# NousResearch/hermes-agent · Cron job loss during updates and migrations

## Open now

- 0 issues, 1 PR open on GitHub.
- PR #35594: fix(backup): atomically restore cron/jobs.json via tempfile + rename

These issues and pull requests concern scheduled cron jobs being silently deleted or cleared during Hermes updates, config migrations, and related backup/restore operations. The work spans bug reports, feature durability questions, and several proposed fixes targeting atomic file handling and payload exclusions.

## TL;DR

- 4 member(s): 0 open issue(s), 1 closed issue(s), 1 open PR(s), 1 merged PR(s), 1 PR(s) closed without merging.
- A fix was merged to main in PR #34840. Verify it addresses your case.
- **Recommended:** read PR #34840 (and any competing PRs below) before filing. Confirm the merged change covers your symptom.

## Maintainer resolution verdict

- Internal-tracker verdict over this cluster's issue members: `resolved` · deciding PR(s): `pr-34840`. This is distinct from the fix status above. Weigh it yourself.

## How this cluster was grouped

- Link evidence (`STRUCTURAL_SPANNING`): every member is connected by structural evidence: shared changed files, or a closing/superseded reference.
- Pairwise link density `0.50`: the share of member pairs that carry a link, counting a structural link in full and a relevance-only link at 0.36. `1.00` means every pair is linked.

## Closed / duplicate issues

- #34600: fix(cron): config migration (23 to 24) may silently clear cron/jobs.json

## Prior & competing PRs

- **#34840: fix(cron): stop silent cron-job loss across update (disk-cleanup + snapshot restore)**. merged to main · fix tier `verified`
  - maintainer direction: category `merged`
  - files: `hermes_cli/backup.py`, `hermes_cli/main.py`, `plugins/disk-cleanup/disk_cleanup.py`, `scripts/release.py`, `tests/hermes_cli/test_backup.py`, `tests/plugins/test_disk_cleanup_plugin.py`
  - fix hunks:
  - `hermes_cli/backup.py`

    ```diff
    @@ -670,6 +670,105 @@ def restore_quick_snapshot(
         return restored > 0
     
     
    +# Relative path of the cron job database inside HERMES_HOME. Kept in sync with
    +# the entry in ``_QUICK_STATE_FILES`` and with ``cron/jobs.py``'s ``JOBS_FILE``.
    +_CRON_JOBS_REL = "cron/jobs.json"
    +
    +
    +def _count_cron_jobs(path: Path) -> Optional[int]:
    +    """Return the number of cron jobs stored in ``path``.
    +
    +    The canonical on-disk shape is ``{"jobs": [...]}`` (see ``cron/jobs.py``).
    +    A legacy bare-list shape (``[...]``) is also honoured.
    +
    +    Returns:
    +        The job count for any *valid, readable* JSON document, or ``None`` if
    +        the file is missing or cannot be parsed. ``None`` means "unknown" —
    +        callers must not treat it as "zero jobs", because acting on an
    +        unreadable file could mask a real corruption the user needs to see.
    +    """
    +    if not path.is_file():
    +        return None
    +    try:
    +        with open(path, "r", encoding="utf-8") as f:
    +            data = json.load(f)
    +    except (OSError, json.JSONDecodeError):
    +        return None
    +    if isinstance(data, dict):
    +        jobs = data.get("jobs", [])
    +        return len(jobs) if isinstance(jobs, list) else None
    +    if isinstance(data, list):
    +        return len(data)
    +    return None
    +
    +
    +def restore_cron_jobs_if_emptied(
    +    snapshot_id: str,
    +    hermes_home: Optional[Path] = None,
    +) -> Optional[Dict[str, Any]]:
    +    """Safety net for silent cron-job loss across ``hermes update``.
    +
    +    Config-version migrations have been observed to leave ``cron/jobs.json``
    +    valid-but-empty after an update, silently dropping every scheduled job
    +    (issue #34600). The existing malformed-shape guards in ``cron/jobs.py``
    +    don't catch this case because ``{"jobs": []}`` is perfectly valid JSON.
    +
    +    This compares the *current* job count against the pre-update snapshot. If
    +    the live file now has **zero** jobs while the snapshot captured **one or
    +    more**, the snapshot copy of ``cron/jobs.json`` is restored in place.
    +
    +    The check is deliberately conservative — it only ever restores when there
    +    is unambiguous evidence of loss (snapshot had jobs, live file has none),
    +    so a user who genuinely deleted all their jobs during/after the update is
    +    never second-guessed, and an unreadable live file (count ``None``) is left
    +    untouched so real corruption still surfaces.
    +
    +    Args:
    +        snapshot_id: The pre-update quick-snapshot id (from
    +            :func:`create_quick_snapshot`).
    +        hermes_home: Override for the Hermes home directory (tests).
    +
    +    Returns:
    +        ``None`` when no action was taken (the common, healthy path). On a
    +        successful restore, a dict ``{"restored": True, "job_count": N,
    +        "snapshot_id": ...}`` so the caller can warn the user.
    +    """
    +    if not snapshot_id:
    +        return None
    +
    +    home = hermes_home or get_hermes_home()
    +    live_path = home / _CRON_JOBS_REL
    +
    +    live_count = _count_cron_jobs(live_path)
    +    # Only act when the live file is readable AND empty. ``None`` (missing or
    +    # unparseable) is intentionally left alone — that's a different failure
    +    # mode the user should see rather than have papered over.
    +    if live_count is None or live_count > 0:
    +        return None
    +
    +    snap_path = _quick_snapshot_root(home) / snapshot_id / _CRON_JOBS_REL
    +    snap_count = _count_cron_jobs(snap_path)
    +    if not snap_count:  # None or 0 — nothing worth restoring
    +        return None
    +
    +    try:
    +        live_path.parent.mkdir(parents=True, exist_ok=True)
    +        shutil.copy2(snap_path, live_path)
    +    except (OSError, PermissionError) as exc:
    +        logger.error(
    +            "Cron jobs were emptied during update but auto-restore failed: %s", exc
    +        )
    +        return None
    +
    +    logger.warning(
    +        "Restored %d cron job(s) from pre-update snapshot %s "
    +        "(cron/jobs.json was emptied during migration)",
    +        snap_count,
    +        snapshot_id,
    +    )
    +    return {"restored": True, "job_count": snap_count, "snapshot_id": snapshot_id}
    +
    +
     def _prune_quick_snapshots(root: Path, keep: int = _QUICK_DEFAULT_KEEP) -> int:
         """Remove oldest quick snapshots beyond the keep limit. Returns count deleted."""
         if not root.exists():
    ```
  - `hermes_cli/main.py`

