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/issues.md DELETED
@@ -1,180 +0,0 @@
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- # docrev — Open Issues
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-
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- Three issues identified during real-world use on the ADAPT proposal build. Working through one by one.
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-
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- Status legend: `[ ]` planned · `[~]` in progress · `[x]` shipped
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-
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- ---
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-
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- ## Issue 1 — Allow custom pandoc filters / args through `rev build` `[x]`
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-
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- ### Problem
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-
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- 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:
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-
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- - `rev build --help` exposes no `--filter` / `--lua-filter` / `--pandoc-arg`.
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- - `rev.yaml` exposes `docx.reference` and `docx.keepComments` but no generic pandoc passthrough.
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-
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- 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`.
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-
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- ### Design (agreed)
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-
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- **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):
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-
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- ```yaml
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- pandoc-args:
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- - --lua-filter=tofill_filter.lua
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- docx:
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- pandoc-args:
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- - --lua-filter=docx_only.lua
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- pdf:
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- pandoc-args:
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- - --variable=papersize:a4
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- ```
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-
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- **CLI**: repeatable `--pandoc-arg <arg>` on `rev build`, appended *after* config args so CLI wins:
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-
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- ```bash
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- rev build docx --pandoc-arg=--lua-filter=tofill.lua --pandoc-arg=--shift-heading-level-by=1
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- ```
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-
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- **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.
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-
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- ### Touch points
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-
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- - `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`).
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- - `lib/commands/build.ts` — add `--pandoc-arg <arg>` (repeatable via custom collector), forward through `BuildOptions`, ensure CLI args are appended last.
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- - `lib/schema.ts` — declare `pandoc-args` (array of strings) at top level and inside each format object.
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- - `skill/SKILL.md` + `skill/REFERENCE.md` — document new field and flag with a `--lua-filter=` example.
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- - `test/build.test.js` — cover (a) top-level only, (b) format-specific only, (c) both concatenated in order, (d) CLI overrides config.
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-
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- ### Open questions
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-
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- 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`).
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-
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- ---
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-
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- ## Issue 2 — Output filename is auto-truncated mid-word and not configurable `[x]`
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-
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- ### Problem
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-
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- 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`.
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-
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- Root cause: `lib/build.ts:1055-1056` (`runPandoc`) and `lib/commands/build.ts:591-592` (`--show-changes` path):
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-
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- ```ts
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- const baseName = config.title
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- ? config.title.toLowerCase().replace(/[^a-z0-9]+/g, '-').slice(0, 50)
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- : 'paper';
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- ```
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-
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- `.slice(0, 50)` is a blind cut.
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-
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- ### Design (agreed)
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-
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- **rev.yaml**: per-format `output:` map. Extensions optional — added if missing.
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-
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- ```yaml
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- output:
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- docx: ADAPT_proposal_draft.docx
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- pdf: ADAPT_proposal_draft.pdf
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- ```
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-
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- **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.
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-
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- **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.
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-
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- **Doc fix**: surface the default `output/` directory in `rev build --help` and SKILL.md "Project Structure" tree (already mentioned in passing — make it explicit).
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-
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- ### Touch points
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-
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- - `lib/build.ts` — `BuildConfig` (`output?: Record<string, string>`), `DEFAULT_CONFIG`, `runPandoc()` (resolve filename: `config.output[format]` → CLI `-o` → slug). Helper: `resolveOutputName(config, format, cliOverride)`.
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- - `lib/commands/build.ts` — add `-o, --output <path>` flag, wire into `BuildOptions`; same fix applied to the `--show-changes` branch's `baseName` construction.
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- - `lib/schema.ts` — declare `output` as object mapping format → string.
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- - `skill/SKILL.md` — "Project Structure" tree explicitly notes `output/`; new `output:` example under config.
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- - `test/build.test.js` — cover (a) `output:` per-format honored, (b) `-o` CLI override, (c) word-boundary truncation when title >50 chars.
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-
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- ### Resolved
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-
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- - `-o` relative paths resolve under `outputDir`; absolute paths bypass it. Same rule applies to values in `output:`.
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- - 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").
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- - `--show-changes` and `--dual` derived filenames (`-changes.docx`, `_comments.docx`, `_comments.pdf`) follow the chosen base name.
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- - 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:`.
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-
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- ---
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-
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- ## Issue 3 — Raw LaTeX figure blocks silently disappear in docx builds `[x]`
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-
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- ### Problem
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- 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.
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- 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.
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-
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- ### Design (agreed)
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- Three layers, combined:
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- **1. Warn during build (always on).** In `applyFormatTransforms()` for docx, scan for raw LaTeX figure environments (`\begin{figure}` … `\end{figure}` containing `\includegraphics`). Emit:
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-
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- ```
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- Warning: 3 raw LaTeX figure block(s) won't render in docx.
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- intro.md:42 \begin{figure}[H] ... \includegraphics{figures/map.pdf} ...
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- methods.md:118
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- results.md:201
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- Hint: use ![caption](path){#fig:label width=80%} for format-portable figures, or
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- pass --pandoc-arg=--lua-filter=<your.lua> to translate them yourself.
