)
+            attrs.push(`width=${width}`);
+        translatedCount++;
+        const attrStr = attrs.length > 0 ? ` {${attrs.join(' ')}}` : '';
+        return `![${caption}](${imgPath})${attrStr}`;
+    });
+    return { translated, translatedCount };
+}
+/**
+ * Format the warning surfaced for raw LaTeX figure blocks that won't render
+ * in docx. `translateEnabled` reflects whether auto-translate ran (true = the
+ * listed blocks are exotic leftovers; false = no translation was attempted).
+ */
+function formatRawLatexFigureWarning(figs, translateEnabled) {
+    const reason = translateEnabled ? 'too complex to auto-translate' : 'translateRawFigures: false';
+    const lines = [
+        `${figs.length} raw LaTeX figure block(s) won't render in docx (${reason}).`,
+    ];
+    for (const f of figs) {
+        const loc = f.file ? `${f.file}:${f.line}` : `line ${f.line}`;
+        const pathMatch = f.block.match(/\\includegraphics\s*(?:\[[^\]]*\])?\s*\{([^}]+)\}/);
+        const pathInfo = pathMatch ? `  ${pathMatch[1].trim()}` : '';
+        lines.push(`  ${loc}${pathInfo}`);
+    }
+    lines.push('  Hint: use ![caption](path){#fig:label width=80%} for format-portable figures,');
+    lines.push('        or pass --pandoc-arg=--lua-filter=<your.lua> to translate them yourself.');
+    return lines.join('\n');
+}
+/**
+ * Walk section files and gather a warning for any raw LaTeX figure blocks that
+ * won't survive the docx build. Returns null when there's nothing to warn about.
+ */
+export function collectRawLatexFigureWarning(directory, config) {
+    const translateEnabled = config.docx?.translateRawFigures !== false;
+    const all = [];
+    for (const section of findSections(directory, config.sections)) {
+        const sectionPath = path.join(directory, section);
+        if (!fs.existsSync(sectionPath))
+            continue;
+        try {
+            const content = fs.readFileSync(sectionPath, 'utf-8');
+            const figs = detectRawLatexFigures(content, section);
+            for (const f of figs) {
+                // When auto-translate is on, non-exotic blocks get rewritten cleanly —
+                // only the exotic leftovers need warning. When opted out, everything
+                // is at risk and we warn about every block.
+                if (translateEnabled && !f.exotic)
+                    continue;
+                all.push(f);
+            }
+        }
+        catch {
+            // ignore unreadable sections
+        }
+    }
+    if (all.length === 0)
+        return null;
+    return formatRawLatexFigureWarning(all, translateEnabled);
+}
+/**
+ * Build pandoc arguments for format.
+ *
+ * Returns only the built-in args derived from config. Passthrough args
+ * (config.pandocArgs, config[format].pandocArgs, CLI --pandoc-arg) are
+ * appended later in runPandoc so they win against pptx/crossref defaults
+ * added there.
+ */
 export function buildPandocArgs(format, config, outputPath) {
@@ -758,2 +989,21 @@ const args = [];
 /**
+ * Collect passthrough pandoc args for a format in the canonical order:
+ * top-level config → format-specific config → CLI extras. Later wins for
+ * repeated flags.
+ */
+export function collectPandocPassthroughArgs(format, config, extraArgs = []) {
+    const out = [];
+    if (config.pandocArgs && config.pandocArgs.length > 0) {
+        out.push(...config.pandocArgs);
+    }
+    const formatConfig = config[format];
+    if (formatConfig?.pandocArgs && formatConfig.pandocArgs.length > 0) {
+        out.push(...formatConfig.pandocArgs);
+    }
+    if (extraArgs.length > 0) {
+        out.push(...extraArgs);
+    }
+    return out;
+}
+/**
  * Write crossref.yaml if needed
@@ -787,3 +1037,81 @@ */
 }
+/** File extension (with leading dot) for each supported pandoc format. */
+const FORMAT_EXTENSIONS = {
+    tex: '.tex',
+    pdf: '.pdf',
+    docx: '.docx',
+    beamer: '.pdf',
+    pptx: '.pptx',
+};
+/** Get file extension for a format, defaulting to `.pdf`. */
+export function getFormatExtension(format) {
+    return FORMAT_EXTENSIONS[format] ?? '.pdf';
+}
 /**
+ * Slugify a title for use as a default output filename. Lowercases, replaces
+ * non-alphanumeric runs with `-`, and truncates at the last `-` boundary
+ * at-or-before MAX_TITLE_FILENAME_LENGTH so words stay whole (the old blind
+ * `.slice` cut mid-word).
+ */
+export function slugifyTitle(title) {
+    if (!title)
+        return 'paper';
+    const slug = title.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+|-+$/g, '');
+    if (!slug)
+        return 'paper';
+    if (slug.length <= MAX_TITLE_FILENAME_LENGTH)
+        return slug;
+    const cut = slug.slice(0, MAX_TITLE_FILENAME_LENGTH);
+    const lastDash = cut.lastIndexOf('-');
+    // Only truncate at a hyphen if it leaves a reasonable amount of content.
+    // Otherwise hard-cut (handles degenerate titles with no spaces at all).
+    if (lastDash >= MAX_TITLE_FILENAME_LENGTH / 2) {
+        return slug.slice(0, lastDash);
+    }
+    return cut;
+}
+/**
+ * Ensure `name` ends with `ext` (case-insensitive). If the user already supplied
+ * the correct extension, return unchanged; if they supplied none or a different
+ * one, append the format's canonical extension.
+ *
+ * Different-extension case (e.g. `output.docx` when building tex): we append
+ * rather than replace, since stripping looks like an unsafe guess. The result
+ * `output.docx.tex` is loud enough to flag the misconfiguration.
+ */
+function ensureExtension(name, ext) {
+    if (name.toLowerCase().endsWith(ext.toLowerCase()))
+        return name;
+    return name + ext;
+}
+/**
+ * Resolve the final output path for a build.
+ *
+ * Priority: `options.outputPath` (internal force) > `cliOverride` (-o flag) >
+ * `config.output[format]` > slugified title fallback.
+ *
+ * Relative paths from `cliOverride`/`config.output` resolve under outputDir;
+ * absolute paths bypass outputDir. The fallback path always lives under
+ * outputDir.
+ *
+ * @param suffix - Appended before the extension (e.g. "-changes", "-slides").
+ *                 Suppressed when user supplied an explicit name via CLI or
+ *                 config — they pick their own suffix.
+ */
+export function resolveOutputPath(directory, config, format, options = {}) {
+    const { cliOverride, suffix = '' } = options;
+    const ext = getFormatExtension(format);
+    const explicit = cliOverride ?? config.output?.[format];
+    if (explicit) {
+        const baseDir = path.isAbsolute(explicit)
+            ? path.dirname(explicit)
+            : resolveOutputDir(directory, config);
+        const baseName = path.basename(explicit);
+        const stem = baseName.replace(/\.[^./\\]+$/, '');
+        return path.join(baseDir, ensureExtension(`${stem}${suffix}`, ext));
+    }
+    const slug = slugifyTitle(config.title);
+    return path.join(resolveOutputDir(directory, config), `${slug}${suffix}${ext}`);
+}
+/**
  * Run pandoc build
@@ -793,22 +1121,11 @@ */
     const directory = path.dirname(inputPath);
-    const baseName = config.title
-        ? config.title.toLowerCase().replace(/[^a-z0-9]+/g, '-').slice(0, 50)
-        : 'paper';
-    // Map format to file extension
-    const extMap = {
-        tex: '.tex',
-        pdf: '.pdf',
-        docx: '.docx',
-        beamer: '.pdf', // beamer outputs PDF
-        pptx: '.pptx',
-    };
-    const ext = extMap[format] || '.pdf';
-    // For beamer, use -slides suffix to distinguish from regular PDF
+    // outputPath (internal force) wins over the resolver. For beamer, we keep
+    // the `-slides` suffix on the slug fallback to distinguish from a regular
+    // PDF build; when the user supplies an explicit name, they pick their own.
     const suffix = format === 'beamer' ? '-slides' : '';
-    // Allow custom output path via options. Auto-named outputs go through the
-    // configured outputDir (default 'output/'); explicit paths are honored as-is
-    // so callers can route temp/intermediate artefacts where they want.
     const outputPath = options.outputPath
-        ? options.outputPath
-        : path.join(resolveOutputDir(directory, config), `${baseName}${suffix}${ext}`);
+        ?? resolveOutputPath(directory, config, format, {
+            cliOverride: options.output,
+            suffix,
+        });
     if (!options.outputPath) {
@@ -873,4 +1190,11 @@ const outDir = path.dirname(outputPath);
     }
+    // Passthrough args go last so they win against built-in defaults.
+    args.push(...collectPandocPassthroughArgs(format, config, options.pandocArgs));
     // Input file (use basename since we set cwd to directory)
     args.push(path.basename(inputPath));
+    if (options.verbose) {
+        const quoted = args.map(a => /[\s"'$`]/.test(a) ? `"${a.replace(/"/g, '\\"')}"` : a).join(' ');
+        console.error(`[pandoc ${format}] (cwd: ${directory})`);
+        console.error(`  pandoc ${quoted}`);
+    }
     return new Promise((resolve) => {
@@ -979,2 +1303,8 @@ const pandoc = spawn('pandoc', args, {
         }
+        // Warn about raw LaTeX figure blocks that won't render in docx (pandoc
+        // drops them silently). With auto-translate on (default), this surfaces
+        // only the exotic leftovers; with it off, every block.
+        const rawFigWarning = collectRawLatexFigureWarning(directory, config);
+        if (rawFigWarning)
+            warnings.push(rawFigWarning);
     }
@@ -981,0 +1311,0 @@ const results = [];

