omnigraph/docs/user/maintenance.md

Maintenance: Optimize & Cleanup

db/omnigraph/optimize.rs.

optimize_all_tables(db) — non-destructive

• Lance compact_files() on every node + edge table on main.
• Rewrites small fragments into fewer large ones; old fragments remain reachable via older manifests.
• Bounded by OMNIGRAPH_MAINTENANCE_CONCURRENCY (default 8).
• Returns [TableOptimizeStats { table_key, fragments_removed, fragments_added, committed, skipped }].
• Blob tables are skipped. A table that declares any Blob property is not compacted: it is reported with skipped: Some(BlobColumnsUnsupportedByLance) (and logged via tracing::warn) instead of compacted, and the rest of the sweep proceeds normally. The current Lance compact_files mis-decodes blob-v2 columns under its forced BlobHandling::AllBinary read; reads and writes are unaffected — only compaction is. This is gated by LANCE_SUPPORTS_BLOB_COMPACTION (db/omnigraph/optimize.rs) and removed when the upstream Lance fix lands (see docs/dev/lance.md). Consequence: fragment count and deleted-row space on blob tables are not reclaimed until then; query results are never affected.

cleanup_all_tables(db, options) — destructive

• Lance cleanup_old_versions() per table.
• Removes manifests (and their unique fragments) older than the retention policy.
• CleanupPolicyOptions { keep_versions: Option<u32>, older_than: Option<Duration> } — at least one is required.
• Returns [TableCleanupStats { table_key, bytes_removed, old_versions_removed, error }].
• Fault-isolated per table. A single table's transient failure (version GC or orphan reclaim) is recorded on that table's stats row (error: Some(..), logged via tracing) and never aborts the healthy tables — cleanup is the convergence backstop, so it does as much as it can and converges on re-run. The CLI reports any failed tables; rerun cleanup to retry them.
• CLI guards with --confirm; without it, prints a preview line.
• Recovery floor: --keep < 3 may garbage-collect Lance versions that the open-time recovery sweep needs as a rollback target (the sweep restores to the branch's manifest-pinned table version, which is HEAD-1 in the typical Phase B → Phase C drift case). Default --keep 10 is safe.
• Orphaned-branch reconciliation: before the version GC, cleanup runs reconcile_orphaned_branches, which force_delete_branches any per-table or commit-graph Lance branch absent from the manifest branch list. These orphans arise when a branch_delete flips the manifest authority but a downstream best-effort reclaim does not complete (see branches-commits.md). The reconciler is authority-derived and idempotent (it no-ops once nothing is orphaned), runs regardless of the keep_versions / older_than values (those gate version GC only), and never reclaims main or system-branch forks. Reclaimed forks are logged via tracing::info.

Tombstones

Logical sub-table delete markers in __manifest; tombstone_object_id(table_key, version) excludes a sub-table version from snapshot reconstruction.

Internal schema migrations (db/manifest/migrations.rs)

Version evolutions of the on-disk __manifest shape are reconciled automatically on the first write under a new binary. INTERNAL_MANIFEST_SCHEMA_VERSION declares the shape the binary expects; the on-disk stamp omnigraph:internal_schema_version (Lance schema-level metadata) records the on-disk shape. The publisher's open-for-write path calls migrate_internal_schema before reading state; reads are side-effect-free. No operator action is required for in-place upgrades. See storage.md → Internal schema versioning for the full mechanism.

A binary opening a manifest stamped at a version higher than it knows about refuses to publish with a clear "upgrade omnigraph first" error — old binaries cannot clobber a newer schema.