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- ```
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- Counted by file/line so the user can jump to fix.
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- **2. Auto-translate the common shape (opt-out via `docx.translateRawFigures: false`).** Convert
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- ```latex
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- \begin{figure}[H]
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- \centering
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- \includegraphics[width=0.8\textwidth]{figures/map.pdf}
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- \caption{Map of study sites.}
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- \label{fig:map}
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- \end{figure}
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- ```
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- ```markdown
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- ![Map of study sites.](figures/map.pdf){#fig:map width=80%}
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- ```
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- 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.
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- Width conversion: `0.8\textwidth` → `80%`; bare `8cm` → `8cm`; missing → omit.
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- **3. Document.** SKILL.md "Cross-References" section currently mentions `@fig:label` and `{#fig:label}` but doesn't show how to *insert* a figure. Add:
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- ```markdown
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- ![Caption text.](figures/foo.pdf){#fig:foo width=80%}
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- ```
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- Note this is the format-portable form. Also mention that raw `\begin{figure}` blocks are PDF-only.
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- ### Touch points
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- - `lib/build.ts` — new helper `detectRawLatexFigures(content): {file?, line, block}[]` and `translateRawLatexFigures(content): {translated, untranslatedCount}`. Wire into `applyFormatTransforms()` for docx (after `convertDynamicRefsToDisplay`).
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- - `lib/build.ts` — propagate warnings up via the existing `warnings: string[]` returned by `build()`. `rev build` already prints from there.
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- - `lib/commands/build.ts` — surface warnings in normal output (not just verbose).
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- - `lib/schema.ts` — declare `docx.translateRawFigures: boolean` (default true).
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- - `skill/SKILL.md` — figure-insertion example under "Cross-References".
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- - `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`.
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- ### Open questions
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- - 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.
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- - Width unit handling: `0.8\textwidth` → `80%` is unambiguous. `\linewidth` → `100%`? Yes. Other relative units → leave raw and warn.
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- ---
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- ## Working order
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- 1. **Issue 1** first — unblocks immediate workflow needs and provides the manual escape hatch for issue 3 even before auto-translate ships.
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- 2. **Issue 2** next — small, low-risk, quality-of-life win.
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- 3. **Issue 3** last — biggest behavior change; benefits from the verbose pandoc echo (Issue 1) for debugging the lua-filter fallback path.
@@ -1,208 +0,0 @@
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- /* ── Base ──────────────────────────────────────────────── */
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- html, body {
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- height: 100%;
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- }
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-
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- body {
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- background-color: #F5F6F8;
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- color: #3E3F3A;
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- display: flex;
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- flex-direction: column;
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- min-height: 100vh;
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- padding-top: 4rem;
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- font-family: "Roboto", -apple-system, BlinkMacSystemFont, "Segoe UI", system-ui, sans-serif;
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- }
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-
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- .container { flex: 1; }
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- footer { margin-top: auto; }
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-
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- /* ── Navbar (pkgdown-style subtle tint, not bg-primary) ── */
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- .navbar {
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- background: color-mix(in oklab, color-mix(in oklab, var(--bs-body-bg) 95%, var(--bs-primary)) 95%, var(--bs-body-color));
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- border-bottom: 1px solid #DFD7CA;
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- line-height: initial;
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- }
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-
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- .navbar .nav-link.active {
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- font-weight: 600;
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- color: var(--bs-primary) !important;
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- }
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-
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- /* ── Links ─────────────────────────────────────────────── */
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- a { color: #325D88; }
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- a:hover { color: #1E3D5C; }
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-
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- /* ── Headings ──────────────────────────────────────────── */
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- h1 { font-size: 2rem; font-weight: 600; margin-bottom: 1rem; }
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- h2 {
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- font-size: 1.4rem; font-weight: 600;
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- margin-top: 2rem; margin-bottom: .65rem;
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- padding-bottom: .3rem;
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- border-bottom: 1px solid #DFD7CA;
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- }
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- h3 { font-size: 1.1rem; font-weight: 600; margin-top: 1.5rem; }
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- h4 { font-size: 1rem; font-weight: 600; margin-top: 1.2rem; }
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-
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- /* ── Code ──────────────────────────────────────────────── */
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- pre, div.sourceCode {
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- background-color: #EEEEED;
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- border: 1px solid #DFD7CA;
