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/session-files.ts

@@ -14,6 +14,8 @@ export type SessionFileEntry = {
   size: number;
   hash: string;
   content: string;
+  /** Maps each content line (0-indexed) to its 1-indexed JSONL source line. */
+  lineMap: number[];
 };
 
 export async function listSessionFilesForAgent(agentId: string): Promise<string[]> {
@@ -75,7 +77,9 @@ export async function buildSessionEntry(absPath: string): Promise<SessionFileEnt
     const raw = await fs.readFile(absPath, "utf-8");
     const lines = raw.split("\n");
     const collected: string[] = [];
-    for (const line of lines) {
+    const lineMap: number[] = [];
+    for (let jsonlIdx = 0; jsonlIdx < lines.length; jsonlIdx++) {
+      const line = lines[jsonlIdx];
       if (!line.trim()) {
         continue;
       }
@@ -108,6 +112,7 @@ export async function buildSessionEntry(absPath: string): Promise<SessionFileEnt
       const safe = redactSensitiveText(text, { mode: "tools" });
       const label = message.role === "user" ? "User" : "Assistant";
       collected.push(`${label}: ${safe}`);
+      lineMap.push(jsonlIdx + 1);
     }
     const content = collected.join("\n");
     return {
@@ -115,8 +120,9 @@ export async function buildSessionEntry(absPath: string): Promise<SessionFileEnt
       absPath,
       mtimeMs: stat.mtimeMs,
       size: stat.size,
-      hash: hashText(content),
+      hash: hashText(content + "\n" + lineMap.join(",")),
       content,
+      lineMap,
     };
   } catch (err) {
     log.debug(`Failed reading session file ${absPath}: ${String(err)}`);