Merge origin/main into cluster-config-docs

docs/user/branches-commits.md

@@ -58,6 +58,6 @@ Internal or legacy branch refs:
 
 ## L2 — Recovery audit trail
 
-The four migrated writers (`MutationStaging::finalize`, `schema_apply`, `branch_merge`, `ensure_indices`) protect their multi-table commits with a sidecar at `__recovery/{ulid}.json` written before Phase B and deleted after Phase C. The next `Omnigraph::open` (gated on `OpenMode::ReadWrite`) runs the recovery sweep in `crates/omnigraph/src/db/manifest/recovery.rs`: classify per-table state, decide all-or-nothing per sidecar, roll forward / back, record an audit row.
+The five migrated writers (`MutationStaging::finalize`, `schema_apply`, `branch_merge`, `ensure_indices`, `optimize_all_tables`) protect their multi-table commits with a sidecar at `__recovery/{ulid}.json` written before Phase B and deleted after Phase C. The next `Omnigraph::open` (gated on `OpenMode::ReadWrite`) runs the recovery sweep in `crates/omnigraph/src/db/manifest/recovery.rs`: classify per-table state, decide all-or-nothing per sidecar, roll forward / back, record an audit row.
 
 Audit rows live in `_graph_commit_recoveries.lance` (sibling to `_graph_commits.lance`) and reference the commit graph by `graph_commit_id`. The linked recovery commit is identified by that same `graph_commit_id`, and `actor_id="omnigraph:recovery"` is stored in `_graph_commit_actors.lance` (joined by `graph_commit_id`) — `_graph_commits.lance` itself does not carry the `actor_id` column. To find recoveries for a specific original actor: `omnigraph commit list --filter actor=omnigraph:recovery`, then join to `_graph_commit_recoveries.lance` by `graph_commit_id` to read `recovery_for_actor`. Schema: see `crates/omnigraph/src/db/recovery_audit.rs`.

docs/user/cli-reference.md

@@ -2,7 +2,7 @@
 
 A reference for the `omnigraph` binary's command surface and `omnigraph.yaml` schema. For a quick-start guide, see [cli.md](cli.md).
 
-18 top-level command families, 40+ subcommands. Graph commands accept either a positional `URI`, `--uri`, or a `--target <name>` resolved against `omnigraph.yaml`; `cluster` commands instead use `--config <dir>`.
+Top-level command families and subcommands. Graph-targeting commands accept either a positional `URI`, `--uri`, or a `--target <name>` resolved against `omnigraph.yaml`; `cluster` commands use `--config <dir>`.
 
 ## Top-level commands
 
@@ -17,12 +17,12 @@ A reference for the `omnigraph` binary's command surface and `omnigraph.yaml` sc
 | `export` | dump to JSONL on stdout (`--type T`, `--table K` filters) |
 | `branch create \| list \| delete \| merge` | branching ops |
 | `commit list \| show` | inspect commit graph |
-| `run list \| show \| publish \| abort` | transactional run ops |
 | `schema plan \| apply \| show (alias: get)` | migrations |
 | `lint` (alias: `check`) | offline / graph-backed query validation. Replaces `query lint` / `query check`, which are kept as deprecated argv-level shims that print a one-line warning and rewrite to `omnigraph lint` |
 | `queries validate \| list` | operate on the server-side stored-query registry (the `queries:` block). `validate` type-checks every stored query against the live schema offline (opens the selected graph; exits non-zero on any breakage), catching schema drift without restarting the server; `list` prints the selected registry's query names, MCP exposure, and typed params. For per-graph registries, pass `--target <graph>` or set `cli.graph`; with no graph selection, `list` shows only top-level `queries:`. Distinct from `lint`, which validates a single `.gq` file |
 | `cluster validate \| plan \| status` | read-only cluster-control preview. `validate` checks a local `cluster.yaml` folder and referenced schema/query/policy files; `plan` diffs it against local JSON state at `__cluster/state.json` while briefly holding `__cluster/lock.json`; `status` reads the state ledger. No apply, graph open, live drift scan, server change, or `state.json` mutation occurs in Stage 2A |
-| `optimize` | non-destructive Lance compaction (skips tables with `Blob` columns; `--json` reports a `skipped` field) |
+| `optimize` | non-destructive Lance compaction (skips tables with `Blob` columns or uncovered drift; `--json` reports `skipped`) |
+| `repair [--confirm] [--force]` | preview or explicitly publish uncovered manifest/head drift. `--confirm` heals verified maintenance drift and exits non-zero if suspicious/unverifiable drift is refused; `--force --confirm` publishes suspicious/unverifiable drift after operator review |
 | `cleanup --keep N --older-than 7d --confirm` | destructive version GC |
 | `embed` | offline JSONL embedding pipeline |
 | `policy validate \| test \| explain` | Cedar tooling. Selects `cli.graph`, else `server.graph`, else top-level `policy.file` |

docs/user/maintenance.md

@@ -1,15 +1,26 @@
-# Maintenance: Optimize & Cleanup
+# Maintenance: Optimize, Repair & Cleanup
 