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dist/lib/commands/build.d.ts.map

@@ -1,1 +0,1 @@
-{"version":3,"file":"build.d.ts","sourceRoot":"","sources":["../../../lib/commands/build.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAqBH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AA+BzC;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,OAAO,EAAE,GAAG,CAAC,EAAE;IAAE,OAAO,CAAC,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAqwB3E"}
+{"version":3,"file":"build.d.ts","sourceRoot":"","sources":["../../../lib/commands/build.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAqBH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAiCzC;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,OAAO,EAAE,GAAG,CAAC,EAAE;IAAE,OAAO,CAAC,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAyxB3E"}

dist/lib/commands/build.js

@@ -405,3 +405,5 @@ /**
         .option('--aspectratio <ratio>', 'Beamer aspect ratio (169, 43)')
-        .option('--verbose', 'Show detailed output including postprocess scripts')
+        .option('--pandoc-arg <arg>', 'Extra arg to pass to pandoc (repeatable). Applied to every format being built; appended after rev.yaml pandoc-args so CLI wins.', (val, prev = []) => [...prev, val], [])
+        .option('-o, --output <path>', 'Output filename or path. Relative paths resolve under outputDir; absolute paths bypass it. Extension auto-added if missing. Applied to every format being built; overrides rev.yaml output.<format>.')
+        .option('--verbose', 'Show detailed output including postprocess scripts and the pandoc invocation')
         .action(async (formats, options) => {
@@ -490,3 +492,3 @@ const dir = path.resolve(options.dir);
             }
-            const { combineSections, resolveOutputDir } = await import('../build.js');
+            const { combineSections, resolveOutputPath } = await import('../build.js');
             const { buildWithTrackChanges } = await import('../trackchanges.js');
@@ -499,9 +501,9 @@ const spin = fmt.spinner('Building with track changes...').start();
                 console.log(chalk.dim(`  ${paperPath}\n`));
-                const baseName = config.title
-                    ? config.title.toLowerCase().replace(/[^a-z0-9]+/g, '-').slice(0, 50)
-                    : 'paper';
-                const outDir = resolveOutputDir(dir, config);
+                const outputPath = resolveOutputPath(dir, config, 'docx', {
+                    cliOverride: options.output,
+                    suffix: '-changes',
+                });
+                const outDir = path.dirname(outputPath);
                 if (!fs.existsSync(outDir))
                     fs.mkdirSync(outDir, { recursive: true });
-                const outputPath = path.join(outDir, `${baseName}-changes.docx`);
                 const spinTc = fmt.spinner('Applying track changes...').start();
@@ -537,6 +539,8 @@ const result = await buildWithTrackChanges(paperPath, outputPath, {
         try {
-            const { results, paperPath, forwardRefsResolved, refsAutoInjected } = await build(dir, targetFormats, {
+            const { results, paperPath, forwardRefsResolved, refsAutoInjected, warnings } = await build(dir, targetFormats, {
                 crossref: options.crossref,
                 config,
                 verbose: options.verbose,
+                pandocArgs: options.pandocArg,
+                output: options.output,
             });
@@ -553,2 +557,13 @@ spin.stop();
             console.log('');
+            if (warnings && warnings.length > 0) {
+                for (const w of warnings) {
+                    // Each warning may span multiple lines — colour the first line as
+                    // a warning header and pass through the rest unchanged.
+                    const [head, ...rest] = w.split('\n');
+                    console.log(chalk.yellow(`Warning: ${head}`));
+                    for (const line of rest)
+                        console.log(chalk.yellow(line));
+                }
+                console.log('');
+            }
             console.log(chalk.cyan('Output:'));
@@ -608,3 +623,3 @@ console.log(formatBuildResults(results));
                         const markedDocxPath = path.join(dir, '.paper-marked.docx');
-                        const pandocResult = await runPandoc(markedPath, 'docx', config, { ...options, outputPath: markedDocxPath });
+                        const pandocResult = await runPandoc(markedPath, 'docx', config, { ...options, outputPath: markedDocxPath, pandocArgs: options.pandocArg });
                         spinBuild.stop();
@@ -685,3 +700,3 @@ if (!pandocResult.success) {
                         spinPdf.text = 'Building annotated PDF...';
-                        const pandocResult = await runPandoc(annotatedPath, 'pdf', annotatedConfig, { ...options, outputPath: annotatedPdfPath });
+                        const pandocResult = await runPandoc(annotatedPath, 'pdf', annotatedConfig, { ...options, outputPath: annotatedPdfPath, pandocArgs: options.pandocArg });
                         spinPdf.stop();
@@ -688,0 +703,0 @@ if (!process.env.DEBUG) {

dist/lib/commands/build.js.map

@@ -1,1 +0,1 @@
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dist/lib/schema.d.ts.map

