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.ts

@@ -246,6 +246,27 @@ export function chunkMarkdown(
   return chunks;
 }
 
+/**
+ * Remap chunk startLine/endLine from content-relative positions to original
+ * source file positions using a lineMap.  Each entry in lineMap gives the
+ * 1-indexed source line for the corresponding 0-indexed content line.
+ *
+ * This is used for session JSONL files where buildSessionEntry() flattens
+ * messages into a plain-text string before chunking.  Without remapping the
+ * stored line numbers would reference positions in the flattened text rather
+ * than the original JSONL file.
+ */
+export function remapChunkLines(chunks: MemoryChunk[], lineMap: number[] | undefined): void {
+  if (!lineMap || lineMap.length === 0) {
+    return;
+  }
+  for (const chunk of chunks) {
+    // startLine/endLine are 1-indexed; lineMap is 0-indexed by content line
+    chunk.startLine = lineMap[chunk.startLine - 1] ?? chunk.startLine;
+    chunk.endLine = lineMap[chunk.endLine - 1] ?? chunk.endLine;
+  }
+}
+
 export function parseEmbedding(raw: string): number[] {
   try {
     const parsed = JSON.parse(raw) as number[];