Delete metadata directories a backup left without a manifest (closes #390)

A backup that stopped between uploading db.zst.age and its manifest
left that directory under metadata/ on the destination for good:
prune deleted nothing there.

The blob step of prune, which snapshot create --prune also runs, now
deletes each directory under metadata/ that has no manifest.json.zst,
that no local snapshot record claims, and all of whose objects are
older than prune_grace_period; an object listed with no time keeps its
directory, and only names that are remote keys are deleted. The prompt
and the --force output name each such directory, the --json result
counts them (metadata_dirs_deleted, metadata_dirs_failed), and a failed
delete fails the run. Every description of the grace period now
covers these directories.

Model: opus-5-5

docs/DATAMODEL.md

@@ -230,6 +230,10 @@ The restore process doesn't use the local database. Instead:
    - Query blobs not referenced by any remaining snapshot
    - Delete from S3, once older than `prune_grace_period`, and from the local
      database
+2. **Delete Metadata Directories With No Manifest**
+   - Delete each directory under `metadata/` that has no `manifest.json.zst`
+     and no local snapshot record, once every object in it is older than
+     `prune_grace_period`
 
 ### 6. Incomplete Snapshot Cleanup
 

docs/REPOSTRUCTURE.md

@@ -163,10 +163,10 @@ These are known, deliberate properties of the format and the tooling, recorded s
 ## Pruning Safety
 
 The prune operation is safe because:
-1. It keeps every blob listed in any snapshot's manifest and deletes only blobs that no manifest references
+1. It keeps every blob listed in any snapshot's manifest and deletes only blobs that no manifest references. Under `metadata/` it deletes only a directory that has no `manifest.json.zst`, whose name is a remote key, and that no local snapshot record claims
 2. Manifests are unencrypted and can be read without keys
 3. If any manifest cannot be downloaded or decoded, prune deletes nothing and exits with an error, rather than treating that snapshot's blobs as unreferenced
-4. It deletes an unreferenced blob only once the blob is older than `prune_grace_period` (default `24h`). A backup uploads its blobs before the manifest that lists them, so a prune running meanwhile, on this host or another sharing the destination, leaves them as long as no backup run takes longer than the grace period. The grace period does not protect a blob a backup reuses from an earlier run that stopped before its manifest: the backup skips the upload of a blob already on the destination, so that blob keeps the time of its first upload, and a prune before the backup's manifest is written can delete it; the new snapshot then cannot be restored. `remote nuke` has no such check
+4. It deletes an unreferenced blob only once the blob is older than `prune_grace_period` (default `24h`), and a directory under `metadata/` with no manifest only once every object in it is. A backup uploads its blobs and its `db.zst.age` before its manifest, so a prune running meanwhile, on this host or another sharing the destination, leaves them as long as no backup run takes longer than the grace period. The grace period does not protect a blob a backup reuses from an earlier run that stopped before its manifest: the backup skips the upload of a blob already on the destination, so that blob keeps the time of its first upload, and a prune before the backup's manifest is written can delete it; the new snapshot then cannot be restored. `remote nuke` has no such check
 
 ## Restoration Requirements