claude: Eliminate circular dependency between core API and engine layer

Moved utility functions from execute/ layer to core/ to break the circular
dependency where core/quarto-api.ts imported from execute/jupyter/percent.ts,
which in turn imported from core/quarto-api.ts.

Changes:
- Move execute/jupyter/percent.ts → core/jupyter/percent.ts (breaks cycle)
  - Updated to import directly from core utilities instead of quartoAPI
- Move languagesInMarkdown() → core/pandoc/pandoc-partition.ts
  - Belongs with other markdown parsing logic
- Move isQmdFile() → core/path.ts
  - Fits naturally with other path utilities
- Move postProcessRestorePreservedHtml() → core/jupyter/preserve.ts
  - Lives with restorePreservedHtml() function it wraps

All functions moved to existing files (zero new files created).
Core utilities no longer depend on engine layer.
Typecheck passes.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: gordonwoodhull

src/core/jupyter/jupyter.ts

@@ -152,7 +152,7 @@ import {
 import { figuresDir, inputFilesDir } from "../render.ts";
 import { lines, trimEmptyLines } from "../lib/text.ts";
 import { partitionYamlFrontMatter, readYamlFromMarkdown } from "../yaml.ts";
-import { languagesInMarkdown } from "../../execute/engine-shared.ts";
+import { languagesInMarkdown } from "../pandoc/pandoc-partition.ts";
 import {
   normalizePath,
   pathWithForwardSlashes,

src/execute/jupyter/percent.ts src/core/jupyter/percent.tssrc/execute/jupyter/percent.ts renamed to src/core/jupyter/percent.ts

@@ -7,10 +7,11 @@
 import { extname } from "../../deno_ral/path.ts";
 
 import { Metadata } from "../../config/types.ts";
-import { pandocAttrKeyvalueFromText } from "../../core/pandoc/pandoc-attr.ts";
+import { pandocAttrKeyvalueFromText } from "../pandoc/pandoc-attr.ts";
 import { kCellRawMimeType } from "../../config/constants.ts";
-import { mdFormatOutput, mdRawOutput } from "../../core/jupyter/jupyter.ts";
-import { quartoAPI as quarto } from "../../core/quarto-api.ts";
+import { mdFormatOutput, mdRawOutput } from "./jupyter.ts";
+import { lines, trimEmptyLines } from "../lib/text.ts";
+import { asYamlText } from "./jupyter-fixups.ts";
 
 export const kJupyterPercentScriptExtensions = [
   ".py",
@@ -37,7 +38,7 @@ export function markdownFromJupyterPercentScript(file: string) {
   // break into cells
   const cells: PercentCell[] = [];
   const activeCell = () => cells[cells.length - 1];
-  for (const line of quarto.text.lines(Deno.readTextFileSync(file).trim())) {
+  for (const line of lines(Deno.readTextFileSync(file).trim())) {
     const header = percentCellHeader(line);
     if (header) {
       cells.push({ header, lines: [] });
@@ -63,11 +64,11 @@ export function markdownFromJupyterPercentScript(file: string) {
   };
 
   return cells.reduce((markdown, cell) => {
-    const cellLines = quarto.text.trimEmptyLines(cell.lines);
+    const cellLines = trimEmptyLines(cell.lines);
     if (cell.header.type === "code") {
       if (cell.header.metadata) {
-        const yamlText = quarto.text.asYamlText(cell.header.metadata);
-        cellLines.unshift(...quarto.text.lines(yamlText).map((line) => `#| ${line}`));
+        const yamlText = asYamlText(cell.header.metadata);
+        cellLines.unshift(...lines(yamlText).map((line) => `#| ${line}`));
       }
       markdown += asCell(["```{" + language + "}", ...cellLines, "```"]);
     } else if (cell.header.type === "markdown") {
@@ -77,10 +78,10 @@ export function markdownFromJupyterPercentScript(file: string) {
       const format = cell.header?.metadata?.["format"];
       const mimeType = cell.header.metadata?.[kCellRawMimeType];
       if (typeof mimeType === "string") {
-        const rawBlock = mdRawOutput(mimeType, quarto.text.lines(rawContent));
+        const rawBlock = mdRawOutput(mimeType, lines(rawContent));
         rawContent = rawBlock || rawContent;
       } else if (typeof format === "string") {
-        rawContent = mdFormatOutput(format, quarto.text.lines(rawContent));
+        rawContent = mdFormatOutput(format, lines(rawContent));
       }
       markdown += rawContent;
     }

