fix(sessions): collapse copied session files onto one entry per native id

packages/agent-runtime/src/native-pi-session.test.ts

@@ -61,6 +61,24 @@ describe("NativePiSessionService", () => {
     expect(readFileSync(f.file)).toEqual(before);
   });
 
+  it("collapses copied session files onto one entry per native id (#1359)", async () => {
+    const f = fixture();
+    // A backup copy of the session under a subdirectory of the scan root:
+    // same header id, different path. It must not become a second session.
+    const backupDir = join(f.sessionRoot, "backup");
+    mkdirSync(backupDir, { recursive: true });
+    writeFileSync(join(backupDir, "fixture-copy.jsonl"), f.text);
+
+    // Control: without the copy, list() names the original file's id.
+    const control = new NativePiSessionService({ agentDir: f.agentDir, sessionRoot: f.sessionRoot });
+    const [original] = await control.list();
+
+    const service = new NativePiSessionService({ agentDir: f.agentDir, sessionRoot: f.sessionRoot });
+    const sessions = await service.list();
+    expect(sessions).toHaveLength(1);
+    expect(sessions[0].id).toBe(original.id);
+  });
+
   it("searches native metadata and active-branch message text without rewriting JSONL", async () => {
     const f = fixture();
     const service = new NativePiSessionService({ agentDir: f.agentDir, sessionRoot: f.sessionRoot });

packages/agent-runtime/src/native-pi-session.ts

@@ -547,7 +547,30 @@ export class NativePiSessionService {
         }
       }),
     );
-    return summaries
+    // A copied session file (backup, manual copy) under the scan root must
+    // not become a second session: identity follows the header id, not the
+    // path. Keep the newest write per native id and drop the stale copies
+    // from the records map so lookups cannot route to a dead duplicate
+    // (#1359).
+    const seenNativeIds = new Set<string>();
+    const deduped: Array<SessionSummary | undefined> = [];
+    const sortedByRecency = [...summaries].sort((a, b) =>
+      (b?.updatedAt ?? "").localeCompare(a?.updatedAt ?? ""),
+    );
+    const winnerIds = new Set<string>();
+    for (const summary of sortedByRecency) {
+      if (!summary) continue;
+      const record = this.records.get(summary.id);
+      if (!record) continue;
+      if (seenNativeIds.has(record.nativeId)) {
+        this.records.delete(summary.id);
+        continue;
+      }
+      seenNativeIds.add(record.nativeId);
+      winnerIds.add(summary.id);
+    }
+    deduped.push(...summaries.filter((summary) => summary && winnerIds.has(summary.id)));
+    return deduped
       .filter((session): session is SessionSummary => Boolean(session))
       .sort((a, b) => b.updatedAt.localeCompare(a.updatedAt));
   }