With both prefix and namespace configured, swamp datastore sync (bidirectional) pulls objects from <prefix>/<namespace>/… and writes them into the local cache at the root (solo) layout instead of under <cache>/<namespace>/. The push half of the same command then hard-errors on the very files the pull just created.

swamp datastore namespace migrate --confirm — the recovery the error message recommends — silently no-ops when the destination files already exist, so there is no supported way out.

Environment

swamp 20260728.221558.0-sha.f1005334
@swamp/s3-datastore 2026.07.25.1 (latest at time of filing)
macOS, Darwin 25.5.0, arm64
Datastore config: {"bucket":"…","region":"us-west-2","prefix":"swamp"}, namespace homelab

Reproduction

Repo on the S3 datastore with both a prefix and a namespace. All data correctly under <prefix>/<namespace>/ in S3; local cache clean (contains only <cache>/<namespace>/).
swamp doctor datastores → overallStatus: pass (all three checks).
swamp datastore sync --push -y → {"mode":"push","filesPushed":0} — converged.
swamp datastore sync ← bidirectional
Observe: [s3-sync] Skipped N solo-layout file(s) outside the bound namespace "homelab". These are stale leftovers — investigate and remove them. together with filesPulled: N. The cache now contains root-level data/, outputs/, auto-definitions/, definitions-evaluated/, workflow-runs/, workflows-evaluated/ alongside homelab/.
swamp datastore sync again → hard error: Cannot push: un-migrated data found at root level (auto-definitions, definitions-evaluated, workflows-evaluated, data, outputs, workflow-runs). Run 'swamp datastore namespace migrate' to preview, then --confirm to move data under the "homelab" namespace before pushing.
swamp datastore namespace migrate --confirm → prints the preview file listing and exits without migrating, because the destinations already exist under homelab/. Root dirs remain; push still errors. Repeating step 7 changes nothing.

Expected

A namespace-scoped pull should write to <cache>/<namespace>/…, matching the layout push expects. With local and remote already in agreement, swamp datastore sync should be a no-op.

Actual

Pull writes namespace-stripped duplicates to the cache root; push rejects them; the documented recovery cannot merge into a non-empty destination. The repo is wedged for all pushes until the root-level directories are manually removed from ~/.swamp/repos/<repoId>/.

Notes

The root-level files are byte-identical duplicates of their counterparts under homelab/ (verified with cmp).
Reads are unaffected — swamp model list and swamp data list keep working and resolve the correct namespace throughout. Data integrity was never at risk in my case.
swamp datastore sync --push alone is unaffected, and is a usable workaround.
swamp doctor datastores does correctly detect the bad state (overallStatus: fail, namespace_migration: passed: false).
However swamp doctor datastores --repair returns {"status":"not_needed"} — it targets foreign-namespace contamination (see #1353), not root-level un-migrated data, so it does not recover this.
Only a manual rm/mv of the root-level dirs in the cache restores a pushable state.

How a clean setup reaches this state

swamp datastore setup extension @swamp/s3-datastore --namespace <ns> … that fails partway through — in my case the credential preflight timed out (PREFLIGHT_TIMEOUT_MS) — still moves local .swamp/ data into the cache at solo layout before erroring. A successful re-run then binds the namespace and correctly refuses to absorb those files. namespace migrate --confirm folds them in (this works while <ns>/ is still empty), and the subsequent push succeeds.

The first bidirectional swamp datastore sync after that re-creates the root layout — and from then on recovery via supported commands is impossible.

Suggested fixes

Namespace-scoped pull should write under <cache>/<namespace>/, symmetric with push.
namespace migrate --confirm should either merge into a non-empty destination (skipping identical files) or fail loudly explaining why it cannot, rather than printing a preview and exiting 0.
Consider extending doctor datastores --repair to cover root-level un-migrated data, since it already detects it.

Upstream repository: https://github.com/systeminit/swamp-extensions

Environment

Extension: @swamp/s3-datastore@2026.07.25.1
swamp: 20260728.221558.0-sha.f1005334
OS: darwin (aarch64)
Deno: 2.8.3
Shell: /bin/zsh

02Bog Flow

Shipped

7/30/2026, 10:04:26 PM

Click a lifecycle step above to view its details.

03Sludge Pulse

stack72 assigned stack727/30/2026, 1:53:18 PM

stack72 commented 7/30/2026, 10:04:44 PM

Thanks @sntxrr for reporting this! The fix has been merged and a release is on its way. We appreciate your contribution to swamp.

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