docrev 0.11.1 → 0.11.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (144) hide show
  1. package/.gitattributes +1 -1
  2. package/CHANGELOG.md +207 -197
  3. package/PLAN-tables-and-postprocess.md +850 -850
  4. package/README.md +433 -433
  5. package/bin/rev.js +11 -11
  6. package/bin/rev.ts +145 -145
  7. package/completions/rev.bash +127 -127
  8. package/completions/rev.ps1 +210 -210
  9. package/completions/rev.zsh +207 -207
  10. package/dist/lib/annotations.d.ts.map +1 -1
  11. package/dist/lib/annotations.js +28 -0
  12. package/dist/lib/annotations.js.map +1 -1
  13. package/dist/lib/build.d.ts +28 -0
  14. package/dist/lib/build.d.ts.map +1 -1
  15. package/dist/lib/build.js +81 -4
  16. package/dist/lib/build.js.map +1 -1
  17. package/dist/lib/commands/comments.d.ts.map +1 -1
  18. package/dist/lib/commands/comments.js +58 -28
  19. package/dist/lib/commands/comments.js.map +1 -1
  20. package/dist/lib/commands/context.d.ts +1 -0
  21. package/dist/lib/commands/context.d.ts.map +1 -1
  22. package/dist/lib/commands/context.js +1 -0
  23. package/dist/lib/commands/context.js.map +1 -1
  24. package/dist/lib/commands/core.d.ts.map +1 -1
  25. package/dist/lib/commands/core.js +25 -8
  26. package/dist/lib/commands/core.js.map +1 -1
  27. package/dist/lib/commands/response.js +1 -1
  28. package/dist/lib/commands/response.js.map +1 -1
  29. package/dist/lib/commands/utilities.js +164 -164
  30. package/dist/lib/commands/word-tools.js +8 -8
  31. package/dist/lib/grammar.js +3 -3
  32. package/dist/lib/import.d.ts +14 -0
  33. package/dist/lib/import.d.ts.map +1 -1
  34. package/dist/lib/import.js +23 -0
  35. package/dist/lib/import.js.map +1 -1
  36. package/dist/lib/input.d.ts +67 -0
  37. package/dist/lib/input.d.ts.map +1 -0
  38. package/dist/lib/input.js +164 -0
  39. package/dist/lib/input.js.map +1 -0
  40. package/dist/lib/macro-filter.lua +201 -201
  41. package/dist/lib/pdf-comments.js +44 -44
  42. package/dist/lib/plugins.js +57 -57
  43. package/dist/lib/pptx-color-filter.lua +37 -37
  44. package/dist/lib/pptx-themes.js +115 -115
  45. package/dist/lib/response.d.ts +1 -1
  46. package/dist/lib/response.d.ts.map +1 -1
  47. package/dist/lib/response.js +5 -2
  48. package/dist/lib/response.js.map +1 -1
  49. package/dist/lib/schema.d.ts.map +1 -1
  50. package/dist/lib/schema.js +8 -2
  51. package/dist/lib/schema.js.map +1 -1
  52. package/dist/lib/spelling.js +2 -2
  53. package/dist/lib/templates.js +387 -387
  54. package/dist/lib/themes.js +51 -51
  55. package/eslint.config.js +27 -27
  56. package/lib/anchor-match.ts +307 -307
  57. package/lib/annotations.ts +695 -664
  58. package/lib/build.ts +2047 -1956
  59. package/lib/citations.ts +160 -160
  60. package/lib/commands/build.ts +885 -885
  61. package/lib/commands/citations.ts +515 -515
  62. package/lib/commands/comments.ts +1077 -1050
  63. package/lib/commands/context.ts +185 -176
  64. package/lib/commands/core.ts +328 -309
  65. package/lib/commands/doi.ts +451 -451
  66. package/lib/commands/file-ops.ts +372 -372
  67. package/lib/commands/history.ts +320 -320
  68. package/lib/commands/index.ts +87 -87
  69. package/lib/commands/init.ts +259 -259
  70. package/lib/commands/merge-resolve.ts +378 -378
  71. package/lib/commands/preview.ts +178 -178
  72. package/lib/commands/project-info.ts +244 -244
  73. package/lib/commands/quality.ts +517 -517
  74. package/lib/commands/response.ts +454 -454
  75. package/lib/commands/section-boundaries.ts +82 -82
  76. package/lib/commands/sections.ts +451 -451
  77. package/lib/commands/sync.ts +689 -689
  78. package/lib/commands/text-ops.ts +449 -449
  79. package/lib/commands/utilities.ts +448 -448
  80. package/lib/commands/verify-anchors.ts +272 -272
  81. package/lib/commands/word-tools.ts +340 -340
  82. package/lib/comment-realign.ts +99 -99
  83. package/lib/config.ts +84 -84
  84. package/lib/crossref.ts +781 -781
