docrev 0.9.3 → 0.9.5

package/bin/rev.js

@@ -1,19 +1,12 @@
 #!/usr/bin/env node
 
-// Wrapper to run the TypeScript entry point via tsx
-// This allows `rev` command to work after npm link / npm install
+// Run the compiled TypeScript entry point directly (no tsx needed)
 
-import { spawnSync } from 'child_process';
-import { fileURLToPath } from 'url';
+import { pathToFileURL, fileURLToPath } from 'url';
 import { dirname, join } from 'path';
 
 const __dirname = dirname(fileURLToPath(import.meta.url));
-const tsEntry = join(__dirname, 'rev.ts');
+const compiled = join(__dirname, '..', 'dist', 'bin', 'rev.js');
 
-// Run tsx with the TypeScript entry point
-const result = spawnSync('npx', ['tsx', tsEntry, ...process.argv.slice(2)], {
-  stdio: 'inherit',
-  shell: true
-});
-
-process.exit(result.status ?? 0);
+// Windows requires file:// URLs for dynamic ESM imports
+await import(pathToFileURL(compiled).href);

package/dist/bin/rev.js

@@ -1,4 +1,4 @@
-#!/usr/bin/env tsx
+#!/usr/bin/env node
 /**
  * rev - Revision workflow for Word ↔ Markdown round-trips
  *
@@ -39,7 +39,7 @@ function suggestCommand(input, commands) {
     return suggestions;
 }
 // Read version from package.json
-const pkgPath = new URL('../package.json', import.meta.url);
+const pkgPath = new URL('../../package.json', import.meta.url);
 const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8'));
 program
     .name('rev')

package/dist/lib/build.d.ts

@@ -18,6 +18,7 @@ export interface CrossrefConfig {
 }
 export interface PdfConfig {
     template?: string | null;
+    headerIncludes?: string | null;
     documentclass?: string;
     fontsize?: string;
     geometry?: string;
@@ -72,6 +73,7 @@ export interface PostprocessConfig {
 export interface BuildConfig {
     title: string;
     authors: (string | Author)[];
+    affiliations: Record<string, string>;
     sections: string[];
     bibliography: string | null;
     csl: string | null;