-`db/omnigraph/optimize.rs`.
+`db/omnigraph/optimize.rs` and `db/omnigraph/repair.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.
+- 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.
+- 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).
+- **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 }]`.
+- 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.
 
+## `repair_all_tables(db, options)` — explicit
+
+- Handles **uncovered manifest/head drift**: a table's Lance HEAD is ahead of the manifest pin and no recovery sidecar records the writer intent.
+- Preview by default. `omnigraph repair --json <uri>` reports each table's `classification`, `action`, manifest/head versions, Lance operation names, and any classification error. `--confirm` publishes only verified maintenance drift; if any suspicious or unverifiable table is refused, the CLI prints the per-table output and exits non-zero. `--force --confirm` also publishes suspicious or unverifiable drift after operator review.
+- Classifies drift by reading Lance transactions from `manifest_version + 1` through `lance_head_version`. Only `ReserveFragments` and `Rewrite` are verified maintenance. Semantic operations such as `Append`, `Delete`, `Update`, `Merge`, or missing transaction history are not auto-healed.
+- Publishes repair by advancing `__manifest` to the existing Lance HEAD; it does **not** rewrite Lance data. If the publish succeeds, normal reads and strict writes use the repaired version. If it fails, no new data-side partial state was created.
+- Requires a clean recovery state. Pending `__recovery` sidecars still belong to automatic sidecar recovery, not manual repair.
+
 ## `cleanup_all_tables(db, options)` — destructive
 
 - Lance `cleanup_old_versions()` per table.

docs/user/storage.md

@@ -94,7 +94,7 @@ flowchart TB
 - **`nodes/`** and **`edges/`** are sibling directories holding one Lance dataset per declared type. Names are `fnv1a64-hex` of the type name to keep paths fixed-length and case-safe.
 - **`_graph_commits.lance`** is an L2 dataset that records the graph-level commit DAG, with a paired `_graph_commit_actors.lance` for the actor map. (Pre-v0.4.0 graphs also have inert `_graph_runs.lance` / `_graph_run_actors.lance` from the removed Run state machine; the v2→v3 migration sweeps their stale `__run__*` branches, and the dataset bytes are reclaimed once `delete_prefix` lands.)
 - **`_graph_commit_recoveries.lance`** — one row per recovery sweep action. Joined to `_graph_commits.lance` by `graph_commit_id`; the linked commit row carries `actor_id=omnigraph:recovery`. Operators correlate recoveries with the original mutations they rolled forward / back via this join. See `crates/omnigraph/src/db/recovery_audit.rs`.
-- **`__recovery/{ulid}.json`** — transient sidecar files written by the four migrated writers (`MutationStaging::finalize`, `schema_apply`, `branch_merge`, `ensure_indices`) before Phase B begins, deleted after Phase C succeeds. A sidecar persisting after process exit means the writer crashed in the Phase B → Phase C window; the next `Omnigraph::open` recovery sweep processes it. Steady-state directory is empty. See `crates/omnigraph/src/db/manifest/recovery.rs`.
+- **`__recovery/{ulid}.json`** — transient sidecar files written by the five migrated writers (`MutationStaging::finalize`, `schema_apply`, `branch_merge`, `ensure_indices`, `optimize_all_tables`) before Phase B begins, deleted after Phase C succeeds. A sidecar persisting after process exit means the writer crashed in the Phase B → Phase C window; the next `Omnigraph::open` recovery sweep processes it. Steady-state directory is empty. See `crates/omnigraph/src/db/manifest/recovery.rs`.
 - **`_refs/branches/{name}.json`** is graph-level branch metadata — pointers from a branch name to the manifest version it heads.
 - **Inside each Lance dataset** (orange): the standard Lance directory layout. `_versions/{n}.manifest` records every commit; `data/` holds the actual Arrow fragments; `_indices/{uuid}/` holds index segments with their own `fragment_bitmap` for partial coverage; `_refs/` holds Lance-native per-dataset branches and tags.