  85. package/lib/csl.ts +191 -191
  86. package/lib/dependencies.ts +132 -132
  87. package/lib/diff-engine.ts +465 -465
  88. package/lib/doi-cache.ts +115 -115
  89. package/lib/doi.ts +879 -879
  90. package/lib/equations.ts +506 -506
  91. package/lib/errors.ts +350 -350
  92. package/lib/format.ts +541 -541
  93. package/lib/git.ts +326 -326
  94. package/lib/grammar.ts +303 -303
  95. package/lib/image-registry.ts +180 -180
  96. package/lib/import.ts +932 -906
  97. package/lib/input.ts +174 -0
  98. package/lib/journals.ts +543 -543
  99. package/lib/macro-filter.lua +201 -201
  100. package/lib/macros.ts +273 -273
  101. package/lib/merge.ts +633 -633
  102. package/lib/ooxml.ts +768 -768
  103. package/lib/orcid.ts +144 -144
  104. package/lib/pdf-comments.ts +263 -263
  105. package/lib/pdf-import.ts +524 -524
  106. package/lib/plugins.ts +362 -362
  107. package/lib/postprocess.ts +188 -188
  108. package/lib/pptx-color-filter.lua +37 -37
  109. package/lib/pptx-template.ts +469 -469
  110. package/lib/pptx-themes.ts +483 -483
  111. package/lib/protect-restore.ts +520 -520
  112. package/lib/rate-limiter.ts +127 -127
  113. package/lib/response.ts +200 -197
  114. package/lib/restore-references.ts +240 -240
  115. package/lib/review.ts +327 -327
  116. package/lib/schema.ts +494 -488
  117. package/lib/scientific-words.ts +73 -73
  118. package/lib/sections.ts +428 -428
  119. package/lib/slides.ts +756 -756
  120. package/lib/spelling.ts +334 -334
  121. package/lib/templates.ts +526 -526
  122. package/lib/themes.ts +742 -742
  123. package/lib/trackchanges.ts +166 -166
  124. package/lib/tui.ts +450 -450
  125. package/lib/types.ts +546 -546
  126. package/lib/undo.ts +250 -250
  127. package/lib/utils.ts +69 -69
  128. package/lib/variables.ts +179 -179
  129. package/lib/word-extraction.ts +525 -525
  130. package/lib/word.ts +526 -526
  131. package/lib/wordcomments.ts +789 -789
  132. package/package.json +1 -1
  133. package/scripts/postbuild.js +47 -47
  134. package/skill/REFERENCE.md +550 -550
  135. package/skill/SKILL.md +302 -302
  136. package/tsconfig.json +26 -26
  137. package/types/index.d.ts +531 -531
  138. package/issues.md +0 -180
  139. package/site/assets/extra.css +0 -208
  140. package/site/commands.html +0 -926
  141. package/site/configuration.html +0 -469
  142. package/site/index.html +0 -288
  143. package/site/troubleshooting.html +0 -461
  144. package/site/workflow.html +0 -518
package/lib/sections.ts CHANGED
@@ -1,428 +1,428 @@
1
- /**
2
- * Section handling - map between section .md files and combined documents
3
- */
4
-
5
- import * as fs from 'fs';
6
- import * as path from 'path';
7
- import YAML from 'yaml';
8
- import type { SectionConfig, SectionsConfig, ExtractedSection } from './types.js';
9
-
10
- /**
11
- * Default section order (common academic paper structure)
12
- */
13
- const DEFAULT_ORDER = [
14
- 'abstract',
15
- 'introduction',
16
- 'background',
17
- 'literature',
18
- 'theory',
19
- 'methods',
20
- 'materials',
21
- 'data',
22
- 'results',
23
- 'analysis',
24
- 'discussion',
25
- 'conclusion',
26
- 'references',
27
- 'appendix',
28
- 'supplementary',
29
- ];
30
-
31
- /**
32
- * Extract header from a markdown file
33
- */
34
- export function extractHeader(filePath: string): string | null {
35
- if (!fs.existsSync(filePath)) return null;
36
-
37
- const content = fs.readFileSync(filePath, 'utf-8');
38
- const lines = content.split('\n');
39
-
40
- for (const line of lines) {
41
- const match = line.match(/^#\s+(.+)$/);
42
- if (match && match[1]) {
43
- return match[1].trim();
44
- }
45
- }
46
-
47
- return null;
48
- }
49
-
50
- /**
51
- * Extract the first markdown heading of ANY level (`#`–`######`) from a file.
52
- *
53
- * Unlike {@link extractHeader} (which is H1-only by contract), this is used to
54
- * derive a section's header from files that lead with a subsection — e.g.