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

@@ -1 +1 @@
-{"version":3,"file":"build.d.ts","sourceRoot":"","sources":["../../lib/build.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAeH,OAAO,KAAK,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAkB5D,MAAM,WAAW,cAAc;IAC7B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,SAAS,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAC9B,SAAS,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAC9B,SAAS,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAC9B,cAAc,CAAC,EAAE,OAAO,CAAC;CAC1B;AAED,MAAM,WAAW,SAAS;IACxB,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,GAAG,CAAC,EAAE,OAAO,CAAC;CACf;AAED,MAAM,WAAW,UAAU;IACzB,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,GAAG,CAAC,EAAE,OAAO,CAAC;CACf;AAED,MAAM,WAAW,SAAS;IACxB,UAAU,CAAC,EAAE,OAAO,CAAC;CACtB;AAED,MAAM,WAAW,YAAY;IAC3B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,UAAU,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,GAAG,KAAK,CAAC;IACvB,UAAU,CAAC,EAAE,OAAO,CAAC;CACtB;AAED,MAAM,WAAW,UAAU;IACzB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,MAAM,CAAC,EAAE;QACP,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,KAAK,CAAC,EAAE,MAAM,CAAC;KAChB,CAAC;IACF,OAAO,CAAC,EAAE;QACR,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,OAAO,CAAC,EAAE,OAAO,CAAC;KACnB,CAAC;CACH;AAED,MAAM,WAAW,YAAY;IAC3B,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;CACnB;AAED,MAAM,WAAW,iBAAiB;IAChC,GAAG,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,IAAI,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACrB,GAAG,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,IAAI,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACrB,MAAM,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,GAAG,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;CAC1C;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAC7B,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,GAAG,EAAE,MAAM,GAAG,IAAI,CAAC;IACnB,QAAQ,EAAE,cAAc,CAAC;IACzB,GAAG,EAAE,SAAS,CAAC;IACf,IAAI,EAAE,UAAU,CAAC;IACjB,GAAG,EAAE,SAAS,CAAC;IACf,MAAM,EAAE,YAAY,CAAC;IACrB,IAAI,EAAE,UAAU,CAAC;IACjB,MAAM,EAAE,YAAY,CAAC;IACrB,WAAW,EAAE,iBAAiB,CAAC;IAC/B,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;CAC7B;AAED,MAAM,WAAW,WAAW;IAC1B,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,OAAO,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,UAAU,YAAY;IACpB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,MAAM,CAAC,EAAE,WAAW,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,oBAAoB,CAAC,EAAE,MAAM,CAAC;CAC/B;AAED,UAAU,cAAe,SAAQ,YAAY;IAC3C,iBAAiB,CAAC,EAAE,OAAO,CAAC;CAC7B;AAMD,UAAU,YAAY;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,UAAU,eAAe;IACvB,OAAO,EAAE,WAAW,EAAE,CAAC;IACvB,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,mBAAmB,EAAE,MAAM,CAAC;IAC5B,gBAAgB,CAAC,EAAE,OAAO,CAAC;CAC5B;AAsBD;;GAEG;AACH,eAAO,MAAM,cAAc,EAAE,WA4D5B,CAAC;AAMF;;;GAGG;AACH,wBAAgB,sBAAsB,CAAC,MAAM,EAAE,WAAW,EAAE,UAAU,EAAE,iBAAiB,EAAE,SAAS,EAAE,MAAM,GAAG,WAAW,CAyDzH;AAED;;;;;;GAMG;AACH,wBAAgB,UAAU,CAAC,SAAS,EAAE,MAAM,GAAG,WAAW,CA2CzD;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAAC,SAAS,EAAE,MAAM,EAAE,cAAc,GAAE,MAAM,EAAO,GAAG,MAAM,EAAE,CAgDvF;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,SAAS,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,OAAO,GAAE,cAAmB,GAAG,MAAM,CAuF5G;AAoCD;;;;;;;GAOG;AACH,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,CA0F1G;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAC9B,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,WAAW,EACnB,OAAO,GAAE,YAAiB,GACzB,MAAM,CAmCR;AAuBD;;GAEG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,EAAE,CAiGjG;AAwBD;;GAEG;AACH,wBAAsB,SAAS,CAC7B,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,WAAW,EACnB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,YAAY,CAAC,CAiJvB;AAED;;GAEG;AACH,wBAAsB,KAAK,CACzB,SAAS,EAAE,MAAM,EACjB,OAAO,GAAE,MAAM,EAAoB,EACnC,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,eAAe,CAAC,CAgE1B;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,WAAW,EAAE,GAAG,MAAM,CAYjE"}