@@ -1,1 +0,1 @@
-{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../lib/schema.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH;;GAEG;AACH,UAAU,eAAe;IACvB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED;;GAEG;AACH,UAAU,iBAAiB;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;GAEG;AACH,UAAU,gBAAgB;IACxB,KAAK,EAAE,OAAO,CAAC;IACf,MAAM,EAAE,eAAe,EAAE,CAAC;IAC1B,QAAQ,EAAE,iBAAiB,EAAE,CAAC;CAC/B;AAED;;GAEG;AACH,UAAU,MAAM;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACpC,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,oBAAoB,CAAC,EAAE,OAAO,CAAC;IAC/B,OAAO,CAAC,EAAE,OAAO,CAAC;CACnB;AAED;;GAEG;AACH,eAAO,MAAM,aAAa,EAAE,MAiI3B,CAAC;AA6HF;;GAEG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,gBAAgB,CAkDhF;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CACpC,MAAM,EAAE,gBAAgB,EACxB,KAAK,EAAE;IAAE,GAAG,EAAE,CAAC,CAAC,EAAE,MAAM,KAAK,MAAM,CAAC;IAAC,MAAM,EAAE,CAAC,CAAC,EAAE,MAAM,KAAK,MAAM,CAAC;IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,KAAK,MAAM,CAAA;CAAE,GACjG,MAAM,CAuBR"}
+{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../lib/schema.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH;;GAEG;AACH,UAAU,eAAe;IACvB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED;;GAEG;AACH,UAAU,iBAAiB;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;GAEG;AACH,UAAU,gBAAgB;IACxB,KAAK,EAAE,OAAO,CAAC;IACf,MAAM,EAAE,eAAe,EAAE,CAAC;IAC1B,QAAQ,EAAE,iBAAiB,EAAE,CAAC;CAC/B;AAED;;GAEG;AACH,UAAU,MAAM;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACpC,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,oBAAoB,CAAC,EAAE,OAAO,CAAC;IAC/B,OAAO,CAAC,EAAE,OAAO,CAAC;CACnB;AAED;;GAEG;AACH,eAAO,MAAM,aAAa,EAAE,MAsK3B,CAAC;AA6HF;;GAEG;AACH,wBAAgB,cAAc,CAAC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,gBAAgB,CAkDhF;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CACpC,MAAM,EAAE,gBAAgB,EACxB,KAAK,EAAE;IAAE,GAAG,EAAE,CAAC,CAAC,EAAE,MAAM,KAAK,MAAM,CAAC;IAAC,MAAM,EAAE,CAAC,CAAC,EAAE,MAAM,KAAK,MAAM,CAAC;IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,MAAM,KAAK,MAAM,CAAA;CAAE,GACjG,MAAM,CAuBR"}

dist/lib/schema.js

@@ -44,2 +44,19 @@ /**
         },
+        'pandoc-args': {
+            type: 'array',
+            description: 'Extra pandoc args applied to every format build (e.g. --lua-filter=...). Format-specific lists are appended after these; --pandoc-arg CLI values are appended last.',
+            items: { type: 'string' },
+        },
+        output: {
+            type: 'object',
+            description: 'Per-format output filenames. Keys are format names (pdf, docx, tex, beamer, pptx); values are paths. Relative paths resolve under outputDir; absolute paths are honored as-is. Extension auto-added if missing. CLI `-o` overrides this map.',
+            properties: {
+                pdf: { type: 'string' },
+                docx: { type: 'string' },
+                tex: { type: 'string' },
+                beamer: { type: 'string' },
+                pptx: { type: 'string' },
+            },
+            additionalProperties: false,
+        },
         sections: {
@@ -114,2 +131,7 @@ type: 'array',
                 footer: { type: 'string' },
+                'pandoc-args': {
+                    type: 'array',
+                    description: 'Extra pandoc args for PDF builds. Appended after the top-level pandoc-args list.',
+                    items: { type: 'string' },
+                },
             },
@@ -125,2 +147,12 @@ additionalProperties: true,
                 toc: { type: 'boolean', default: false },
+                translateRawFigures: {
+                    type: 'boolean',
+                    default: true,
+                    description: 'Auto-translate the common \\begin{figure}...\\end{figure} shape to portable ![](){#fig: ...} markdown so figures render in docx. Pandoc strips raw LaTeX in docx output silently otherwise.',
+                },
+                'pandoc-args': {
+                    type: 'array',
+                    description: 'Extra pandoc args for DOCX builds. Appended after the top-level pandoc-args list.',
+                    items: { type: 'string' },
+                },
             },
@@ -134,2 +166,7 @@ additionalProperties: true,
                 standalone: { type: 'boolean', default: true },
+                'pandoc-args': {
+                    type: 'array',
+                    description: 'Extra pandoc args for TeX builds. Appended after the top-level pandoc-args list.',
+                    items: { type: 'string' },
+                },
             },
@@ -136,0 +173,0 @@ additionalProperties: true,

dist/lib/schema.js.map

@@ -1,1 +0,1 @@
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lib/anchor-match.ts

@@ -14,4 +14,2 @@ /**
   | 'partial-start-stripped'
-  | 'partial-window'
-  | 'partial-window-stripped'
   | 'context-both'
@@ -177,25 +175,20 @@ | 'context-before'
 
-  // Strategy 4: word window from anchor (prefix or interior).
-  // Sliding the window across the anchor catches the case where the
-  // anchor's prefix has been edited but a chunk in the middle/end
-  // survived intact (e.g. "Sensitivity analyses were performed by
-  // perturbing the prior variance" → drifted "Sensitivity analyses
-  // perturbed the prior variance" still contains "the prior variance").
+  // Strategy 4: first N words of anchor (long anchors)
   const words = anchor.split(/\s+/);
   if (words.length > 3) {
     for (let n = Math.min(6, words.length); n >= 3; n--) {
-      for (let start = 0; start + n <= words.length; start++) {
-        const window = words.slice(start, start + n).join(' ');
-        const windowLower = window.toLowerCase();
-        if (windowLower.length < 15) continue;
-
-        let occ = findAllOccurrences(textLower, windowLower);
-        if (occ.length > 0) {
-          const strategy: AnchorStrategy = start === 0 ? 'partial-start' : 'partial-window';
-          return { occurrences: occ, matchedAnchor: window, strategy };
+      const partialAnchor = words.slice(0, n).join(' ').toLowerCase();
+      if (partialAnchor.length >= 15) {
+        occurrences = findAllOccurrences(textLower, partialAnchor);
+        if (occurrences.length > 0) {
+          return { occurrences, matchedAnchor: words.slice(0, n).join(' '), strategy: 'partial-start' };
         }
-        occ = findAllOccurrences(strippedLower, windowLower);
-        if (occ.length > 0) {
-          const strategy: AnchorStrategy = start === 0 ? 'partial-start-stripped' : 'partial-window-stripped';
-          return { occurrences: occ, matchedAnchor: window, strategy, stripped: true };
+        occurrences = findAllOccurrences(strippedLower, partialAnchor);
+        if (occurrences.length > 0) {
+          return {
+            occurrences,
+            matchedAnchor: words.slice(0, n).join(' '),
+            strategy: 'partial-start-stripped',
+            stripped: true,
+          };
         }
@@ -206,16 +199,6 @@ }
 
