Orphan pruning decides a project is gone from a single probe:
if delete_orphans and (not workdir or not Path(workdir).exists()):
reason = "orphan"
then deletes its ref, index, and metadata — the project's entire checkpoint
history. `Path.exists()` is False for a deleted directory, but it is equally
False for one whose storage is not attached right now: an unplugged external
drive, a share behind a downed VPN, a bind-mount absent from this container,
an offline Windows mapped drive. The project is fine; only our view of it is.
This is not an opt-in maintenance command. `maybe_auto_prune_checkpoints`
runs unattended at startup from both `cli.py` and `gateway/run.py`, with
`delete_orphans=True` by default. So starting Hermes once while the drive is
unplugged silently destroys the restore points for every project on it — the
one thing checkpoints exist to provide, and there is nothing to restore from
afterwards.
Reproduced against the real store: a project registered under an unmounted
path and one on local disk, then a startup prune —
prune: {'scanned': 2, 'deleted_orphan': 1}
unreachable project index still on disk: False
The legacy pre-v2 branch has the same flaw plus a second one: a
`HERMES_WORKDIR` marker that exists but cannot be read leaves `workdir = None`,
which the same condition treats as an orphan. Failing to read a file is not
evidence that a project was deleted.
Require corroboration before deleting: the workdir's parent must be present,
so its absence is something we actually observed. A missing parent means the
volume is not there and we know nothing, so the entry is left alone — and an
unreadable marker never deletes at all. Genuinely abandoned projects are still
reclaimed, both by the unchanged orphan path (parent present, project gone)
and by the retention/stale rule, which runs off `last_touch` rather than a
filesystem probe.
tests/tools/test_checkpoint_manager.py: a project whose whole mount disappears
keeps its history; controls prove a genuinely deleted project is still pruned
and a live project is untouched. The data-loss test fails on main; both
controls pass there. 81 passed across the checkpoint suites (2 failures in
test_checkpoint_manager.py are pre-existing and fail identically on clean
main).
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