+{"version":3,"file":"build.d.ts","sourceRoot":"","sources":["../../lib/build.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAeH,OAAO,KAAK,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAkB5D,MAAM,WAAW,cAAc;IAC7B,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,SAAS,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAC9B,SAAS,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAC9B,SAAS,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IAC9B,cAAc,CAAC,EAAE,OAAO,CAAC;CAC1B;AAED,MAAM,WAAW,SAAS;IACxB,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,cAAc,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC/B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,GAAG,CAAC,EAAE,OAAO,CAAC;CACf;AAED,MAAM,WAAW,UAAU;IACzB,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,GAAG,CAAC,EAAE,OAAO,CAAC;CACf;AAED,MAAM,WAAW,SAAS;IACxB,UAAU,CAAC,EAAE,OAAO,CAAC;CACtB;AAED,MAAM,WAAW,YAAY;IAC3B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,UAAU,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,GAAG,KAAK,CAAC;IACvB,UAAU,CAAC,EAAE,OAAO,CAAC;CACtB;AAED,MAAM,WAAW,UAAU;IACzB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,KAAK,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,MAAM,CAAC,EAAE;QACP,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,KAAK,CAAC,EAAE,MAAM,CAAC;KAChB,CAAC;IACF,OAAO,CAAC,EAAE;QACR,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,OAAO,CAAC,EAAE,OAAO,CAAC;KACnB,CAAC;CACH;AAED,MAAM,WAAW,YAAY;IAC3B,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;CACnB;AAED,MAAM,WAAW,iBAAiB;IAChC,GAAG,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,IAAI,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACrB,GAAG,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,IAAI,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACrB,MAAM,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACvB,GAAG,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,GAAG,SAAS,CAAC;CAC1C;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAC7B,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,GAAG,EAAE,MAAM,GAAG,IAAI,CAAC;IACnB,QAAQ,EAAE,cAAc,CAAC;IACzB,GAAG,EAAE,SAAS,CAAC;IACf,IAAI,EAAE,UAAU,CAAC;IACjB,GAAG,EAAE,SAAS,CAAC;IACf,MAAM,EAAE,YAAY,CAAC;IACrB,IAAI,EAAE,UAAU,CAAC;IACjB,MAAM,EAAE,YAAY,CAAC;IACrB,WAAW,EAAE,iBAAiB,CAAC;IAC/B,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;CAC7B;AAED,MAAM,WAAW,WAAW;IAC1B,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,OAAO,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,UAAU,YAAY;IACpB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,MAAM,CAAC,EAAE,WAAW,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,oBAAoB,CAAC,EAAE,MAAM,CAAC;CAC/B;AAED,UAAU,cAAe,SAAQ,YAAY;IAC3C,iBAAiB,CAAC,EAAE,OAAO,CAAC;CAC7B;AAMD,UAAU,YAAY;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,UAAU,eAAe;IACvB,OAAO,EAAE,WAAW,EAAE,CAAC;IACvB,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,mBAAmB,EAAE,MAAM,CAAC;IAC5B,gBAAgB,CAAC,EAAE,OAAO,CAAC;CAC5B;AAsBD;;GAEG;AACH,eAAO,MAAM,cAAc,EAAE,WA6D5B,CAAC;AAMF;;;GAGG;AACH,wBAAgB,sBAAsB,CAAC,MAAM,EAAE,WAAW,EAAE,UAAU,EAAE,iBAAiB,EAAE,SAAS,EAAE,MAAM,GAAG,WAAW,CAyDzH;AAED;;;;;;GAMG;AACH,wBAAgB,UAAU,CAAC,SAAS,EAAE,MAAM,GAAG,WAAW,CA2CzD;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAAC,SAAS,EAAE,MAAM,EAAE,cAAc,GAAE,MAAM,EAAO,GAAG,MAAM,EAAE,CAgDvF;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,SAAS,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,OAAO,GAAE,cAAmB,GAAG,MAAM,CAgG5G;AAkJD;;;;;;;GAOG;AACH,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,CA0F1G;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAC9B,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,WAAW,EACnB,OAAO,GAAE,YAAiB,GACzB,MAAM,CAmDR;AAuBD;;GAEG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,EAAE,CAoGjG;AAwBD;;GAEG;AACH,wBAAsB,SAAS,CAC7B,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,WAAW,EACnB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,YAAY,CAAC,CAiJvB;AAED;;GAEG;AACH,wBAAsB,KAAK,CACzB,SAAS,EAAE,MAAM,EACjB,OAAO,GAAE,MAAM,EAAoB,EACnC,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,eAAe,CAAC,CAgE1B;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,WAAW,EAAE,GAAG,MAAM,CAYjE"}