55
- * `02_objectives.md` starting with `## 1.2 Objectives`. Using the real first
56
- * heading lets the derived header match the corresponding docx heading.
57
- */
58
- export function extractFirstHeading(filePath: string): string | null {
59
- if (!fs.existsSync(filePath)) return null;
60
-
61
- const content = fs.readFileSync(filePath, 'utf-8');
62
- for (const line of content.split('\n')) {
63
- const match = line.match(/^#{1,6}\s+(.+)$/);
64
- if (match && match[1]) {
65
- return match[1].trim();
66
- }
67
- }
68
-
69
- return null;
70
- }
71
-
72
- /**
73
- * Generate sections.yaml from existing .md files
74
- */
75
- export function generateConfig(
76
- directory: string,
77
- excludePatterns: string[] = ['paper.md', 'README.md', 'CLAUDE.md']
78
- ): SectionsConfig {
79
- const files = fs.readdirSync(directory).filter((f) => {
80
- if (!f.endsWith('.md')) return false;
81
- if (excludePatterns.some((p) => f.toLowerCase().includes(p.toLowerCase()))) return false;
82
- return true;
83
- });
84
-
85
- const sections: Record<string, SectionConfig> = {};
86
-
87
- for (const file of files) {
88
- const filePath = path.join(directory, file);
89
- // Use the first heading at any level: a section file may be headed by a
90
- // subsection (## 1.2 Objectives). H1-only extraction left such files with a
91
- // filename-derived header that never matched the reviewed document.
92
- const header = extractFirstHeading(filePath);
93
- const baseName = path.basename(file, '.md').toLowerCase();
94
-
95
- // Determine order based on common patterns
96
- let order = DEFAULT_ORDER.findIndex((s) => baseName.includes(s));
97
- if (order === -1) order = 999;
98
-
99
- sections[file] = {
100
- header: header || titleCase(baseName),
101
- aliases: [],
102
- order: order,
103
- };
104
- }
105
-
106
- // Sort by order
107
- const sorted = Object.entries(sections)
108
- .sort((a, b) => (a[1].order ?? 999) - (b[1].order ?? 999))
109
- .reduce((acc, [k, v]) => {
110
- acc[k] = v;
111
- return acc;
112
- }, {} as Record<string, SectionConfig>);
113
-
114
- return {
115
- version: 1,
116
- description: 'Section configuration for rev import/split',
117
- sections: sorted,
118
- };
119
- }
120
-
121
- /**
122
- * Convert string to title case
123
- */
124
- function titleCase(str: string): string {
125
- return str
126
- .split(/[-_\s]+/)
127
- .map((word) => word.charAt(0).toUpperCase() + word.slice(1))
128
- .join(' ');
129
- }
130
-
131
- /**
132
- * Load sections config from yaml file
133
- */
134
- export function loadConfig(configPath: string): SectionsConfig {
135
- const content = fs.readFileSync(configPath, 'utf-8');
136
- const config = YAML.parse(content);
137
-
138
- // Normalize: convert string values to full config objects
139
- const normalized: SectionsConfig = {
140
- version: config.version || 1,
141
- description: config.description,
142
- sections: {},
143
- };
144
-
145
- for (const [file, value] of Object.entries(config.sections || {})) {
146
- if (typeof value === 'string') {
147
- normalized.sections[file] = {
148
- header: value,
149
- aliases: [],
150
- };
151
- } else {
152
- const typedValue = value as SectionConfig;
153
- normalized.sections[file] = {
154
- header: typedValue.header,
155
- aliases: typedValue.aliases || [],
156
- order: typedValue.order,
157
- };
158
- }
159
- }
160
-
161
- return normalized;
162
- }
163
-
164
- /**
165
- * Save sections config to yaml file
166
- */
167
- export function saveConfig(configPath: string, config: SectionsConfig): void {
168
- const yamlStr = YAML.stringify(config, { indent: 2, lineWidth: 100 });
169
- fs.writeFileSync(configPath, yamlStr, 'utf-8');
170
- }
171
-
172
- /**
173
- * Derive a SectionsConfig from the `sections:` list in rev.yaml.
174
- *
175
- * Each listed file's header is its first markdown H1 (falling back to a
176
- * title-cased file name); order follows the list order in rev.yaml. This is
177
- * the same section list that `build` consumes, so a project that only has a
178
- * `rev.yaml` needs no separate `sections.yaml`.
179
- *
180
- * Returns null when rev.yaml is absent, unparseable, or has no `sections` list.
