fix: remap session JSONL chunk line numbers to original source positions (#12102)

* fix: remap session JSONL chunk line numbers to original source positions

buildSessionEntry() flattens JSONL messages into plain text before
chunkMarkdown() assigns line numbers. The stored startLine/endLine
values therefore reference positions in the flattened text, not the
original JSONL file.

- Add lineMap to SessionFileEntry tracking which JSONL line each
  extracted message came from
- Add remapChunkLines() to translate chunk positions back to original
  JSONL lines after chunking
- Guard remap with source === "sessions" to prevent misapplication
- Include lineMap in content hash so existing sessions get re-indexed

Fixes #12044

* memory: dedupe session JSONL parsing

---------

Co-authored-by: Tak Hoffman <781889+Takhoffman@users.noreply.github.com>

src/memory/internal.test.ts

@@ -2,7 +2,12 @@ import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
-import { chunkMarkdown, listMemoryFiles, normalizeExtraMemoryPaths } from "./internal.js";
+import {
+  chunkMarkdown,
+  listMemoryFiles,
+  normalizeExtraMemoryPaths,
+  remapChunkLines,
+} from "./internal.js";
 
 describe("normalizeExtraMemoryPaths", () => {
   it("trims, resolves, and dedupes paths", () => {
@@ -123,3 +128,65 @@ describe("chunkMarkdown", () => {
     }
   });
 });
+
+describe("remapChunkLines", () => {
+  it("remaps chunk line numbers using a lineMap", () => {
+    // Simulate 5 content lines that came from JSONL lines [4, 6, 7, 10, 13] (1-indexed)
+    const lineMap = [4, 6, 7, 10, 13];
+
+    // Create chunks from content that has 5 lines
+    const content = "User: Hello\nAssistant: Hi\nUser: Question\nAssistant: Answer\nUser: Thanks";
+    const chunks = chunkMarkdown(content, { tokens: 400, overlap: 0 });
+    expect(chunks.length).toBeGreaterThan(0);
+
+    // Before remapping, startLine/endLine reference content line numbers (1-indexed)
+    expect(chunks[0].startLine).toBe(1);
+
+    // Remap
+    remapChunkLines(chunks, lineMap);
+
+    // After remapping, line numbers should reference original JSONL lines
+    // Content line 1 → JSONL line 4, content line 5 → JSONL line 13
+    expect(chunks[0].startLine).toBe(4);
+    const lastChunk = chunks[chunks.length - 1];
+    expect(lastChunk.endLine).toBe(13);
+  });
+
+  it("preserves original line numbers when lineMap is undefined", () => {
+    const content = "Line one\nLine two\nLine three";
+    const chunks = chunkMarkdown(content, { tokens: 400, overlap: 0 });
+    const originalStart = chunks[0].startLine;
+    const originalEnd = chunks[chunks.length - 1].endLine;
+
+    remapChunkLines(chunks, undefined);
+
+    expect(chunks[0].startLine).toBe(originalStart);
+    expect(chunks[chunks.length - 1].endLine).toBe(originalEnd);
+  });
+
+  it("handles multi-chunk content with correct remapping", () => {
+    // Use small chunk size to force multiple chunks
+    // lineMap: 10 content lines from JSONL lines [2, 5, 8, 11, 14, 17, 20, 23, 26, 29]
+    const lineMap = [2, 5, 8, 11, 14, 17, 20, 23, 26, 29];
+    const contentLines = lineMap.map((_, i) =>
+      i % 2 === 0 ? `User: Message ${i}` : `Assistant: Reply ${i}`,
+    );
+    const content = contentLines.join("\n");
+
+    // Use very small chunk size to force splitting
+    const chunks = chunkMarkdown(content, { tokens: 10, overlap: 0 });
+    expect(chunks.length).toBeGreaterThan(1);
+
+    remapChunkLines(chunks, lineMap);
+
+    // First chunk should start at JSONL line 2
+    expect(chunks[0].startLine).toBe(2);
+    // Last chunk should end at JSONL line 29
+    expect(chunks[chunks.length - 1].endLine).toBe(29);
+
+    // Each chunk's startLine should be ≤ its endLine
+    for (const chunk of chunks) {
+      expect(chunk.startLine).toBeLessThanOrEqual(chunk.endLine);
+    }
+  });
+});