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- border-radius: .375rem;
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- padding: .9rem 1.1rem;
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- font-size: .85rem;
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- overflow-x: auto;
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- margin: 1em 0;
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- }
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- code {
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- background-color: #EEEEED;
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- color: #3E3F3A;
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- border-radius: .25rem;
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- padding: .1em .35em;
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- font-size: .875em;
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- }
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- pre code, div.sourceCode code {
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- background: none;
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- padding: 0;
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- border-radius: 0;
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- font-size: inherit;
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- color: inherit;
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- }
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- div.sourceCode { padding: 0; }
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- div.sourceCode pre { border: none; margin: 0; }
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-
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- /* ── Tables ────────────────────────────────────────────── */
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- table {
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- width: 100%;
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- border-collapse: collapse;
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- margin: 1em 0;
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- font-size: .9rem;
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- }
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-
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- thead th {
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- background-color: #DFD7CA;
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- color: #3E3F3A;
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- font-weight: 600;
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- padding: .5rem .75rem;
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- border-bottom: 2px solid #c8c0b4;
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- text-align: left;
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- }
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-
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- td, th { padding: .4rem .75rem; border-bottom: 1px solid #e8e2d8; }
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- tbody tr:hover { background-color: rgba(223,215,202,.2); }
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-
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- /* ── TOC sidebar ───────────────────────────────────────── */
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- aside#toc, aside .toc, aside nav.toc { font-size: .875rem; }
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-
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- aside h2.h6 {
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- text-transform: uppercase;
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- font-size: .68rem;
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- letter-spacing: .07em;
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- color: #6c757d;
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- font-weight: 600;
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- margin-bottom: .5rem;
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- border: none;
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- padding: 0;
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- }
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-
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- aside .toc, aside #TOC {
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- position: sticky;
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- top: 5rem;
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- max-height: calc(100vh - 6rem);
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- overflow-y: auto;
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- }
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-
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- aside ul {
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- list-style: none;
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- padding-left: .9rem;
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- margin: 0;
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- }
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- aside > nav > .toc > ul,
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- aside .toc > ul { padding-left: 0; }
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-
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- aside li { margin: .1rem 0; }
126
-
127
- aside a {
128
- color: #6c757d;
129
- text-decoration: none;
130
- display: block;
131
- line-height: 1.55;
132
- }
133
- aside a:hover { color: #325D88; }
134
-
135
- /* ── Home page cards ───────────────────────────────────── */
136
- .doc-card {
137
- border: 1px solid #DFD7CA;
138
- border-radius: .375rem;
139
- padding: 1.1rem 1.25rem;
140
- height: 100%;
141
- background: #fff;
142
- transition: border-color .15s, box-shadow .15s;
143
- }
144
- .doc-card:hover {
145
- border-color: #325D88;
146
- box-shadow: 0 2px 8px rgba(50,93,136,.1);
147
- }
148
- .doc-card h5 { font-size: 1rem; font-weight: 600; margin-bottom: .4rem; }
149
- .doc-card p { font-size: .875rem; color: #6c757d; margin-bottom: .6rem; }
150
- .doc-card a.stretched-link::after { z-index: 1; }
151
-
152
- /* ── Badges row ────────────────────────────────────────── */
153
- .badge-row { margin-bottom: 1rem; line-height: 2; }
154
- .badge-row img { margin-right: .25rem; }
155
-
156
- /* ── ── ── DARK MODE ── ── ── ──────────────────────────── */
157
-
158
- [data-bs-theme="dark"] body { background-color: #343739; color: #DFD7CA; }
159
-
160
- [data-bs-theme="dark"] .navbar {
161
- background: color-mix(in oklab, color-mix(in oklab, #343739 92%, var(--bs-primary)) 95%, #DFD7CA);
162
- border-bottom-color: #495057;
163
- }
164
-
165
- [data-bs-theme="dark"] a { color: #7ba8d0; }
166
- [data-bs-theme="dark"] a:hover { color: #a5c4e8; }
167
-
168
- [data-bs-theme="dark"] .navbar .nav-link.active { color: #7ba8d0 !important; }
169
-
170
- [data-bs-theme="dark"] h1,
171
- [data-bs-theme="dark"] h2,
172
- [data-bs-theme="dark"] h3,
173
- [data-bs-theme="dark"] h4 { color: #DFD7CA; }
174
-
175
- [data-bs-theme="dark"] h2 { border-color: #495057; }
176
-
177
- [data-bs-theme="dark"] pre,
178
- [data-bs-theme="dark"] div.sourceCode {
179
- background-color: #2C2F31;
180
- border-color: #495057;
181
- color: #DFD7CA;
182
- }
183
-
184
- [data-bs-theme="dark"] code {
185
- background-color: #2C2F31;
186
- color: #DFD7CA;
187
- }
188
-
189
- [data-bs-theme="dark"] div.sourceCode span[class] { color: #DFD7CA !important; }
190
-
191
- [data-bs-theme="dark"] thead th {
192
- background-color: #3d4043;
193
- color: #DFD7CA;
194
- border-color: #495057;
195
- }
196
- [data-bs-theme="dark"] td,
197
- [data-bs-theme="dark"] th { border-color: #3d4043; }
198
- [data-bs-theme="dark"] tbody tr:hover { background-color: rgba(73,80,87,.3); }
199
-
200
- [data-bs-theme="dark"] aside a { color: #8e9499; }
201
- [data-bs-theme="dark"] aside a:hover { color: #7ba8d0; }
202
-
203
- [data-bs-theme="dark"] .doc-card {
204
- background: #2C2F31;
205
- border-color: #495057;
206
- }
207
- [data-bs-theme="dark"] .doc-card:hover { border-color: #7ba8d0; }
208
- [data-bs-theme="dark"] .doc-card p { color: #8e9499; }