-  // Strategy 5: context (before/after) only.
-  //
-  // For a non-empty anchor that already failed every text-based strategy
-  // above, we treat context as a degraded placement: classify it
-  // 'context-only' so callers can warn the user. We also reject
-  // implausible brackets — if both contexts match but the gap between
-  // them is far too small to contain the anchor (e.g. the anchored
-  // sentence was deleted), do not silently land the comment between
-  // the surviving sentences. Return 'failed' so the user is told to
-  // place it manually.
+  // Strategy 5: context (before/after) only
   if (before || after) {
     const beforeLower = before.toLowerCase();
     const afterLower = after.toLowerCase();
-    const anchorLen = anchor.length;
 
@@ -227,17 +210,4 @@ if (before && after) {
         const afterIdx = textLower.indexOf(afterLower.slice(0, 50), searchStart);
-        if (afterIdx !== -1) {
-          const gap = afterIdx - searchStart;
-          // Require the bracket to plausibly contain a remnant of the anchor.
-          // Below 30% of anchor length: anchor was deleted — refuse to place.
-          // Above 2× anchor length + slack: brackets are too far apart, the
-          // matcher has latched onto unrelated repeats of common context.
-          const minGap = Math.floor(anchorLen * 0.3);
-          const maxGap = Math.min(500, anchorLen * 2 + 50);
-          if (gap >= minGap && gap <= maxGap) {
-            return { occurrences: [searchStart], matchedAnchor: null, strategy: 'context-both' };
-          }
-          // Both brackets found but gap implausible: anchor likely deleted.
-          // Don't fall back to single-side context — that would silently
-          // place the comment in the wrong location.
-          return { occurrences: [], matchedAnchor: null, strategy: 'failed' };
+        if (afterIdx !== -1 && afterIdx - searchStart < 500) {
+          return { occurrences: [searchStart], matchedAnchor: null, strategy: 'context-both' };
         }
@@ -299,4 +269,2 @@ }
     case 'partial-start-stripped':
-    case 'partial-window':
-    case 'partial-window-stripped':
     case 'split-match':
@@ -303,0 +271,0 @@ return 'drift';

lib/build.ts

@@ -35,4 +35,9 @@ /**
 
-/** Maximum title length for output filename */
-const MAX_TITLE_FILENAME_LENGTH = 50;
+/**
+ * Maximum length for slugified-title output filenames. Only used when no
+ * explicit `output:` filename is configured. Long titles are truncated at the
+ * last `-` boundary at-or-before this length so words stay intact (the old
+ * blind `.slice(0, 50)` cut mid-word).
+ */
+const MAX_TITLE_FILENAME_LENGTH = 80;
 
@@ -73,2 +78,4 @@ // =============================================================================
   monofont?: string;
+  /** Extra pandoc args appended for this format (after top-level pandocArgs). */
+  pandocArgs?: string[];
 }
@@ -81,2 +88,10 @@
   toc?: boolean;
+  pandocArgs?: string[];
+  /**
+   * Auto-translate the common-shape raw `\begin{figure}...\end{figure}` block
+   * to portable `![caption](path){#fig:label width=N%}` markdown so figures
+   * survive the docx build (pandoc otherwise drops raw LaTeX silently).
+   * Default true. Set false to opt out — blocks then warn and are left alone.
+   */
+  translateRawFigures?: boolean;
 }
@@ -86,2 +101,3 @@
   standalone?: boolean;
+  pandocArgs?: string[];
 }
@@ -98,2 +114,3 @@
   fit_images?: boolean;
+  pandocArgs?: string[];
 }
@@ -114,2 +131,3 @@
   };
+  pandocArgs?: string[];
 }
@@ -152,2 +170,15 @@
   outputDir?: string | null;
+  /**
+   * Per-format output filenames. Keys are format names (pdf/docx/tex/beamer/
+   * pptx); values are paths. Relative paths resolve under outputDir; absolute
+   * paths are honored as-is. Extension is added if missing. CLI `-o` wins
+   * over this map.
+   */
+  output?: Record<string, string>;
+  /**
+   * Extra pandoc args applied to every format. Format-specific args
+   * (e.g. docx.pandocArgs) are appended *after* these, and CLI --pandoc-arg
+   * values are appended last.
+   */
+  pandocArgs?: string[];
   _configPath?: string | null;
@@ -166,4 +197,16 @@ }
   config?: BuildConfig;
+  /**
+   * Internal: forces the exact output path. Used by dual-mode/temp builds that
+   * route to specific temp files. Bypasses the `output:` resolver.
+   */
   outputPath?: string;
+  /**
+   * CLI override (`-o, --output <path>`). Beats `config.output[format]` but
+   * loses to `options.outputPath`. Relative paths resolve under outputDir;
+   * absolute paths bypass outputDir.
+   */
+  output?: string;
   crossref?: boolean;
+  /** Extra pandoc args from CLI (--pandoc-arg). Appended after config args. */
+  pandocArgs?: string[];
   _refsAutoInjected?: boolean;
@@ -247,2 +290,3 @@ _forwardRefsResolved?: number;
     toc: false,
+    translateRawFigures: true,
   },
@@ -354,2 +398,16 @@ tex: {
 /**
+ * In-place: copy `pandoc-args` → `pandocArgs` on an object (if not already set).
+ * Idempotent. Coerces a single string into a one-element array.
+ */
+function normalizePandocArgsKey(obj: Record<string, unknown>): void {
+  if (!obj || typeof obj !== 'object') return;
+  const hy = obj['pandoc-args'];
+  if (hy === undefined) return;
+  if (obj.pandocArgs === undefined) {
+    obj.pandocArgs = Array.isArray(hy) ? hy : [hy];
+  }
+  delete obj['pandoc-args'];
+}
+
+/**
  * Load rev.yaml config from directory
@@ -376,2 +434,12 @@ * @param directory - Project directory path
 
+    // Accept hyphenated `pandoc-args` (the form pandoc itself uses) in addition
+    // to camelCase `pandocArgs`. Hyphenated is what we document; camelCase is
+    // accepted for users who already prefer that convention.
+    normalizePandocArgsKey(userConfig);
+    for (const fmt of ['pdf', 'docx', 'tex', 'beamer', 'pptx'] as const) {
+      if (userConfig[fmt] && typeof userConfig[fmt] === 'object') {
+        normalizePandocArgsKey(userConfig[fmt]);
+      }
+    }
+
     // Deep merge with defaults
@@ -844,2 +912,10 @@ let config: BuildConfig = {
 