181
- */
182
- export function deriveSectionsFromRev(directory: string): SectionsConfig | null {
183
- const revPath = path.join(directory, 'rev.yaml');
184
- if (!fs.existsSync(revPath)) return null;
185
-
186
- let parsed: { sections?: unknown };
187
- try {
188
- parsed = YAML.parse(fs.readFileSync(revPath, 'utf-8')) || {};
189
- } catch {
190
- return null;
191
- }
192
-
193
- const list = parsed.sections;
194
- if (!Array.isArray(list) || list.length === 0) return null;
195
-
196
- const sections: Record<string, SectionConfig> = {};
197
- list.forEach((entry, index) => {
198
- if (typeof entry !== 'string') return;
199
- const header = extractFirstHeading(path.join(directory, entry)) || titleCase(path.basename(entry, '.md'));
200
- sections[entry] = { header, aliases: [], order: index };
201
- });
202
-
203
- if (Object.keys(sections).length === 0) return null;
204
-
205
- return {
206
- version: 1,
207
- description: 'Derived from rev.yaml sections list',
208
- sections,
209
- };
210
- }
211
-
212
- /**
213
- * Resolve the effective sections config for a project directory.
214
- *
215
- * Precedence (single source of truth, with optional override):
216
- * 1. An explicit sections config file (default `sections.yaml`) when it
217
- * exists — lets users override headers/aliases/order.
218
- * 2. Otherwise the `sections:` list in `rev.yaml`, via {@link deriveSectionsFromRev}.
219
- *
220
- * Returns null only when neither source yields any sections; callers turn that
221
- * into a user-facing error.
222
- */
223
- export function resolveSectionsConfig(
224
- directory: string,
225
- configFileName = 'sections.yaml'
226
- ): { config: SectionsConfig; source: string } | null {
227
- const explicitPath = path.resolve(directory, configFileName);
228
- if (fs.existsSync(explicitPath)) {
229
- return { config: loadConfig(explicitPath), source: explicitPath };
230
- }
231
-
232
- const derived = deriveSectionsFromRev(directory);
233
- if (derived) {
234
- return { config: derived, source: path.resolve(directory, 'rev.yaml') };
235
- }
236
-
237
- return null;
238
- }
239
-
240
- /**
241
- * Match a heading to a section file
242
- */
243
- export function matchHeading(
244
- heading: string,
245
- sections: Record<string, SectionConfig>
246
- ): { file: string; config: SectionConfig } | null {
247
- // Strip markdown header prefix (# or ##, etc.) before matching
248
- const normalizedHeading = heading.replace(/^#{1,6}\s+/, '').toLowerCase().trim();
249
-
250
- for (const [file, config] of Object.entries(sections)) {
251
- // Check primary header
252
- if (config.header.toLowerCase().trim() === normalizedHeading) {
253
- return { file, config };
254
- }
255
-
256
- // Check aliases
257
- if (config.aliases) {
258
- for (const alias of config.aliases) {
259
- if (alias.toLowerCase().trim() === normalizedHeading) {
260
- return { file, config };
261
- }
262
- }
263
- }
264
-
265
- // Fuzzy match: check if heading contains the key words
266
- const headerWords = config.header.toLowerCase().split(/\s+/);
267
- const headingWords = normalizedHeading.split(/\s+/);
268
- const matchCount = headerWords.filter((w) => headingWords.includes(w)).length;
269
- if (matchCount >= headerWords.length * 0.7) {
270
- return { file, config };
271
- }
272
- }
273
-
274
- return null;
275
- }
276
-
277
- /**
278
- * Extract sections from Word document text
279
- */
280
- export function extractSectionsFromText(
281
- text: string,
282
- sections: Record<string, SectionConfig>
283
- ): ExtractedSection[] {
284
- const result: ExtractedSection[] = [];
285
-
286
- // Process line by line to detect markdown headers
287
- const lines = text.split('\n');
288
- let currentSection: { file: string; header: string } | null = null;
289
- let currentContent: string[] = [];
290
-
291
- for (let i = 0; i < lines.length; i++) {
292
- const line = lines[i];
293
- if (!line) continue;
294
- const trimmed = line.trim();
295
-
296
- // Explicitly check for markdown headers (# Header)
297
- const headerMatch = trimmed.match(/^(#{1,6})\s+(.+)$/);
298
-
299
- let matchedSection: { file: string; config: SectionConfig } | null = null;
300
- if (headerMatch) {
301
- // This is a markdown header - try to match it to a section
302
- matchedSection = matchHeading(trimmed, sections);
303
- } else if (trimmed.length > 0 && trimmed.length < 100 && !trimmed.includes('.')) {
304
- // Fallback: check if short text without periods matches a section (for plain text headings)
305
- matchedSection = matchHeading(trimmed, sections);
306
- }
307
-
308
- if (matchedSection) {
309
- // Save previous section
310
- if (currentSection) {
311
