@vignesh07 you might be interested in this fix. I just rebased and squashed when I saw you pushed some changes and remembered your focus on memory enhancements

+1 — we hit this exact scenario tonight. After a session cleanup, dozens of .jsonl.deleted.* files were invisible to the indexer. Had to manually mv them back to .jsonl as a workaround before we could even begin indexing them (which itself required working around #20148).

This PR + #20148 together would fully resolve the issue. 🙏

+1 from a production deployment.

We have 92 .reset/.deleted session transcript files totaling 37.9 MB that are completely invisible to the memory indexer. This represents ~213% of our currently indexed content — more than double what's searchable is sitting in the dark.

After a session cleanup cycle, memory_search effectively loses access to the majority of historical context. This PR would fix that.

Happy to help test if needed.

Been actively using and debasing since I opened the PR with no issues. Hopefully someone takes a peek soon 🤞

Thanks all for the production feedback and +1s it's actually helpful in a place where there are literally thousands of PRs/issues.

I pushed an update to scope this PR to reset archives only. This changes the scope to indexes *.jsonl and *.jsonl.reset.* only and no longer indexes *.jsonl.deleted.*

Why the change?

From the session lifecycle paths:

• .reset is created when a session is explicitly replaced/reset (for example /new, /reset, or sessions.reset), i.e. “continue conversation lineage from a fresh session”.
• .deleted is created when sessions are explicitly removed/pruned (for example sessions.delete, maintenance prune/cap in enforce mode, and cron run-session reaping).

So .reset is a continuity artifact, while .deleted is a removal artifact. This PR now targets continuity recall only.

Result

This fixes missing memory recall from reset snapshots while intentionally keeping deleted transcripts out of indexing.

If you're looking for *.jsonl.reset.* files to not get deleted then you should also set the following:

• session.maintenance.mode: "warn"
• session.maintenance.resetArchiveRetention: false

If there’s demand for deleted indexing, that should likely be a separate, explicit follow-up (probably as an opt-in and scoped by session type).

@codex review

@greptile-apps review

Greptile Summary

This PR adds opt-in recall of reset-archive transcripts (*.jsonl.reset.<timestamp>) to both the builtin memory-search sync path and the QMD manager. The implementation wires a new includeResetArchives boolean through schema validation, config types, help text, labels, merge logic, and runtime meta tracking — all consistent with existing patterns. Archive lifecycle events (archiveFileOnDisk, cleanupArchivedSessionTranscripts) now emit emitSessionTranscriptUpdate so index entries can be invalidated after cleanup. Two issues were found:

• emitSessionTranscriptUpdate emitted after a silently-swallowed rm failure (src/gateway/session-utils.fs.ts:269-273): if fs.promises.rm fails and the error is caught, the removal signal still fires — potentially causing the memory manager to drop an index entry for a file that remains on disk.
• Stale session-row cleanup skipped on full reindex (src/memory/manager-sync-ops.ts:784-789): sessionRowsBefore is set to [] when needsFullReindex is true, making the stale-row deletion loop a no-op. The old code always queried and cleaned stale rows regardless of reindex mode. This is safe only if the parent sync path already bulk-deletes session rows before calling syncSessionFiles — please confirm this assumption or restore the unconditional query for the cleanup pass.

Confidence Score: 3/5

• Safe to merge only after confirming that stale session rows are cleaned on full reindex and the emitSessionTranscriptUpdate emit is guarded against failed rm calls.
• Config plumbing, filtering logic, and most of the lifecycle emit work are solid and well-tested. Two logic concerns reduce confidence: (1) the emitSessionTranscriptUpdate call fires even when rm silently fails, sending a false removal signal downstream, and (2) the sessionRowsBefore = [] optimization on full reindex may prevent stale rows from being cleaned up unless a bulk-delete exists elsewhere in the sync path — the test at line 814 should surface this if broken, but the assumption is not documented in the code.
• src/memory/manager-sync-ops.ts (stale cleanup on full reindex) and src/gateway/session-utils.fs.ts (emit after failed rm).

This is a comment left during a code review.
Path: src/gateway/session-utils.fs.ts
Line: 269-273

Comment:
**Transcript update emitted even when `rm` fails silently**

`fs.promises.rm` errors are swallowed by `.catch(() => undefined)`, but `emitSessionTranscriptUpdate` is called unconditionally afterward. If the file removal fails, downstream subscribers (memory index manager) will receive a "file removed" signal for a file that still exists on disk. This can cause the index entry to be deleted and then re-added on the next sync cycle — at minimum, unnecessary churn.

Compare with `archiveFileOnDisk` where `renameSync` throws on failure so the emit is implicitly guarded. The cleanup path should apply the same guard:

```typescript
const removed_ = await fs.promises.rm(fullPath).then(() => true, () => false);
if (removed_) {
  removed += 1;
  if (reason === "reset") {
    emitSessionTranscriptUpdate(fullPath);
  }
}
```

How can I resolve this? If you propose a fix, please make it concise.

---

This is a comment left during a code review.
Path: src/memory/manager-sync-ops.ts
Line: 784-789

Comment:
**Stale session rows not cleaned up on full reindex**

`sessionRowsBefore` is set to `[]` when `needsFullReindex` is `true`, which means the stale-row cleanup loop at the bottom of `syncSessionFiles` becomes a no-op during full reindexes. Prior to this PR, the `staleRows` query ran *after* indexing regardless of `needsFullReindex`, so it always cleaned up paths no longer in `activePaths`.

The practical impact is visible in the toggle scenario: when `includeResetArchives` flips from `true` → `false`, a full reindex is triggered (via `metaSessionIncludeResetArchivesDiffers`), `activePaths` no longer includes reset archive paths, but because `sessionRowsBefore = []` the stale reset archive rows are never deleted from the `files`/`chunks` tables.

The test `triggers a full session reindex when includeResetArchives toggles` expects `withoutArchivesFiles` to equal `1` after the toggle, which would fail unless there is a pre-existing bulk-delete of session rows elsewhere in the parent sync path (not visible in this diff). If that bulk-delete exists, this is intentional; if not, it is a regression. Please confirm that the full reindex path clears session rows before calling `syncSessionFiles({ needsFullReindex: true })`, or restore the unconditional query for the cleanup pass:

```typescript
const sessionRowsBefore =
  (this.db.prepare(`SELECT path FROM files WHERE source = ?`).all("sessions") as Array<{
    path: string;
  }>);
const knownPaths = params.needsFullReindex
  ? new Set<string>()
  : new Set(sessionRowsBefore.map((row) => row.path));
```

This preserves the optimization (skip known unchanged paths on incremental sync) while still ensuring stale rows are cleaned up on full reindex.

How can I resolve this? If you propose a fix, please make it concise.

_{Last reviewed commit: cd22347}

@greptile-apps review
@codex review

Codex Review: Didn't find any major issues. What shall we delve into next?

@vignesh07 would you mind taking a look?

@greptile-apps review
@codex review

Codex Review: Didn't find any major issues. 🎉

@greptile-apps review
@codex review

Codex Review: Didn't find any major issues. Delightful!

@vignesh07 rebased with main and addressed additional bot reviews 🤞

+1 — this PR fixes a real pain point (92 .reset files / 37.9MB excluded from search). Codex review passed, rebased clean. Would love to see this merged! 🙏

Taking a look.