Harden branch recovery and cleanup retention (#344)

* Harden branch recovery and cleanup retention

* Fail closed on blocked partial rollback

AGENTS.md

@@ -252,11 +252,11 @@ omnigraph policy explain --cluster ./company-brain --graph knowledge --actor act
 |---|---|---|
 | Columnar storage on object store | ✅ Arrow/Lance | URI normalization, S3 env-var plumbing |
 | Per-dataset versioning + time travel | ✅ | `snapshot_at_version`, `entity_at`, snapshot-pinned reads across many tables |
-| Per-dataset branches | ✅ | **Graph-level** branches (atomic across all sub-tables), lazy fork, system branch filtering |
+| Per-dataset branches | ✅ | **Graph-level** refs are logically atomic through authoritative `__manifest` `BranchContents`; native create/delete crash gaps are classified and reclaimed under a single-writer-process boundary; live names are path-prefix-disjoint; data-table forks are lazy; system branches are filtered |
 | Atomic single-dataset commits | ✅ | **Multi-table publish via three layers**, NOT a single Lance primitive: (1) per-table Lance `commit_staged` for the data write, (2) `__manifest` row-level CAS via `ManifestBatchPublisher` for cross-table ordering, (3) the open-time recovery sweep for the residual gap between (1) and (2). All three layers ship; the five migrated writers (`MutationStaging::commit_all`, `schema_apply`, `branch_merge`, `ensure_indices`, `optimize_all_tables`) write a `__recovery/{ulid}.json` sidecar before Phase B and delete it after Phase C. The next `Omnigraph::open` (gated on `OpenMode::ReadWrite`) runs the sweep in `db/manifest/recovery.rs`: classify, decide all-or-nothing per sidecar, roll forward via single `ManifestBatchPublisher::publish` or roll back via `Dataset::restore` followed by a manifest publish of the restored version (so both directions converge to `manifest == HEAD` — no residual drift), and record an internal audit row in `_graph_commit_recoveries.lance`. A v3 roll-forward preserves the interrupted writer's fixed commit lineage and actor; rollback and legacy recovery commits use `omnigraph:recovery`. There is currently no public CLI query for the recovery-audit table, and ordinary commit history is not a complete recovery enumeration. The write entry points (`load_as`, `mutate_as`, `apply_schema_as`, `branch_merge_as`) and `refresh` additionally run an in-process roll-forward-only heal, serialized against same-process live writers through the shared root-scoped gate manager, so a long-lived server converges on its next write without restart; only rollback-eligible sidecars still defer to the next read-write open (a future background reconciler's goal). Engine writes route through a sealed `TableStorage` trait (`db.storage()`) exposing only `stage_*` + `commit_staged` + reads; the sole inline-commit residual (`create_vector_index`) is split onto a separate sealed `InlineCommitResidual` trait reached via `db.storage_inline_residual()` (MR-854), so the default surface cannot couple a write with a HEAD advance — §1 holds by construction. `delete` migrated to the staged path in MR-A (`stage_delete` via Lance 7.0 `DeleteBuilder::execute_uncommitted`, [#6658](https://github.com/lance-format/lance/issues/6658)); `create_vector_index` stays inline until upstream Lance ships a public two-phase API ([#6666](https://github.com/lance-format/lance/issues/6666)); `LoadMode::Overwrite` uses Lance `Overwrite` staged transactions. |
 | Compaction (`compact_files`) + reindex (`optimize_indices`) | ✅ | `omnigraph optimize` orchestrates over all node/edge tables, bounded concurrency; per table runs `compact_files` **then Lance `optimize_indices`** (folds appended/rewritten fragments back into existing indexes — incremental merge, not retrain) and **publishes the resulting version to `__manifest`** (so the manifest tracks the Lance HEAD — required for reads to observe the work and for schema apply / strict writes to pass their HEAD-vs-manifest precondition), under the per-`(table, main)` write queue with `SidecarKind::Optimize` recovery coverage spanning both ops; **commits even with no compaction work if index coverage is stale**; **refuses on an unrecovered graph**; **skips uncovered HEAD > manifest drift** with `DriftNeedsRepair`; **compacts blob-bearing tables** (the pre-9 `LANCE_SUPPORTS_BLOB_COMPACTION` skip was removed once Lance 8.0.0+ shipped blob-v2 compaction — see [docs/dev/invariants.md](docs/dev/invariants.md) Known Gaps) |
 | Repair uncovered drift | — | `omnigraph repair` explicitly classifies uncovered table `HEAD > manifest` drift: verified maintenance drift (`ReserveFragments`/`Rewrite`) can be published with `--confirm`; suspicious or unverifiable drift requires `--force --confirm`. Sidecar-covered crash residuals still recover automatically on open. |
-| Cleanup (`cleanup_old_versions`) | ✅ | `omnigraph cleanup` with `--keep` / `--older-than` policy |
+| Cleanup (`cleanup_old_versions`) | ✅ | `omnigraph cleanup` derives requested `--keep` / `--older-than` cutoffs from each table's available versions; Lance refs plus OmniGraph's live-lazy-branch and recovery floors may retain additional versions. It fails closed on unopenable pins, recovery intent, or uncovered main-table HEAD drift |
 | BTREE / inverted (FTS) / vector indexes | ✅ | `@index`/`@key` declares intent; the physical index is derived state that never fails a logical op. Built per column through one chokepoint (`build_indices_on_dataset_for_catalog`, type-dispatched by `node_prop_index_kind`: enum + orderable scalar → BTREE, free-text String → FTS, Vector → vector); idempotent; lazy across branches. **Schema apply and mutation/load build no indexes inline**: the latter publish only their exact data effects, leaving physical intent pending. `ensure_indices`/`optimize` materializes declared-but-missing indexes, restores fragment coverage, and continues to report untrainable Vector columns as pending. |
 | `merge_insert` upsert | ✅ | `LoadMode::Merge`, mutation `update`/`insert`/`delete` lowering |
 | Vector search | ✅ | `nearest()` query op; embedding pipeline (Gemini / OpenAI clients); `@embed` in schema |