- // Include header in content for proper diffing
312
- const fullContent = currentSection.header + '\n\n' + currentContent.join('\n').trim();
313
- result.push({
314
- file: currentSection.file,
315
- header: currentSection.header,
316
- content: fullContent.trim(),
317
- matched: true,
318
- });
319
- }
320
-
321
- currentSection = {
322
- file: matchedSection.file,
323
- header: trimmed,
324
- };
325
- currentContent = [];
326
- } else {
327
- currentContent.push(line);
328
- }
329
- }
330
-
331
- // Save last section
332
- if (currentSection) {
333
- // Include header in content for proper diffing
334
- const fullContent = currentSection.header + '\n\n' + currentContent.join('\n').trim();
335
- result.push({
336
- file: currentSection.file,
337
- header: currentSection.header,
338
- content: fullContent.trim(),
339
- matched: true,
340
- });
341
- }
342
-
343
- return result;
344
- }
345
-
346
- /**
347
- * Parse annotated paper.md and split back to section files
348
- */
349
- export function splitAnnotatedPaper(
350
- paperContent: string,
351
- sections: Record<string, SectionConfig>
352
- ): Map<string, string> {
353
- const result = new Map<string, string>();
354
-
355
- // Look for section markers: <!-- @section:filename.md -->
356
- const markerPattern = /<!--\s*@section:(\S+\.md)\s*-->/g;
357
- const markers = [...paperContent.matchAll(markerPattern)];
358
-
359
- if (markers.length > 0) {
360
- // Use markers
361
- for (let i = 0; i < markers.length; i++) {
362
- const marker = markers[i];
363
- if (!marker || !marker[1]) continue;
364
- const file = marker[1];
365
- const start = (marker.index || 0) + marker[0].length;
366
- const end = markers[i + 1]?.index || paperContent.length;
367
-
368
- let content = paperContent.slice(start, end).trim();
369
-
370
- // Remove trailing marker if present
371
- content = content.replace(/<!--\s*@section:\S+\.md\s*-->$/, '').trim();
372
-
373
- result.set(file, content);
374
- }
375
- } else {
376
- // Fall back to header detection
377
- const lines = paperContent.split('\n');
378
- let currentFile: string | null = null;
379
- let currentContent: string[] = [];
380
-
381
- for (const line of lines) {
382
- const headerMatch = line.match(/^#{1,6}\s+(.+)$/);
383
-
384
- if (headerMatch && headerMatch[1]) {
385
- // Save previous section
386
- if (currentFile) {
387
- result.set(currentFile, currentContent.join('\n').trim());
388
- }
389
-
390
- // Find matching section file
391
- const heading = headerMatch[1].trim();
392
- const match = matchHeading(heading, sections);
393
-
394
- if (match) {
395
- currentFile = match.file;
396
- currentContent = [line];
397
- } else {
398
- // Unknown section - keep accumulating to previous
399
- currentContent.push(line);
400
- }
401
- } else {
402
- currentContent.push(line);
403
- }
404
- }
405
-
406
- // Save last section
407
- if (currentFile) {
408
- result.set(currentFile, currentContent.join('\n').trim());
409
- }
410
- }
411
-
412
- return result;
413
- }
414
-
415
- /**
416
- * Get ordered list of section files from config
417
- */
418
- export function getOrderedSections(config: SectionsConfig): string[] {
419
- const entries = Object.entries(config.sections || {});
420
-
421
- return entries
422
- .sort((a, b) => {
423
- const orderA = a[1].order ?? 999;
424
- const orderB = b[1].order ?? 999;
425
- return orderA - orderB;
426
- })
427
- .map(([file]) => file);
428
- }
1
+ /**
2
+ * Section handling - map between section .md files and combined documents
3
+ */
4
+
5
+ import * as fs from 'fs';
6
+ import * as path from 'path';
7
+ import YAML from 'yaml';
8
+ import type { SectionConfig, SectionsConfig, ExtractedSection } from './types.js';
9
+
10
+ /**
11
+ * Default section order (common academic paper structure)
12
+ */
13
+ const DEFAULT_ORDER = [
14
+ 'abstract',
15
+ 'introduction',
16
+ 'background',
17
+ 'literature',
18
+ 'theory',
19
+ 'methods',
20
+ 'materials',
21
+ 'data',
22
+ 'results',
23
+ 'analysis',
24
+ 'discussion',
25
+ 'conclusion',
26
+ 'references',
27
+ 'appendix',
28
+ 'supplementary',
29
+ ];
30
+
31
+ /**
32
+ * Extract header from a markdown file
33
+ */
34
+ export function extractHeader(filePath: string): string | null {
35
+ if (!fs.existsSync(filePath)) return null;
36
+
37
+ const content = fs.readFileSync(filePath, 'utf-8');
38
+ const lines = content.split('\n');
39
+
40
+ for (const line of lines) {
41
+ const match = line.match(/^#\s+(.+)$/);
42
+ if (match && match[1]) {
43
+ return match[1].trim();
44
+ }
45
+ }
46
+
47
+ return null;
48
+ }
49
+
50
+ /**
51
+ * Extract the first markdown heading of ANY level (`#`–`######`) from a file.