package/dist/lib/build.js

@@ -12,7 +12,7 @@ import * as path from 'path';
 import { spawn } from 'child_process';
 import YAML from 'yaml';
 import { stripAnnotations } from './annotations.js';
-import { buildRegistry, labelToDisplay, detectDynamicRefs, resolveForwardRefs } from './crossref.js';
+import { buildRegistry, labelToDisplay, detectDynamicRefs, resolveForwardRefs, resolveSupplementaryRefs } from './crossref.js';
 import { processVariables, hasVariables } from './variables.js';
 import { processSlideMarkdown, hasSlideSyntax } from './slides.js';
 import { injectMediaIntoPptx, injectSlideNumbers, applyBuildupColors } from './pptx-template.js';
@@ -35,6 +35,7 @@ const MAX_TITLE_FILENAME_LENGTH = 50;
 export const DEFAULT_CONFIG = {
     title: 'Untitled Document',
     authors: [],
+    affiliations: {},
     sections: [],
     bibliography: null,
     csl: null,
@@ -321,6 +322,14 @@ export function combineSections(directory, config, options = {}) {
             // Store resolved count for optional reporting
             options._forwardRefsResolved = resolved.length;
         }
+        // Resolve supplementary references and strip their anchors.
+        // pandoc-crossref cannot produce "Figure S1" numbering — it numbers all
+        // figures sequentially. We resolve supplementary refs to plain text and
+        // remove the {#fig:...} attributes so crossref ignores them.
+        const supp = resolveSupplementaryRefs(paperContent, registry);
+        if (supp.resolved.length > 0) {
+            paperContent = supp.text;
+        }
     }
     const paperPath = path.join(directory, 'paper.md');
     fs.writeFileSync(paperPath, paperContent, 'utf-8');
@@ -333,7 +342,9 @@ function buildFrontmatter(config) {
     const fm = {};
     if (config.title)
         fm.title = config.title;
-    if (config.authors && config.authors.length > 0) {
+    // Skip author in frontmatter when using numbered affiliations —
+    // the author block is injected separately per format
+    if (config.authors && config.authors.length > 0 && !hasNumberedAffiliations(config)) {
         fm.author = config.authors;
     }
     if (config.bibliography) {
@@ -354,6 +365,104 @@ function stripFrontmatter(content) {
     }
     return content;
 }
+/**
+ * Check if config uses numbered affiliation mode
+ * (authors have `affiliations` arrays and an affiliations map is defined)
+ */
+function hasNumberedAffiliations(config) {
+    if (!config.affiliations || Object.keys(config.affiliations).length === 0)
+        return false;
+    return config.authors.some(a => typeof a !== 'string' && a.affiliations && a.affiliations.length > 0);
+}
+/**
+ * Generate LaTeX author block using authblk package for numbered superscript affiliations.
+ * Returns LaTeX code to be injected via header-includes.
+ */
+function generateLatexAuthorBlock(config) {
+    const lines = [];
+    lines.push('\\usepackage{authblk}');
+    lines.push('\\renewcommand\\Authfont{\\normalsize}');
+    lines.push('\\renewcommand\\Affilfont{\\small}');
+    lines.push('');
+    // Map affiliation keys to numbers
+    const affiliationKeys = Object.keys(config.affiliations);
+    const keyToNum = new Map();
+    affiliationKeys.forEach((key, i) => keyToNum.set(key, i + 1));
+    // Authors
+    for (const author of config.authors) {
+        if (typeof author === 'string') {
+            lines.push(`\\author{${author}}`);
+            continue;
+        }
+        const marks = (author.affiliations || [])
+            .map(k => keyToNum.get(k))
+            .filter((n) => n !== undefined);
+        const markStr = marks.length > 0 ? `[${marks.join(',')}]` : '';
+        let nameStr = author.name;
+        if (author.corresponding && author.email) {
+            nameStr += `\\thanks{Corresponding author: ${author.email}}`;
+        }
+        else if (author.corresponding) {
+            nameStr += '\\thanks{Corresponding author}';
+        }
+        lines.push(`\\author${markStr}{${nameStr}}`);
+    }
+    // Affiliations
+    for (const [key, text] of Object.entries(config.affiliations)) {
+        const num = keyToNum.get(key);
