Fix paragraph chunking to ignore blank lines inside code fences

src/auto-reply/chunk.test.ts

@@ -343,6 +343,17 @@ describe("chunkMarkdownTextWithMode", () => {
     const text = "```js\nconst a = 1;\nconst b = 2;\n```\nAfter";
     expect(chunkMarkdownTextWithMode(text, 1000, "newline")).toEqual([text]);
   });
+
+  it("does not split on blank lines inside a fenced code block", () => {
+    const text = "```python\ndef my_function():\n    x = 1\n\n    y = 2\n    return x + y\n```";
+    expect(chunkMarkdownTextWithMode(text, 1000, "newline")).toEqual([text]);
+  });
+
+  it("splits on blank lines between a code fence and following paragraph", () => {
+    const fence = "```python\ndef my_function():\n    x = 1\n\n    y = 2\n    return x + y\n```";
+    const text = `${fence}\n\nAfter`;
+    expect(chunkMarkdownTextWithMode(text, 1000, "newline")).toEqual([fence, "After"]);
+  });
 });
 
 describe("resolveChunkMode", () => {

src/auto-reply/chunk.ts

@@ -189,11 +189,19 @@ export function chunkByParagraph(text: string, limit: number): string[] {
     return normalized.length <= limit ? [normalized] : chunkText(normalized, limit);
   }
 
+  const spans = parseFenceSpans(normalized);
+
   const parts: string[] = [];
   const re = /\n[\t ]*\n+/g; // paragraph break: blank line(s), allowing whitespace
   let lastIndex = 0;
   for (const match of normalized.matchAll(re)) {
     const idx = match.index ?? 0;
+
+    // Do not split on blank lines that occur inside fenced code blocks.
+    if (!isSafeFenceBreak(spans, idx)) {
+      continue;
+    }
+
     parts.push(normalized.slice(lastIndex, idx));
     lastIndex = idx + match[0].length;
   }