+    // Pandoc strips raw LaTeX in docx output. Translate the common
+    // `\begin{figure}...\end{figure}` shape to portable markdown so figures
+    // actually appear; exotic blocks are left alone (warned about in build()).
+    if (config.docx?.translateRawFigures !== false) {
+      const { translated } = translateRawLatexFigures(content);
+      content = translated;
+    }
+
     if (hasNumberedAffiliations(config)) {
@@ -912,5 +988,204 @@ const mdBlock = generateMarkdownAuthorBlock(config);
 
+// =============================================================================
+// Raw LaTeX figure detection / translation (docx)
+// =============================================================================
+
 /**
- * Build pandoc arguments for format
+ * A raw LaTeX `\begin{figure}...\end{figure}` block found in source markdown.
+ * `exotic` blocks contain features we don't auto-translate (multiple
+ * `\includegraphics`, `\subfloat`, `\rotatebox`, unrecognised width units);
+ * pandoc strips raw LaTeX silently in docx output, so users get warned about
+ * anything that won't be translated.
  */
+export interface RawLatexFigure {
+  file?: string;
+  line: number;
+  block: string;
+  exotic: boolean;
+}
+
+/** Match `\begin{figure}` / `\begin{figure*}` … `\end{figure}` blocks. */
+function makeRawFigureRegex(): RegExp {
+  return /\\begin\{figure\*?\}(?:\[[^\]]*\])?[\s\S]*?\\end\{figure\*?\}/g;
+}
+
+/**
+ * Convert a LaTeX width spec to a markdown image attribute value.
+ * - `0.8\textwidth` → `80%`
+ * - `\linewidth` → `100%`
+ * - `8cm`, `2in`, `12pt` → kept verbatim
+ * Returns null for anything we don't translate (block stays "exotic").
+ */
+function convertLatexWidth(raw: string): string | null {
+  const trimmed = raw.trim();
+  // Coefficient × relative length
+  const rel = trimmed.match(/^([\d.]+)\s*\\(textwidth|linewidth|columnwidth)$/);
+  if (rel) {
+    const pct = Math.round(parseFloat(rel[1]!) * 100);
+    if (!isFinite(pct) || pct <= 0) return null;
+    return `${pct}%`;
+  }
+  // Bare relative length
+  if (/^\\(textwidth|linewidth|columnwidth)$/.test(trimmed)) return '100%';
+  // Absolute units
+  if (/^[\d.]+\s*(cm|mm|in|pt|px|em|ex)$/.test(trimmed)) return trimmed.replace(/\s+/g, '');
+  return null;
+}
+
+/** Extract a balanced `{...}` argument that follows `command` in `text`. */
+function extractBracedArg(text: string, command: string): string | null {
+  const idx = text.indexOf(command);
+  if (idx === -1) return null;
+  let i = idx + command.length;
+  while (i < text.length && /\s/.test(text[i]!)) i++;
+  if (text[i] !== '{') return null;
+  i++;
+  const start = i;
+  let depth = 1;
+  while (i < text.length) {
+    const ch = text[i]!;
+    if (ch === '\\' && i + 1 < text.length) { i += 2; continue; }
+    if (ch === '{') depth++;
+    else if (ch === '}') {
+      depth--;
+      if (depth === 0) return text.slice(start, i);
+    }
+    i++;
+  }
+  return null;
+}
+
+/** True if a `\begin{figure}` block contains features we don't auto-translate. */
+function isExoticFigureBlock(block: string): boolean {
+  if (/\\subfloat\b/.test(block)) return true;
+  if (/\\rotatebox\b/.test(block)) return true;
+  const includes = (block.match(/\\includegraphics\b/g) || []).length;
+  if (includes !== 1) return true;
+  const m = block.match(/\\includegraphics\s*(?:\[([^\]]*)\])?\s*\{([^}]+)\}/);
+  if (!m) return true;
+  const opts = m[1] || '';
+  const widthMatch = opts.match(/(?:^|,)\s*width\s*=\s*([^,]+)/);
+  if (widthMatch && !convertLatexWidth(widthMatch[1]!)) return true;
+  return false;
+}
+
+/**
+ * Find raw LaTeX figure blocks containing `\includegraphics` in markdown.
+ * `file`, if given, is attached to each result. `line` is 1-based within the
+ * supplied content (the line where `\begin{figure}` sits).
+ */
+export function detectRawLatexFigures(content: string, file?: string): RawLatexFigure[] {
+  const figures: RawLatexFigure[] = [];
+  const re = makeRawFigureRegex();
+  let m: RegExpExecArray | null;
+  while ((m = re.exec(content)) !== null) {
+    const block = m[0];
+    if (!block.includes('\\includegraphics')) continue;
+    const line = content.slice(0, m.index).split(/\r?\n/).length;
+    figures.push({ file, line, block, exotic: isExoticFigureBlock(block) });
+  }
+  return figures;
+}
+
+/**
+ * Translate the 80% case: single `\includegraphics` figure with optional
+ * `\caption{...}` and `\label{...}`, wrapped in `\begin{figure}...\end{figure}`,
+ * to portable `![caption](path){#fig:label width=N%}` markdown. Exotic blocks
+ * (see `isExoticFigureBlock`) are left untouched.
+ */
+export function translateRawLatexFigures(content: string): { translated: string; translatedCount: number } {
+  let translatedCount = 0;
+  const re = makeRawFigureRegex();
+  const translated = content.replace(re, (block) => {
+    if (!block.includes('\\includegraphics')) return block;
+    if (isExoticFigureBlock(block)) return block;
+
+    const inc = block.match(/\\includegraphics\s*(?:\[([^\]]*)\])?\s*\{([^}]+)\}/);
+    if (!inc) return block;
+    const optsStr = inc[1] || '';
+    const imgPath = inc[2]!.trim();
+
+    let width: string | undefined;
+    const widthMatch = optsStr.match(/(?:^|,)\s*width\s*=\s*([^,]+)/);
+    if (widthMatch) {
+      const w = convertLatexWidth(widthMatch[1]!);
+      if (!w) return block; // already filtered by isExoticFigureBlock, defensive
+      width = w;
+    }
+
+    const caption = (extractBracedArg(block, '\\caption') ?? '').trim();
+    const labelRaw = extractBracedArg(block, '\\label');
+
+    const attrs: string[] = [];
+    if (labelRaw) {
+      const label = labelRaw.trim();
+      const labelWithPrefix = /^[a-z]+:/i.test(label) ? label : `fig:${label}`;
+      attrs.push(`#${labelWithPrefix}`);
+    }
+    if (width) attrs.push(`width=${width}`);
+
+    translatedCount++;
+    const attrStr = attrs.length > 0 ? ` {${attrs.join(' ')}}` : '';
+    return `![${caption}](${imgPath})${attrStr}`;
+  });
+  return { translated, translatedCount };
+}
+
+/**
+ * Format the warning surfaced for raw LaTeX figure blocks that won't render
+ * in docx. `translateEnabled` reflects whether auto-translate ran (true = the
+ * listed blocks are exotic leftovers; false = no translation was attempted).
+ */
+function formatRawLatexFigureWarning(figs: RawLatexFigure[], translateEnabled: boolean): string {
+  const reason = translateEnabled ? 'too complex to auto-translate' : 'translateRawFigures: false';
+  const lines: string[] = [
+    `${figs.length} raw LaTeX figure block(s) won't render in docx (${reason}).`,
+  ];
+  for (const f of figs) {
+    const loc = f.file ? `${f.file}:${f.line}` : `line ${f.line}`;
+    const pathMatch = f.block.match(/\\includegraphics\s*(?:\[[^\]]*\])?\s*\{([^}]+)\}/);
+    const pathInfo = pathMatch ? `  ${pathMatch[1]!.trim()}` : '';
+    lines.push(`  ${loc}${pathInfo}`);
+  }
+  lines.push('  Hint: use ![caption](path){#fig:label width=80%} for format-portable figures,');
+  lines.push('        or pass --pandoc-arg=--lua-filter=<your.lua> to translate them yourself.');
+  return lines.join('\n');
+}
+
+/**
+ * Walk section files and gather a warning for any raw LaTeX figure blocks that
+ * won't survive the docx build. Returns null when there's nothing to warn about.
+ */
+export function collectRawLatexFigureWarning(directory: string, config: BuildConfig): string | null {
+  const translateEnabled = config.docx?.translateRawFigures !== false;
+  const all: RawLatexFigure[] = [];
+  for (const section of findSections(directory, config.sections)) {
+    const sectionPath = path.join(directory, section);
+    if (!fs.existsSync(sectionPath)) continue;
+    try {
+      const content = fs.readFileSync(sectionPath, 'utf-8');
+      const figs = detectRawLatexFigures(content, section);
+      for (const f of figs) {
+        // When auto-translate is on, non-exotic blocks get rewritten cleanly —
+        // only the exotic leftovers need warning. When opted out, everything
+        // is at risk and we warn about every block.
+        if (translateEnabled && !f.exotic) continue;
+        all.push(f);
+      }
+    } catch {
+      // ignore unreadable sections
+    }
+  }
+  if (all.length === 0) return null;
+  return formatRawLatexFigureWarning(all, translateEnabled);
+}
+
+/**
+ * Build pandoc arguments for format.
+ *
+ * Returns only the built-in args derived from config. Passthrough args
+ * (config.pandocArgs, config[format].pandocArgs, CLI --pandoc-arg) are
+ * appended later in runPandoc so they win against pptx/crossref defaults
+ * added there.
+ */
 export function buildPandocArgs(format: string, config: BuildConfig, outputPath: string): string[] {
@@ -1033,2 +1308,26 @@ const args: string[] = [];
 /**
+ * Collect passthrough pandoc args for a format in the canonical order:
+ * top-level config → format-specific config → CLI extras. Later wins for
+ * repeated flags.
+ */
+export function collectPandocPassthroughArgs(
+  format: string,
+  config: BuildConfig,
+  extraArgs: string[] = []
+): string[] {
+  const out: string[] = [];
+  if (config.pandocArgs && config.pandocArgs.length > 0) {
+    out.push(...config.pandocArgs);
+  }
+  const formatConfig = (config as unknown as Record<string, { pandocArgs?: string[] } | undefined>)[format];
+  if (formatConfig?.pandocArgs && formatConfig.pandocArgs.length > 0) {
+    out.push(...formatConfig.pandocArgs);
+  }
+  if (extraArgs.length > 0) {
+    out.push(...extraArgs);
+  }
+  return out;
+}
+
+/**
  * Write crossref.yaml if needed
@@ -1065,3 +1364,89 @@ */
 