+        if (num !== undefined) {
+            lines.push(`\\affil[${num}]{${text}}`);
+        }
+    }
+    return lines.join('\n');
+}
+/**
+ * Generate markdown author block for DOCX output with superscript affiliations.
+ * Returns markdown text to insert after the YAML frontmatter.
+ */
+function generateMarkdownAuthorBlock(config) {
+    const lines = [];
+    // Map affiliation keys to numbers
+    const affiliationKeys = Object.keys(config.affiliations);
+    const keyToNum = new Map();
+    affiliationKeys.forEach((key, i) => keyToNum.set(key, i + 1));
+    // Author line: Name^1,2^, Name^3^, ...
+    const authorParts = [];
+    for (const author of config.authors) {
+        if (typeof author === 'string') {
+            authorParts.push(author);
+            continue;
+        }
+        const marks = (author.affiliations || [])
+            .map(k => keyToNum.get(k))
+            .filter((n) => n !== undefined);
+        let entry = author.name;
+        const superParts = marks.map(String);
+        if (author.corresponding)
+            superParts.push('\\*');
+        if (superParts.length > 0) {
+            entry += `^${superParts.join(',')}^`;
+        }
+        authorParts.push(entry);
+    }
+    lines.push(authorParts.join(', '));
+    lines.push('');
+    // Affiliation lines: ^1^ Department of ...
+    for (const [key, text] of Object.entries(config.affiliations)) {
+        const num = keyToNum.get(key);
+        if (num !== undefined) {
+            lines.push(`^${num}^ ${text}`);
+        }
+    }
+    // Corresponding author footnote
+    const corresponding = config.authors.find(a => typeof a !== 'string' && a.corresponding);
+    if (corresponding?.email) {
+        lines.push('');
+        lines.push(`^\\*^ Corresponding author: ${corresponding.email}`);
+    }
+    lines.push('');
+    return lines.join('\n');
+}
 /**
  * Process markdown tables to apply nowrap formatting to specified columns.
  * Converts distribution notation (Normal, Student-t, Gamma) to LaTeX math.
@@ -448,12 +557,26 @@ export function prepareForFormat(paperPath, format, config, options = {}) {
         content = stripAnnotations(content);
         // Process tables for nowrap columns (convert Normal() → $\mathcal{N}()$ etc.)
         content = processTablesForFormat(content, config.tables, format);
+        // Inject LaTeX author block with numbered affiliations
+        if (hasNumberedAffiliations(config)) {
+            const latexBlock = generateLatexAuthorBlock(config);
+            // Inject as header-includes in the YAML frontmatter
+            content = content.replace(/^(---\r?\n[\s\S]*?)(---\r?\n)/, (match, yamlContent, closing) => {
+                return `${yamlContent}header-includes: |\n${latexBlock.split('\n').map(l => '  ' + l).join('\n')}\n${closing}`;
+            });
+        }
     }
     else if (format === 'docx') {
         // Strip track changes, optionally keep comments
         content = stripAnnotations(content, { keepComments: config.docx.keepComments });
         // Convert @fig:label to "Figure 1" for Word readers
         content = convertDynamicRefsToDisplay(content, registry);
+        // Inject markdown author block with superscript affiliations
+        if (hasNumberedAffiliations(config)) {
+            const mdBlock = generateMarkdownAuthorBlock(config);
+            // Insert after YAML frontmatter, before body content
+            content = content.replace(/^(---\r?\n[\s\S]*?---\r?\n)/, `$1\n${mdBlock}\n`);
+        }
     }
     else if (format === 'beamer' || format === 'pptx') {
         // Strip annotations for slide output
@@ -528,6 +651,9 @@ export function buildPandocArgs(format, config, outputPath) {
         args.push('-V', `documentclass=${config.pdf.documentclass}`);
         args.push('-V', `fontsize=${config.pdf.fontsize}`);
         args.push('-V', `geometry:${config.pdf.geometry}`);
+        if (config.pdf.headerIncludes) {
+            args.push('-H', config.pdf.headerIncludes);
+        }
         if (config.pdf.linestretch !== 1) {
             args.push('-V', `linestretch=${config.pdf.linestretch}`);
         }