src/core/jupyter/preserve.ts

@@ -1,10 +1,10 @@
 /*
-* preserve.ts
-*
-* Copyright (C) 2020-2022 Posit Software, PBC
-*
-*/
+ * preserve.ts
+ *
+ * Copyright (C) 2020-2022 Posit Software, PBC
+ */
 
+import { dirname, isAbsolute, join } from "../../deno_ral/path.ts";
 import { kTextHtml, kTextMarkdown } from "../mime.ts";
 import { isDisplayData } from "./display-data.ts";
 import { JupyterNotebook, JupyterOutputDisplayData } from "./types.ts";
@@ -58,3 +58,27 @@ export function restorePreservedHtml(
 export function isPreservedHtml(_html: string) {
   return false;
 }
+
+export function postProcessRestorePreservedHtml(options: PostProcessOptions) {
+  // read the output file
+
+  const outputPath = isAbsolute(options.output)
+    ? options.output
+    : join(dirname(options.target.input), options.output);
+  let output = Deno.readTextFileSync(outputPath);
+
+  // substitute
+  output = restorePreservedHtml(
+    output,
+    options.preserve,
+  );
+
+  // re-write the output
+  Deno.writeTextFileSync(outputPath, output);
+}
+
+interface PostProcessOptions {
+  target: { input: string };
+  output: string;
+  preserve?: Record<string, string>;
+}

src/core/pandoc/pandoc-partition.ts

@@ -109,3 +109,24 @@ export function markdownWithExtractedHeading(markdown: string) {
     contentBeforeHeading,
   };
 }
+
+export function languagesInMarkdownFile(file: string) {
+  return languagesInMarkdown(Deno.readTextFileSync(file));
+}
+
+export function languagesInMarkdown(markdown: string) {
+  // see if there are any code chunks in the file
+  const languages = new Set<string>();
+  const kChunkRegex = /^[\t >]*```+\s*\{([a-zA-Z0-9_]+)( *[ ,].*)?\}\s*$/gm;
+  kChunkRegex.lastIndex = 0;
+  let match = kChunkRegex.exec(markdown);
+  while (match) {
+    const language = match[1].toLowerCase();
+    if (!languages.has(language)) {
+      languages.add(language);
+    }
+    match = kChunkRegex.exec(markdown);
+  }
+  kChunkRegex.lastIndex = 0;
+  return languages;
+}

src/core/path.ts

@@ -92,6 +92,12 @@ export function dirAndStem(file: string): [string, string] {
   ];
 }
 
+export function isQmdFile(file: string) {
+  const ext = extname(file).toLowerCase();
+  const kQmdExtensions = [".qmd"];
+  return kQmdExtensions.includes(ext);
+}
+
 export function expandPath(path: string) {
   if (path === "~") {
     return getenv("HOME", "~");

src/core/quarto-api.ts

@@ -43,11 +43,10 @@ import type { PandocIncludes, PostProcessOptions } from "../execute/types.ts";
 import {
   isJupyterPercentScript,
   markdownFromJupyterPercentScript,
-} from "../execute/jupyter/percent.ts";
+} from "./jupyter/percent.ts";
+import { postProcessRestorePreservedHtml } from "./jupyter/preserve.ts";
 import { runExternalPreviewServer } from "../preview/preview-server.ts";
 import type { PreviewServer } from "../preview/preview-server.ts";
-import { isQmdFile } from "../execute/qmd.ts";
-import { postProcessRestorePreservedHtml } from "../execute/engine-shared.ts";
 import { onCleanup } from "./cleanup.ts";
 import { inputFilesDir, isServerShiny, isServerShinyPython } from "./render.ts";
 import { quartoDataDir } from "./appdirs.ts";
@@ -224,8 +223,10 @@ export interface QuartoAPI {
 