+/** File extension (with leading dot) for each supported pandoc format. */
+const FORMAT_EXTENSIONS: Record<string, string> = {
+  tex: '.tex',
+  pdf: '.pdf',
+  docx: '.docx',
+  beamer: '.pdf',
+  pptx: '.pptx',
+};
+
+/** Get file extension for a format, defaulting to `.pdf`. */
+export function getFormatExtension(format: string): string {
+  return FORMAT_EXTENSIONS[format] ?? '.pdf';
+}
+
 /**
+ * Slugify a title for use as a default output filename. Lowercases, replaces
+ * non-alphanumeric runs with `-`, and truncates at the last `-` boundary
+ * at-or-before MAX_TITLE_FILENAME_LENGTH so words stay whole (the old blind
+ * `.slice` cut mid-word).
+ */
+export function slugifyTitle(title: string): string {
+  if (!title) return 'paper';
+  const slug = title.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+|-+$/g, '');
+  if (!slug) return 'paper';
+  if (slug.length <= MAX_TITLE_FILENAME_LENGTH) return slug;
+  const cut = slug.slice(0, MAX_TITLE_FILENAME_LENGTH);
+  const lastDash = cut.lastIndexOf('-');
+  // Only truncate at a hyphen if it leaves a reasonable amount of content.
+  // Otherwise hard-cut (handles degenerate titles with no spaces at all).
+  if (lastDash >= MAX_TITLE_FILENAME_LENGTH / 2) {
+    return slug.slice(0, lastDash);
+  }
+  return cut;
+}
+
+/**
+ * Ensure `name` ends with `ext` (case-insensitive). If the user already supplied
+ * the correct extension, return unchanged; if they supplied none or a different
+ * one, append the format's canonical extension.
+ *
+ * Different-extension case (e.g. `output.docx` when building tex): we append
+ * rather than replace, since stripping looks like an unsafe guess. The result
+ * `output.docx.tex` is loud enough to flag the misconfiguration.
+ */
+function ensureExtension(name: string, ext: string): string {
+  if (name.toLowerCase().endsWith(ext.toLowerCase())) return name;
+  return name + ext;
+}
+
+/**
+ * Resolve the final output path for a build.
+ *
+ * Priority: `options.outputPath` (internal force) > `cliOverride` (-o flag) >
+ * `config.output[format]` > slugified title fallback.
+ *
+ * Relative paths from `cliOverride`/`config.output` resolve under outputDir;
+ * absolute paths bypass outputDir. The fallback path always lives under
+ * outputDir.
+ *
+ * @param suffix - Appended before the extension (e.g. "-changes", "-slides").
+ *                 Suppressed when user supplied an explicit name via CLI or
+ *                 config — they pick their own suffix.
+ */
+export function resolveOutputPath(
+  directory: string,
+  config: BuildConfig,
+  format: string,
+  options: { cliOverride?: string; suffix?: string } = {}
+): string {
+  const { cliOverride, suffix = '' } = options;
+  const ext = getFormatExtension(format);
+
+  const explicit = cliOverride ?? config.output?.[format];
+  if (explicit) {
+    const baseDir = path.isAbsolute(explicit)
+      ? path.dirname(explicit)
+      : resolveOutputDir(directory, config);
+    const baseName = path.basename(explicit);
+    const stem = baseName.replace(/\.[^./\\]+$/, '');
+    return path.join(baseDir, ensureExtension(`${stem}${suffix}`, ext));
+  }
+
+  const slug = slugifyTitle(config.title);
+  return path.join(resolveOutputDir(directory, config), `${slug}${suffix}${ext}`);
+}
+
+/**
  * Run pandoc build
@@ -1076,24 +1461,12 @@ */
   const directory = path.dirname(inputPath);
-  const baseName = config.title
-    ? config.title.toLowerCase().replace(/[^a-z0-9]+/g, '-').slice(0, 50)
-    : 'paper';
 