    ```diff
    @@ -9125,12 +9125,13 @@ def _cmd_update_impl(args, gateway_mode: bool):
             # though `git pull` can't touch $HERMES_HOME, this is cheap
             # belt-and-suspenders insurance and gives the user something to
             # restore from via `/snapshot list` / `/snapshot restore <id>`.
    +        pre_update_snapshot_id = None
             try:
                 from hermes_cli.backup import create_quick_snapshot
     
    -            snap_id = create_quick_snapshot(label="pre-update", keep=1)
    -            if snap_id:
    -                print(f"  ✓ Pre-update snapshot: {snap_id}")
    +            pre_update_snapshot_id = create_quick_snapshot(label="pre-update", keep=1)
    +            if pre_update_snapshot_id:
    +                print(f"  ✓ Pre-update snapshot: {pre_update_snapshot_id}")
             except Exception as exc:
                 # Never let a snapshot failure block an update.
                 logger.debug("Pre-update snapshot failed: %s", exc)
    ```

    ```diff
    @@ -9467,6 +9468,25 @@ def _cmd_update_impl(args, gateway_mode: bool):
             else:
                 print("  ✓ Configuration is up to date")
     
    +        # Safety net: config-version migrations have been observed to leave
    +        # cron/jobs.json valid-but-empty, silently dropping every scheduled
    +        # job (issue #34600). If the live file is now empty while the
    +        # pre-update snapshot held jobs, restore it and warn loudly.
    +        try:
    +            from hermes_cli.backup import restore_cron_jobs_if_emptied
    +
    +            cron_restore = restore_cron_jobs_if_emptied(pre_update_snapshot_id)
    +            if cron_restore:
    +                print()
    +                print(
    +                    "  ⚠️  cron/jobs.json was emptied during this update — "
    +                    f"restored {cron_restore['job_count']} job(s) from "
    +                    f"pre-update snapshot {cron_restore['snapshot_id']}."
    +                )
    +        except Exception as exc:
    +            # Never let the cron safety net break an otherwise-good update.
    +            logger.debug("Cron jobs auto-restore check failed: %s", exc)
    +
             print()
             print("✓ Update complete!")
     