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package/dist/lib/commands/comments.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"comments.d.ts","sourceRoot":"","sources":["../../../lib/commands/comments.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAkJpC;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAm4B/C"}
+{"version":3,"file":"comments.d.ts","sourceRoot":"","sources":["../../../lib/commands/comments.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAkJpC;;GAEG;AACH,wBAAgB,QAAQ,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CA83B/C"}

package/dist/lib/commands/comments.js

@@ -3,9 +3,7 @@
  *
  * Commands for viewing, navigating, and managing reviewer comments and track changes.
  */
-import { chalk, fs, path, fmt, findFiles, getComments, setCommentStatus, getTrackChanges, applyDecision, cleanupOrphanedMarkers, interactiveCommentReview, 
-// tuiCommentReview, // TUI module not yet migrated
-getUserName, exitWithError, getAnnotationSuggestions, requireFile, } from './context.js';
+import { chalk, fs, path, fmt, findFiles, getComments, setCommentStatus, getTrackChanges, applyDecision, cleanupOrphanedMarkers, interactiveCommentReview, tuiCommentReview, getUserName, exitWithError, getAnnotationSuggestions, requireFile, } from './context.js';
 /**
  * Add a reply after a comment
  * @param text - Full document text
@@ -98,30 +96,24 @@ export function register(program) {
         const text = fs.readFileSync(file, 'utf-8');
         // TUI review mode
         if (options.tui) {
-            console.error(chalk.yellow('TUI mode is temporarily unavailable (module migration in progress)'));
-            console.error(chalk.dim('Use --interactive mode instead: rev comments --interactive ' + file));
-            process.exit(1);
-            // TODO: Re-enable when tui.ts is migrated
-            // let author = options.author || getUserName();
-            // if (!author) {
-            //   exitWithError('No user name set for replies', getAnnotationSuggestions('no_author'));
-            // }
-            //
-            // const result = await tuiCommentReview(text, {
-            //   author,
-            //   addReply: (txt: string, comment: Comment, auth: string, msg: string) => {
-            //     const replyAnnotation = `{>>${auth}: ${msg}<<}`;
-            //     const insertPos = comment.position + comment.match.length;
-            //     return txt.slice(0, insertPos) + ' ' + replyAnnotation + txt.slice(insertPos);
-            //   },
-            //   setStatus: setCommentStatus,
-            // });
-            //
-            // if (result.resolved > 0 || result.replied > 0) {
-            //   fs.writeFileSync(file, result.text, 'utf-8');
-            //   console.log(fmt.status('success', `Changes saved to ${file}`));
-            // }
-            // return;
+            let author = options.author || getUserName();
+            if (!author) {
+                exitWithError('No user name set for replies', getAnnotationSuggestions('no_author'));
+            }
+            const result = await tuiCommentReview(text, {
+                author,
+                addReply: (txt, comment, auth, msg) => {
+                    const replyAnnotation = `{>>${auth}: ${msg}<<}`;
+                    const insertPos = comment.position + comment.match.length;
+                    return txt.slice(0, insertPos) + ' ' + replyAnnotation + txt.slice(insertPos);
+                },
+                setStatus: setCommentStatus,
+            });
+            if (result.resolved > 0 || result.replied > 0) {
+                fs.writeFileSync(file, result.text, 'utf-8');
+                console.log(fmt.status('success', `Changes saved to ${file}`));
+            }
+            return;
         }
         // Interactive review mode
         if (options.interactive) {