-  // Map format to file extension
-  const extMap: Record<string, string> = {
-    tex: '.tex',
-    pdf: '.pdf',
-    docx: '.docx',
-    beamer: '.pdf', // beamer outputs PDF
-    pptx: '.pptx',
-  };
-  const ext = extMap[format] || '.pdf';
-
-  // For beamer, use -slides suffix to distinguish from regular PDF
+  // outputPath (internal force) wins over the resolver. For beamer, we keep
+  // the `-slides` suffix on the slug fallback to distinguish from a regular
+  // PDF build; when the user supplies an explicit name, they pick their own.
   const suffix = format === 'beamer' ? '-slides' : '';
-  // Allow custom output path via options. Auto-named outputs go through the
-  // configured outputDir (default 'output/'); explicit paths are honored as-is
-  // so callers can route temp/intermediate artefacts where they want.
   const outputPath = options.outputPath
-    ? options.outputPath
-    : path.join(resolveOutputDir(directory, config), `${baseName}${suffix}${ext}`);
+    ?? resolveOutputPath(directory, config, format, {
+      cliOverride: options.output,
+      suffix,
+    });
 
@@ -1165,5 +1538,14 @@ if (!options.outputPath) {
 
+  // Passthrough args go last so they win against built-in defaults.
+  args.push(...collectPandocPassthroughArgs(format, config, options.pandocArgs));
+
   // Input file (use basename since we set cwd to directory)
   args.push(path.basename(inputPath));
 
+  if (options.verbose) {
+    const quoted = args.map(a => /[\s"'$`]/.test(a) ? `"${a.replace(/"/g, '\\"')}"` : a).join(' ');
+    console.error(`[pandoc ${format}] (cwd: ${directory})`);
+    console.error(`  pandoc ${quoted}`);
+  }
+
   return new Promise((resolve) => {
@@ -1285,2 +1667,8 @@ const pandoc: ChildProcess = spawn('pandoc', args, {
     }
+
+    // Warn about raw LaTeX figure blocks that won't render in docx (pandoc
+    // drops them silently). With auto-translate on (default), this surfaces
+    // only the exotic leftovers; with it off, every block.
+    const rawFigWarning = collectRawLatexFigureWarning(directory, config);
+    if (rawFigWarning) warnings.push(rawFigWarning);
   }
@@ -1287,0 +1675,0 @@

lib/commands/build.ts

@@ -55,2 +55,4 @@ /**
   verbose?: boolean;
+  pandocArg?: string[];
+  output?: string;
 }
@@ -491,3 +493,10 @@
     .option('--aspectratio <ratio>', 'Beamer aspect ratio (169, 43)')
-    .option('--verbose', 'Show detailed output including postprocess scripts')
+    .option(
+      '--pandoc-arg <arg>',
+      'Extra arg to pass to pandoc (repeatable). Applied to every format being built; appended after rev.yaml pandoc-args so CLI wins.',
+      (val: string, prev: string[] = []) => [...prev, val],
+      []
+    )
+    .option('-o, --output <path>', 'Output filename or path. Relative paths resolve under outputDir; absolute paths bypass it. Extension auto-added if missing. Applied to every format being built; overrides rev.yaml output.<format>.')
+    .option('--verbose', 'Show detailed output including postprocess scripts and the pandoc invocation')
     .action(async (formats: string[], options: BuildOptions) => {
@@ -582,3 +591,3 @@ const dir = path.resolve(options.dir);
 
-        const { combineSections, resolveOutputDir } = await import('../build.js');
+        const { combineSections, resolveOutputPath } = await import('../build.js');
         const { buildWithTrackChanges } = await import('../trackchanges.js');
@@ -594,8 +603,8 @@
 
-          const baseName = config.title
-            ? config.title.toLowerCase().replace(/[^a-z0-9]+/g, '-').slice(0, 50)
-            : 'paper';
-          const outDir = resolveOutputDir(dir, config);
+          const outputPath = resolveOutputPath(dir, config, 'docx', {
+            cliOverride: options.output,
+            suffix: '-changes',
+          });
+          const outDir = path.dirname(outputPath);
           if (!fs.existsSync(outDir)) fs.mkdirSync(outDir, { recursive: true });
-          const outputPath = path.join(outDir, `${baseName}-changes.docx`);
 
@@ -632,6 +641,8 @@ const spinTc = fmt.spinner('Applying track changes...').start();
       try {
-        const { results, paperPath, forwardRefsResolved, refsAutoInjected } = await build(dir, targetFormats, {
+        const { results, paperPath, forwardRefsResolved, refsAutoInjected, warnings } = await build(dir, targetFormats, {
           crossref: options.crossref,
           config,
           verbose: options.verbose,
+          pandocArgs: options.pandocArg,
+          output: options.output,
         });
@@ -651,2 +662,13 @@
 
+        if (warnings && warnings.length > 0) {
+          for (const w of warnings) {
+            // Each warning may span multiple lines — colour the first line as
+            // a warning header and pass through the rest unchanged.
+            const [head, ...rest] = w.split('\n');
+            console.log(chalk.yellow(`Warning: ${head}`));
+            for (const line of rest) console.log(chalk.yellow(line));
+          }
+          console.log('');
+        }
+
         console.log(chalk.cyan('Output:'));
@@ -712,3 +734,3 @@ console.log(formatBuildResults(results));
               const markedDocxPath = path.join(dir, '.paper-marked.docx');
-              const pandocResult = await runPandoc(markedPath, 'docx', config, { ...options, outputPath: markedDocxPath });
+              const pandocResult = await runPandoc(markedPath, 'docx', config, { ...options, outputPath: markedDocxPath, pandocArgs: options.pandocArg });
               spinBuild.stop();
@@ -796,3 +818,3 @@
               spinPdf.text = 'Building annotated PDF...';
-              const pandocResult = await runPandoc(annotatedPath, 'pdf', annotatedConfig, { ...options, outputPath: annotatedPdfPath });
+              const pandocResult = await runPandoc(annotatedPath, 'pdf', annotatedConfig, { ...options, outputPath: annotatedPdfPath, pandocArgs: options.pandocArg });
               spinPdf.stop();
@@ -799,0 +821,0 @@