    ```
  - `plugins/disk-cleanup/disk_cleanup.py`

    ```diff
    @@ -481,7 +481,14 @@ def guess_category(path: Path) -> Optional[str]:
             }:
                 return None
             if top == "cron" or top == "cronjobs":
    -            return "cron-output"
    +            # Only files under the disposable ``output/`` subtree are
    +            # cleanup candidates. Top-level cron control-plane state
    +            # (e.g. ``jobs.json``, ``.tick.lock``) must never be
    +            # auto-tracked — deleting it wipes the live scheduler
    +            # registry. See issue #32164.
    +            if len(rel.parts) >= 2 and rel.parts[1] == "output":
    +                return "cron-output"
    +            return None
             if top == "cache":
                 return "temp"
         except ValueError:
    ```
  - `scripts/release.py`

    ```diff
    @@ -645,6 +645,7 @@
         "[redacted:email]": "AntAISecurityLab",
         "252620095+briandevans@users.noreply.github.com": "briandevans",
         "[redacted:email]": "Bartok9",
    +    "96944678+ymylive@users.noreply.github.com": "sweetcornna",
         "[redacted:email]": "CruxExperts",
         "154585401+LeonSGP43@users.noreply.github.com": "LeonSGP43",
         "12250313+Kailigithub@users.noreply.github.com": "Kailigithub",
    ```
  - `tests/hermes_cli/test_backup.py`

    ```diff
    @@ -1679,3 +1679,105 @@ def test_does_not_touch_pre_update_backups(self, hermes_home):
                 _t.sleep(1.05)
             # Update backup must still be there
             assert update_backup.exists(), "pre-migration rotation wrongly pruned the pre-update backup"
    +
    +
    +# ---------------------------------------------------------------------------
    +# Cron jobs auto-restore after silent migration loss (issue #34600)
    +# ---------------------------------------------------------------------------
    +
    +class TestRestoreCronJobsIfEmptied:
    +    """`hermes update` config migration can leave cron/jobs.json valid-but-empty,
    +    silently dropping every scheduled job. `restore_cron_jobs_if_emptied` is the
    +    post-migration safety net that restores from the pre-update snapshot."""
    +
    +    @staticmethod
    +    def _seed_jobs(path: Path, jobs):
    +        path.parent.mkdir(parents=True, exist_ok=True)
    +        path.write_text(json.dumps({"jobs": jobs}))
    +
    +    def _make_snapshot(self, hermes_home: Path, label="pre-update"):
    +        from hermes_cli.backup import create_quick_snapshot
    +        return create_quick_snapshot(label=label, hermes_home=hermes_home, keep=5)
    +
    +    def test_restores_when_emptied_after_migration(self, tmp_path):
    +        from hermes_cli.backup import restore_cron_jobs_if_emptied
    +        hermes_home = tmp_path / ".hermes"
    +        jobs_path = hermes_home / "cron" / "jobs.json"
    +        # Pre-update: 3 real jobs.
    +        self._seed_jobs(jobs_path, [{"id": "a"}, {"id": "b"}, {"id": "c"}])
    +        snap_id = self._make_snapshot(hermes_home)
    +        assert snap_id
    +
    +        # Migration silently empties the file (valid JSON, zero jobs).
    +        jobs_path.write_text(json.dumps({"jobs": []}))
    +
    +        result = restore_cron_jobs_if_emptied(snap_id, hermes_home=hermes_home)
    +        assert result is not None
    +        assert result["restored"] is True
    +        assert result["job_count"] == 3
    +        assert result["snapshot_id"] == snap_id
    +
    +        # The live file now has the jobs back.
    +        restored = json.loads(jobs_path.read_text())
    +        assert len(restored["jobs"]) == 3
    +
    +    def test_noop_when_live_file_still_has_jobs(self, tmp_path):
    +        from hermes_cli.backup import restore_cron_jobs_if_emptied
    +        hermes_home = tmp_path / ".hermes"
    +        jobs_path = hermes_home / "cron" / "jobs.json"
    +        self._seed_jobs(jobs_path, [{"id": "a"}, {"id": "b"}])
    +        snap_id = self._make_snapshot(hermes_home)
    +
    +        # Healthy path: file unchanged after update.
    +        result = restore_cron_jobs_if_emptied(snap_id, hermes_home=hermes_home)
    +        assert result is None
    +
    +    def test_noop_when_snapshot_had_no_jobs(self, tmp_path):
    +        from hermes_cli.backup import restore_cron_jobs_if_emptied
    +        hermes_home = tmp_path / ".hermes"
    +        jobs_path = hermes_home / "cron" / "jobs.json"
    +        # Pre-update genuinely had zero jobs; current is also empty.
    +        self._seed_jobs(jobs_path, [])
    +        snap_id = self._make_snapshot(hermes_home)
    +        jobs_path.write_text(json.dumps({"jobs": []}))
    +
    +        result = restore_cron_jobs_if_emptied(snap_id, hermes_home=hermes_home)
    +        assert result is None
    +
    +    def test_noop_when_live_file_unreadable(self, tmp_path):
    +        """An unparseable live file is left alone — that's a different failure
    +        mode the user should see, not silently overwrite."""
    +        from hermes_cli.backup import restore_cron_jobs_if_emptied
    +        hermes_home = tmp_path / ".hermes"
    +        jobs_path = hermes_home / "cron" / "jobs.json"
    +        self._seed_jobs(jobs_path, [{"id": "a"}])
    +        snap_id = self._make_snapshot(hermes_home)
    +        jobs_path.write_text("{ this is not valid json")
    +
    +        result = restore_cron_jobs_if_emptied(snap_id, hermes_home=hermes_home)
    +        assert result is None
    +        # File left untouched.
    +        assert jobs_path.read_text() == "{ this is not valid json"
    +
    +    def test_noop_when_snapshot_id_missing(self, tmp_path):
    +        from hermes_cli.backup import restore_cron_jobs_if_emptied
    +        hermes_home = tmp_path / ".hermes"
    +        jobs_path = hermes_home / "cron" / "jobs.json"
    +        self._seed_jobs(jobs_path, [])
    +        assert restore_cron_jobs_if_emptied(None, hermes_home=hermes_home) is None
    +        assert restore_cron_jobs_if_emptied("", hermes_home=hermes_home) is None
    +
    +    def test_restores_legacy_bare_list_snapshot_shape(self, tmp_path):
    +        """A legacy snapshot storing a bare JSON list (not {"jobs": [...]}) is
    +        still counted and restored."""
    +        from hermes_cli.backup import restore_cron_jobs_if_emptied
    +        hermes_home = tmp_path / ".hermes"
    +        jobs_path = hermes_home / "cron" / "jobs.json"
    +        jobs_path.parent.mkdir(parents=True, exist_ok=True)
    +        jobs_path.write_text(json.dumps([{"id": "a"}, {"id": "b"}]))
    +        snap_id = self._make_snapshot(hermes_home)
    +
    +        jobs_path.write_text(json.dumps({"jobs": []}))
    +        result = restore_cron_jobs_if_emptied(snap_id, hermes_home=hermes_home)
    +        assert result is not None
    +        assert result["job_count"] == 2
    ```
  - `tests/plugins/test_disk_cleanup_plugin.py`

