feat(engine): reindex in optimize to keep index coverage current

A scalar/FTS/vector index only covers the fragments it was built over. Rows
appended after the build (e.g. `ingest --mode merge`, whose commit does not
rebuild an existing index) are scanned unindexed, and `compact_files` rewrites
fragments out of coverage. Nothing folded them back in, so coverage decayed as
the graph grew — even the id/src/dst BTREEs that power traversal.

`optimize_one_table` now runs Lance `optimize_indices` after `compact_files`
(incremental merge, not retrain — the same compact->optimize_indices sequence
LanceDB's `optimize()` uses) and enters the publish path on compaction work OR
stale index coverage (new `TableStore::has_unindexed_fragments`, reusing the
fragment_bitmap logic). `optimize_indices` is a committing call with no
uncommitted variant in lance-6.0.1, so it is an inline-commit residual covered
by the existing `SidecarKind::Optimize` recovery sidecar spanning both ops.
Blob-bearing tables are still skipped (the Lance blob-compaction bug is
compaction-specific; reindex-for-blob deferred as a noted follow-up).

Tests: maintenance.rs asserts an appended fragment is uncovered before and
covered after optimize, and idempotency holds (second pass is a no-op).
lance_surface_guards pins the `optimize_indices` signature and its incremental-
coverage behavior. The existing optimize Phase-B recovery failpoint now also
exercises a crash after reindex. Docs: maintenance.md, writes.md, invariants.md,
lance.md, AGENTS.md.
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Ragnor Comerford 2026-06-13 18:47:41 +02:00
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commit 0edcf3ec59
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@ -4,14 +4,15 @@
## `optimize_all_tables(db)` — non-destructive
- Lance `compact_files()` on every node + edge table on `main`, then **publishes the compacted version to the `__manifest`** so the manifest's `table_version` tracks the compacted Lance HEAD. Reads pin the manifest version, so without this publish compaction would be invisible to readers *and* would break the HEAD-vs-manifest precondition of the next schema apply / strict update/delete ("stale view … refresh and retry"). The publish advances the graph version (a system-attributed commit) only for tables that actually compacted.
- Lance `compact_files()` then `optimize_indices()` on every node + edge table on `main`, then **publishes the resulting version to the `__manifest`** so the manifest's `table_version` tracks the compacted-and-reindexed Lance HEAD. Reads pin the manifest version, so without this publish the work would be invisible to readers *and* would break the HEAD-vs-manifest precondition of the next schema apply / strict update/delete ("stale view … refresh and retry"). The publish advances the graph version (a system-attributed commit) only for tables that actually changed.
- Rewrites small fragments into fewer large ones; old fragments remain reachable via older manifests until `cleanup` runs.
- Each table's compact→publish runs under its per-`(table, main)` write queue (serializing with concurrent mutations — compaction is a Lance `Rewrite` op that retryable-conflicts with a concurrent merge/update/delete on overlapping fragments). The Lance-HEAD-before-manifest-publish gap is covered by a `SidecarKind::Optimize` recovery sidecar (loose-match): a crash in that window rolls the compacted version forward on the next `Omnigraph::open` (compaction is content-preserving, so roll-forward is always safe).
- **Reindex (index coverage maintenance).** A scalar/FTS/vector index only covers the fragments it was built over. Rows appended after the index was built (e.g. by `ingest --mode merge`, whose commit does not rebuild an already-existing index) are scanned unindexed, and `compact_files` itself rewrites fragments out of an index's coverage. `optimize` runs Lance's incremental `optimize_indices` after compaction to fold those fragments back in (a delta merge, not a full retrain), restoring full coverage so equality/range/traversal predicates stay index-accelerated. This is why a table with **no compaction work but stale index coverage still commits** a new version under `optimize`. Run `optimize` on a cadence at least as frequent as your freshness window so recently-ingested rows do not linger in the unindexed flat-scan tail. `optimize_indices` is an inline-commit residual (Lance exposes no uncommitted variant), so it advances Lance HEAD like compaction and is covered by the same `SidecarKind::Optimize` recovery sidecar.
- Each table's compact→reindex→publish runs under its per-`(table, main)` write queue (serializing with concurrent mutations — compaction is a Lance `Rewrite` op that retryable-conflicts with a concurrent merge/update/delete on overlapping fragments). The Lance-HEAD-before-manifest-publish gap (now spanning both compaction and `optimize_indices`) is covered by a single `SidecarKind::Optimize` recovery sidecar (loose-match): a crash in that window rolls the compacted-and-reindexed version forward on the next `Omnigraph::open` (both ops are content-preserving, so roll-forward is always safe).
- **Requires a recovered graph.** `optimize` refuses (errors) when an unresolved recovery sidecar is present under `__recovery` — operating on an unrecovered graph could publish a partial write the open-time recovery sweep would roll back. Reopen the graph to run the recovery sweep, then re-run `optimize`.
- **Uncovered drift is skipped, not interpreted.** If a table's Lance HEAD is ahead of the version recorded in `__manifest` and no recovery sidecar covers that movement, `optimize` reports `skipped: Some(DriftNeedsRepair)` with the manifest/head versions and leaves the table untouched. Run `omnigraph repair` to classify and explicitly publish that drift.
- Bounded by `OMNIGRAPH_MAINTENANCE_CONCURRENCY` (default 8).
- Returns `[TableOptimizeStats { table_key, fragments_removed, fragments_added, committed, skipped, manifest_version, lance_head_version }]`.
- **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](../dev/lance.md)). Consequence: fragment count and deleted-row space on blob tables are not reclaimed until then; query results are never affected.
- **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](../dev/lance.md)). Consequence: fragment count and deleted-row space on blob tables are not reclaimed until then; query results are never affected. A skipped blob table is also **not reindexed** in the same sweep (the skip happens before the reindex step), so its index coverage on appended rows is not refreshed by `optimize` today — a follow-up may split reindex out of the blob skip since `optimize_indices` does not hit the blob-compaction bug.
## `repair_all_tables(db, options)` — explicit