lib/schema.ts

@@ -94,2 +94,19 @@ /**
     },
+    'pandoc-args': {
+      type: 'array',
+      description: 'Extra pandoc args applied to every format build (e.g. --lua-filter=...). Format-specific lists are appended after these; --pandoc-arg CLI values are appended last.',
+      items: { type: 'string' },
+    },
+    output: {
+      type: 'object',
+      description: 'Per-format output filenames. Keys are format names (pdf, docx, tex, beamer, pptx); values are paths. Relative paths resolve under outputDir; absolute paths are honored as-is. Extension auto-added if missing. CLI `-o` overrides this map.',
+      properties: {
+        pdf: { type: 'string' },
+        docx: { type: 'string' },
+        tex: { type: 'string' },
+        beamer: { type: 'string' },
+        pptx: { type: 'string' },
+      },
+      additionalProperties: false,
+    },
     sections: {
@@ -164,2 +181,7 @@ type: 'array',
         footer: { type: 'string' },
+        'pandoc-args': {
+          type: 'array',
+          description: 'Extra pandoc args for PDF builds. Appended after the top-level pandoc-args list.',
+          items: { type: 'string' },
+        },
       },
@@ -175,2 +197,12 @@ additionalProperties: true,
         toc: { type: 'boolean', default: false },
+        translateRawFigures: {
+          type: 'boolean',
+          default: true,
+          description: 'Auto-translate the common \\begin{figure}...\\end{figure} shape to portable ![](){#fig: ...} markdown so figures render in docx. Pandoc strips raw LaTeX in docx output silently otherwise.',
+        },
+        'pandoc-args': {
+          type: 'array',
+          description: 'Extra pandoc args for DOCX builds. Appended after the top-level pandoc-args list.',
+          items: { type: 'string' },
+        },
       },
@@ -184,2 +216,7 @@ additionalProperties: true,
         standalone: { type: 'boolean', default: true },
+        'pandoc-args': {
+          type: 'array',
+          description: 'Extra pandoc args for TeX builds. Appended after the top-level pandoc-args list.',
+          items: { type: 'string' },
+        },
       },
@@ -186,0 +223,0 @@ additionalProperties: true,

package.json

 {
   "name": "docrev",
-  "version": "0.9.17",
+  "version": "0.9.18",
   "description": "Academic paper revision workflow: Word ↔ Markdown round-trips, DOI validation, reviewer comments",
@@ -5,0 +5,0 @@ "type": "module",

skill/REFERENCE.md

@@ -65,2 +65,5 @@ # docrev Command Reference
 rev build docx --show-changes  # DOCX with visible track changes (audit)
+rev build docx --pandoc-arg=--lua-filter=tofill.lua   # Pass extra args to pandoc
+rev build -o Final_Report     # Override output filename (extension auto-added)
+rev build pdf --verbose      # Echo the pandoc invocation (useful for filter debugging)
 ```
@@ -71,2 +74,65 @@
 
+#### Choosing output filenames
+
+By default, the output basename is derived from `title:` (slugified — e.g.
+"My Paper" → `my-paper.docx`). Long titles are truncated at word boundaries
+(at the last `-` at-or-before 80 chars), so `communities` stays whole instead
+of becoming `communitie`.
+
+To pick your own filename, set per-format names in `rev.yaml`:
+
+```yaml
+output:
+  docx: ADAPT_proposal_draft.docx
+  pdf: ADAPT_proposal_draft.pdf
+```
+
+Extensions are optional — `ADAPT_proposal_draft` is fine, the right extension
+is added per format. Relative paths resolve under `outputDir`; absolute paths
+bypass `outputDir`.
+
+Or override on the command line with `-o, --output <path>`:
+
+```bash
+rev build docx -o Final_Report           # → output/Final_Report.docx
+rev build pdf docx -o Final_Report       # Applies to both formats
+rev build -o /tmp/draft.docx docx        # Absolute path bypasses outputDir
+```
+
+CLI `-o` wins over `output:` in `rev.yaml`. When `--dual` is on, the
+`_comments` variant piggybacks on the chosen name (e.g.
+`Final_Report_comments.docx`). When `--show-changes` is on, the audit DOCX
+uses the chosen name with a `-changes` suffix
+(e.g. `Final_Report-changes.docx`).
+
+#### Passing custom pandoc args
+
+For pandoc flags rev doesn't surface directly (Lua/JSON filters, custom
+templates, variables, etc.), use the repeatable `--pandoc-arg` flag or the
+`pandoc-args` field in `rev.yaml`:
+
+```yaml
+# rev.yaml — applies to every format
+pandoc-args:
+  - --lua-filter=tofill.lua
+  - --shift-heading-level-by=1
+
+# Format-specific (concatenated after the top-level list)
+docx:
+  pandoc-args:
+    - --lua-filter=docx_only.lua
+pdf:
+  pandoc-args:
+    - --variable=papersize:a4
+```
+
+```bash
+# CLI overrides — appended last, so pandoc's last-wins rule lets CLI flags
+# beat repeated config flags
+rev build docx --pandoc-arg=--lua-filter=cli.lua --pandoc-arg=--metadata=draft:true
+```
+
+Run with `--verbose` to print the full pandoc command line (one per format).
+Copy-paste it into a terminal to reproduce a build manually.
+
 The `--dual` flag produces:
@@ -73,0 +139,0 @@ - `output/<title>.docx` — clean, for submission

skill/SKILL.md

@@ -20,5 +20,4 @@ ---
 title: "My Document"
-output:
-  docx:
-    reference-doc: template.docx
+docx:
+  reference: template.docx
 ```
@@ -102,4 +101,12 @@
 Outputs land in `output/` by default; set `outputDir: null` in `rev.yaml`
-to keep them alongside `paper.md` (legacy layout).
+to keep them alongside `paper.md` (legacy layout). The basename is derived
+from `title:` unless overridden — set `output: { docx: foo.docx, pdf: foo.pdf }`
+in `rev.yaml` or pass `-o, --output <path>` on the CLI. See REFERENCE.md →
+"Choosing output filenames".
 
+For pandoc flags rev doesn't surface directly (Lua filters, custom variables,
+templates), use `--pandoc-arg` (repeatable) or `pandoc-args:` in `rev.yaml`
+(both top-level and per-format). Run with `--verbose` to see the exact pandoc
+invocation. See REFERENCE.md → "Passing custom pandoc args" for details.
+
 ### 8. Archive reviewer files
@@ -188,2 +195,16 @@
 
+Insert a figure with the format-portable syntax (renders in both PDF and Word):
+
+```markdown
+![Caption text.](figures/foo.pdf){#fig:foo width=80%}
+```
+
+Raw `\begin{figure}...\end{figure}` LaTeX blocks are PDF-only. For docx
+builds, `rev` auto-translates the common shape (single `\includegraphics`
+with optional `\caption{...}` and `\label{...}`) to the markdown form above
+so figures still render. Exotic blocks (`\subfloat`, `\rotatebox`, multiple
+`\includegraphics`) are left alone and warned about — convert them by hand
+or supply a custom Lua filter via `--pandoc-arg`. Opt out of auto-translate
+with `docx.translateRawFigures: false` in `rev.yaml`.
+
 ## Template Variables
@@ -190,0 +211,0 @@

.claude/settings.local.json

-{
-  "permissions": {
-    "allow": [
-      "Skill(code-quality)"
-    ],
-    "deny": [],
-    "ask": []
-  }
-}

New alerts

URL strings

Supply chain risk

Package contains fragments of external URLs or IP addresses, which the package may be accessing at runtime.

Found 1 instance in 1 package

Fixed alerts

URL strings

Supply chain risk

Package contains fragments of external URLs or IP addresses, which the package may be accessing at runtime.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

3540522

6.51%

Number of package files

394

1.55%

Lines of code

55231

1.87%

No dependency changes