    ```diff
    @@ -129,12 +129,40 @@ def test_skips_protected_top_level(self, _isolate_env):
     
         def test_cron_subtree_categorised(self, _isolate_env):
             dg = _load_lib()
    -        cron_dir = _isolate_env / "cron"
    -        cron_dir.mkdir()
    -        p = cron_dir / "job_output.md"
    +        # Only files under ``cron/output/`` are disposable run artifacts.
    +        output_dir = _isolate_env / "cron" / "output" / "job_123"
    +        output_dir.mkdir(parents=True)
    +        p = output_dir / "run.md"
             p.write_text("x")
             assert dg.guess_category(p) == "cron-output"
     
    +    def test_cron_jobs_json_not_tracked(self, _isolate_env):
    +        """Regression for #32164: the cron registry must never be tracked."""
    +        dg = _load_lib()
    +        cron_dir = _isolate_env / "cron"
    +        cron_dir.mkdir()
    +        p = cron_dir / "jobs.json"
    +        p.write_text("[]")
    +        assert dg.guess_category(p) is None
    +
    +    def test_cron_tick_lock_not_tracked(self, _isolate_env):
    +        """Regression for #32164: cron tick-lock is control-plane state."""
    +        dg = _load_lib()
    +        cron_dir = _isolate_env / "cron"
    +        cron_dir.mkdir()
    +        p = cron_dir / ".tick.lock"
    +        p.write_text("")
    +        assert dg.guess_category(p) is None
    +
    +    def test_cronjobs_top_level_not_tracked(self, _isolate_env):
    +        """The legacy ``cronjobs`` alias is also control-plane at the top."""
    +        dg = _load_lib()
    +        cron_dir = _isolate_env / "cronjobs"
    +        cron_dir.mkdir()
    +        p = cron_dir / "jobs.json"
    +        p.write_text("[]")
    +        assert dg.guess_category(p) is None
    +
         def test_ordinary_file_returns_none(self, _isolate_env):
             dg = _load_lib()
             p = _isolate_env / "notes.md"
    ```
- **#34602: fix(cron): restore jobs.json emptied by config migration on update**. closed without merge
  - maintainer direction: category `merged_via`; implication `superseded`; refs `3845d86b9`, `#34840`, `#33834`
- **#35594: fix(backup): atomically restore cron/jobs.json via tempfile + rename**. open
  - maintainer direction: category `partial_fix`; implication `needs_llm`
  - files: `hermes_cli/backup.py`

## Fix status

- Merged to main in PR #34840 (cited above). No release data is tracked. Verify downstream.
- Fix last verified (merged) `2026-05-29`.
- Subsystem: `cron`