52
+ *
53
+ * Unlike {@link extractHeader} (which is H1-only by contract), this is used to
54
+ * derive a section's header from files that lead with a subsection — e.g.
55
+ * `02_objectives.md` starting with `## 1.2 Objectives`. Using the real first
56
+ * heading lets the derived header match the corresponding docx heading.
57
+ */
58
+ export function extractFirstHeading(filePath: string): string | null {
59
+ if (!fs.existsSync(filePath)) return null;
60
+
61
+ const content = fs.readFileSync(filePath, 'utf-8');
62
+ for (const line of content.split('\n')) {
63
+ const match = line.match(/^#{1,6}\s+(.+)$/);
64
+ if (match && match[1]) {
65
+ return match[1].trim();
66
+ }
67
+ }
68
+
69
+ return null;
70
+ }
71
+
72
+ /**
73
+ * Generate sections.yaml from existing .md files
74
+ */
75
+ export function generateConfig(
76
+ directory: string,
77
+ excludePatterns: string[] = ['paper.md', 'README.md', 'CLAUDE.md']
78
+ ): SectionsConfig {
79
+ const files = fs.readdirSync(directory).filter((f) => {
80
+ if (!f.endsWith('.md')) return false;
81
+ if (excludePatterns.some((p) => f.toLowerCase().includes(p.toLowerCase()))) return false;
82
+ return true;
83
+ });
84
+
85
+ const sections: Record<string, SectionConfig> = {};
86
+
87
+ for (const file of files) {
88
+ const filePath = path.join(directory, file);
89
+ // Use the first heading at any level: a section file may be headed by a
90
+ // subsection (## 1.2 Objectives). H1-only extraction left such files with a
91
+ // filename-derived header that never matched the reviewed document.
92
+ const header = extractFirstHeading(filePath);
93
+ const baseName = path.basename(file, '.md').toLowerCase();
94
+
95
+ // Determine order based on common patterns
96
+ let order = DEFAULT_ORDER.findIndex((s) => baseName.includes(s));
97
+ if (order === -1) order = 999;
98
+
99
+ sections[file] = {
100
+ header: header || titleCase(baseName),
101
+ aliases: [],
102
+ order: order,
103
+ };
104
+ }
105
+
106
+ // Sort by order
107
+ const sorted = Object.entries(sections)
108
+ .sort((a, b) => (a[1].order ?? 999) - (b[1].order ?? 999))
109
+ .reduce((acc, [k, v]) => {
110
+ acc[k] = v;
111
+ return acc;
112
+ }, {} as Record<string, SectionConfig>);
113
+
114
+ return {
115
+ version: 1,
116
+ description: 'Section configuration for rev import/split',
117
+ sections: sorted,
118
+ };
119
+ }
120
+
121
+ /**
122
+ * Convert string to title case
123
+ */
124
+ function titleCase(str: string): string {
125
+ return str
126
+ .split(/[-_\s]+/)
127
+ .map((word) => word.charAt(0).toUpperCase() + word.slice(1))
128
+ .join(' ');
129
+ }
130
+
131
+ /**
132
+ * Load sections config from yaml file
133
+ */
134
+ export function loadConfig(configPath: string): SectionsConfig {
135
+ const content = fs.readFileSync(configPath, 'utf-8');
136
+ const config = YAML.parse(content);
137
+
138
+ // Normalize: convert string values to full config objects
139
+ const normalized: SectionsConfig = {
140
+ version: config.version || 1,
141
+ description: config.description,
142
+ sections: {},
143
+ };
144
+
145
+ for (const [file, value] of Object.entries(config.sections || {})) {
146
+ if (typeof value === 'string') {
147
+ normalized.sections[file] = {
148
+ header: value,
149
+ aliases: [],
150
+ };
151
+ } else {
152
+ const typedValue = value as SectionConfig;
153
+ normalized.sections[file] = {
154
+ header: typedValue.header,
155
+ aliases: typedValue.aliases || [],
156
+ order: typedValue.order,
157
+ };
158
+ }
159
+ }
160
+
161
+ return normalized;
162
+ }
163
+
164
+ /**
165
+ * Save sections config to yaml file
166
+ */
167
+ export function saveConfig(configPath: string, config: SectionsConfig): void {
168
+ const yamlStr = YAML.stringify(config, { indent: 2, lineWidth: 100 });
169
+ fs.writeFileSync(configPath, yamlStr, 'utf-8');
170
+ }
171
+
172
+ /**
173
+ * Derive a SectionsConfig from the `sections:` list in rev.yaml.