 // Create the implementation of the quartoAPI
 import { readYamlFromMarkdown } from "./yaml.ts";
-import { partitionMarkdown } from "./pandoc/pandoc-partition.ts";
-import { languagesInMarkdown } from "../execute/engine-shared.ts";
+import {
+  languagesInMarkdown,
+  partitionMarkdown,
+} from "./pandoc/pandoc-partition.ts";
 import {
   asMappedString,
   mappedIndexToLineCol,
@@ -241,7 +242,12 @@ import {
   isMarkdownOutput,
   isPresentationOutput,
 } from "../config/format.ts";
-import { dirAndStem, normalizePath, pathWithForwardSlashes } from "./path.ts";
+import {
+  dirAndStem,
+  isQmdFile,
+  normalizePath,
+  pathWithForwardSlashes,
+} from "./path.ts";
 import { quartoRuntimeDir } from "./appdirs.ts";
 import { resourcePath } from "./resources.ts";
 import { isInteractiveSession } from "./platform.ts";

src/execute/jupyter/jupyter.ts

@@ -69,7 +69,7 @@ interface JupyterTargetData {
 // Import quartoAPI directly since we're in core codebase
 import { quartoAPI as quarto } from "../../core/quarto-api.ts";
 import { MappedString } from "../../core/mapped-text.ts";
-import { kJupyterPercentScriptExtensions } from "./percent.ts";
+import { kJupyterPercentScriptExtensions } from "../../core/jupyter/percent.ts";
 import type { CheckConfiguration } from "../../command/check/check.ts";
 
 export const jupyterEngineDiscovery: ExecutionEngineDiscovery = {

src/project/types/manuscript/manuscript-render.ts

@@ -41,7 +41,7 @@ import { logProgress } from "../../../core/log.ts";
 import { kOutputFile } from "../../../config/constants.ts";
 import { readBaseInputIndex } from "../../project-index.ts";
 import { outputFile } from "../../../render/notebook/notebook-contributor-ipynb.ts";
-import { isQmdFile } from "../../../execute/qmd.ts";
+import { isQmdFile } from "../../../core/path.ts";
 
 interface ManuscriptCompletion {
   completion: PandocRenderCompletion;

src/project/types/manuscript/manuscript.ts

@@ -102,10 +102,9 @@ import { manuscriptRenderer } from "./manuscript-render.ts";
 import { outputFile } from "../../../render/notebook/notebook-contributor-html.ts";
 import { Document } from "../../../core/deno-dom.ts";
 import { kHtmlEmptyPostProcessResult } from "../../../command/render/constants.ts";
-import { isQmdFile } from "../../../execute/qmd.ts";
 
 import * as ld from "../../../core/lodash.ts";
-import { safeExistsSync } from "../../../core/path.ts";
+import { isQmdFile, safeExistsSync } from "../../../core/path.ts";
 
 import {
   copySync,

src/render/notebook/notebook-contributor-html.ts

@@ -45,8 +45,7 @@ import { kNotebookViewStyleNotebook } from "../../format/html/format-html-consta
 import { kAppendixStyle } from "../../format/html/format-html-shared.ts";
 import { basename, dirname, join, relative } from "../../deno_ral/path.ts";
 import { Format } from "../../config/types.ts";
-import { isQmdFile } from "../../execute/qmd.ts";
-import { dirAndStem } from "../../core/path.ts";
+import { dirAndStem, isQmdFile } from "../../core/path.ts";
 import { projectOutputDir } from "../../project/project-shared.ts";
 import { existsSync } from "../../deno_ral/fs.ts";
 import { safeCloneDeep } from "../../core/safe-clone-deep.ts";