174
+ *
175
+ * Each listed file's header is its first markdown H1 (falling back to a
176
+ * title-cased file name); order follows the list order in rev.yaml. This is
177
+ * the same section list that `build` consumes, so a project that only has a
178
+ * `rev.yaml` needs no separate `sections.yaml`.
179
+ *
180
+ * Returns null when rev.yaml is absent, unparseable, or has no `sections` list.
181
+ */
182
+ export function deriveSectionsFromRev(directory: string): SectionsConfig | null {
183
+ const revPath = path.join(directory, 'rev.yaml');
184
+ if (!fs.existsSync(revPath)) return null;
185
+
186
+ let parsed: { sections?: unknown };
187
+ try {
188
+ parsed = YAML.parse(fs.readFileSync(revPath, 'utf-8')) || {};
189
+ } catch {
190
+ return null;
191
+ }
192
+
193
+ const list = parsed.sections;
194
+ if (!Array.isArray(list) || list.length === 0) return null;
195
+
196
+ const sections: Record<string, SectionConfig> = {};
197
+ list.forEach((entry, index) => {
198
+ if (typeof entry !== 'string') return;
199
+ const header = extractFirstHeading(path.join(directory, entry)) || titleCase(path.basename(entry, '.md'));
200
+ sections[entry] = { header, aliases: [], order: index };
201
+ });
202
+
203
+ if (Object.keys(sections).length === 0) return null;
204
+
205
+ return {
206
+ version: 1,
207
+ description: 'Derived from rev.yaml sections list',
208
+ sections,
209
+ };
210
+ }
211
+
212
+ /**
213
+ * Resolve the effective sections config for a project directory.
214
+ *
215
+ * Precedence (single source of truth, with optional override):
216
+ * 1. An explicit sections config file (default `sections.yaml`) when it
217
+ * exists — lets users override headers/aliases/order.
218
+ * 2. Otherwise the `sections:` list in `rev.yaml`, via {@link deriveSectionsFromRev}.
219
+ *
220
+ * Returns null only when neither source yields any sections; callers turn that
221
+ * into a user-facing error.
222
+ */
223
+ export function resolveSectionsConfig(
224
+ directory: string,
225
+ configFileName = 'sections.yaml'
226
+ ): { config: SectionsConfig; source: string } | null {
227
+ const explicitPath = path.resolve(directory, configFileName);
228
+ if (fs.existsSync(explicitPath)) {
229
+ return { config: loadConfig(explicitPath), source: explicitPath };
230
+ }
231
+
232
+ const derived = deriveSectionsFromRev(directory);
233
+ if (derived) {
234
+ return { config: derived, source: path.resolve(directory, 'rev.yaml') };
235
+ }
236
+
237
+ return null;
238
+ }
239
+
240
+ /**
241
+ * Match a heading to a section file
242
+ */
243
+ export function matchHeading(
244
+ heading: string,
245
+ sections: Record<string, SectionConfig>
246
+ ): { file: string; config: SectionConfig } | null {
247
+ // Strip markdown header prefix (# or ##, etc.) before matching
248
+ const normalizedHeading = heading.replace(/^#{1,6}\s+/, '').toLowerCase().trim();
249
+
250
+ for (const [file, config] of Object.entries(sections)) {
251
+ // Check primary header
252
+ if (config.header.toLowerCase().trim() === normalizedHeading) {
253
+ return { file, config };
254
+ }
255
+
256
+ // Check aliases
257
+ if (config.aliases) {
258
+ for (const alias of config.aliases) {
259
+ if (alias.toLowerCase().trim() === normalizedHeading) {
260
+ return { file, config };
261
+ }
262
+ }
263
+ }
264
+
265
+ // Fuzzy match: check if heading contains the key words
266
+ const headerWords = config.header.toLowerCase().split(/\s+/);
267
+ const headingWords = normalizedHeading.split(/\s+/);
268
+ const matchCount = headerWords.filter((w) => headingWords.includes(w)).length;
269
+ if (matchCount >= headerWords.length * 0.7) {
270
+ return { file, config };
271
+ }
272
+ }
273
+
274
+ return null;
275
+ }
276
+
277
+ /**
278
+ * Extract sections from Word document text
279
+ */
280
+ export function extractSectionsFromText(
281
+ text: string,
282
+ sections: Record<string, SectionConfig>
283
+ ): ExtractedSection[] {
284
+ const result: ExtractedSection[] = [];
285
+
286
+ // Process line by line to detect markdown headers
287
+ const lines = text.split('\n');
288
+ let currentSection: { file: string; header: string } | null = null;
289
+ let currentContent: string[] = [];
290
+
291
+ for (let i = 0; i < lines.length; i++) {
292
+ const line = lines[i];
293
+ if (!line) continue;
294
+ const trimmed = line.trim();
295
+
296
+ // Explicitly check for markdown headers (# Header)
297
+ const headerMatch = trimmed.match(/^(#{1,6})\s+(.+)$/);
298
+
299
+ let matchedSection: { file: string; config: SectionConfig } | null = null;
300
+ if (headerMatch) {
301
+ // This is a markdown header - try to match it to a section
302
+ matchedSection = matchHeading(trimmed, sections);
303
+ } else if (trimmed.length > 0 && trimmed.length < 100 && !trimmed.includes('.')) {
304
+ // Fallback: check if short text without periods matches a section (for plain text headings)
305
+ matchedSection = matchHeading(trimmed, sections);
306
+ }
307
+
308
+ if (matchedSection) {
309
+ // Save previous section
310
+ if (currentSection) {
311
+ // Include header in content for proper diffing
312
+ const fullContent = currentSection.header + '\n\n' + currentContent.join('\n').trim();
313
+ result.push({
314
+ file: currentSection.file,
315
+ header: currentSection.header,
316
+ content: fullContent.trim(),
317
+ matched: true,
318
+ });
319
+ }
320
+
321
+ currentSection = {
322
+ file: matchedSection.file,
323
+ header: trimmed,
324
+ };
325
+ currentContent = [];
326
+ } else {
327
+ currentContent.push(line);
328
+ }
329
+ }
330
+
331
+ // Save last section
332
+ if (currentSection) {
333
+ // Include header in content for proper diffing
334
+ const fullContent = currentSection.header + '\n\n' + currentContent.join('\n').trim();
335
+ result.push({
336
+ file: currentSection.file,
337
+ header: currentSection.header,
338
+ content: fullContent.trim(),
339
+ matched: true,
340
+ });
341
+ }
342
+
343
+ return result;
344
+ }
345
+
346
+ /**
347
+ * Parse annotated paper.md and split back to section files
348
+ */
349
+ export function splitAnnotatedPaper(
350
+ paperContent: string,
351
+ sections: Record<string, SectionConfig>
352
+ ): Map<string, string> {
353
+ const result = new Map<string, string>();
354
+
355
+ // Look for section markers: <!-- @section:filename.md -->
356
+ const markerPattern = /<!--\s*@section:(\S+\.md)\s*-->/g;
357
+ const markers = [...paperContent.matchAll(markerPattern)];
358
+
359
+ if (markers.length > 0) {
360
+ // Use markers
361
+ for (let i = 0; i < markers.length; i++) {
362
+ const marker = markers[i];
363
+ if (!marker || !marker[1]) continue;
364
+ const file = marker[1];
365
+ const start = (marker.index || 0) + marker[0].length;
366
+ const end = markers[i + 1]?.index || paperContent.length;
367
+
368
+ let content = paperContent.slice(start, end).trim();
369
+
370
+ // Remove trailing marker if present
371
+ content = content.replace(/<!--\s*@section:\S+\.md\s*-->$/, '').trim();
372
+
373
+ result.set(file, content);
374
+ }
375
+ } else {
376
+ // Fall back to header detection
377
+ const lines = paperContent.split('\n');
378
+ let currentFile: string | null = null;
379
+ let currentContent: string[] = [];
380
+
381
+ for (const line of lines) {
382
+ const headerMatch = line.match(/^#{1,6}\s+(.+)$/);
383
+
384
+ if (headerMatch && headerMatch[1]) {
385
+ // Save previous section
386
+ if (currentFile) {
387
+ result.set(currentFile, currentContent.join('\n').trim());
388
+ }
389
+
390
+ // Find matching section file
391
+ const heading = headerMatch[1].trim();
392
+ const match = matchHeading(heading, sections);
393
+
394
+ if (match) {
395
+ currentFile = match.file;
396
+ currentContent = [line];
397
+ } else {
398
+ // Unknown section - keep accumulating to previous
399
+ currentContent.push(line);
400
+ }
401
+ } else {
402
+ currentContent.push(line);
403
+ }
404
+ }
405
+
406
+ // Save last section
407
+ if (currentFile) {
408
+ result.set(currentFile, currentContent.join('\n').trim());
409
+ }
410
+ }
411
+
412
+ return result;
413
+ }
414
+
415
+ /**
416
+ * Get ordered list of section files from config
417
+ */
418
+ export function getOrderedSections(config: SectionsConfig): string[] {
419
+ const entries = Object.entries(config.sections || {});
420
+
421
+ return entries
422
+ .sort((a, b) => {
423
+ const orderA = a[1].order ?? 999;
424
+ const orderB = b[1].order ?? 999;
425
+ return orderA - orderB;
426
+ })
427
+ .map(([file]) => file);
428
+ }