omnigraph/docs/dev/architecture.md
Ragnor Comerford 0dcdcf5a9d
feat(engine): Stage the delete path; retire the inline-delete residual (#308)
* test(engine): pin zero-row cascade delete must not drift an edge table (red)

A delete <Node> cascades a delete_where into every incident edge type. The
inline delete_where (Dataset::delete) advances Lance HEAD even when zero edges
match, but the cascade records the new version only if deleted_rows > 0 — so a
node with no incident edges leaves edge:Knows HEAD>manifest drift, which trips
the next strict write's ExpectedVersionMismatch and repair refuses it.

Red today: edge:Knows manifest=v5, Lance HEAD=v6. Goes green when delete moves
to the staged two-phase path (iss-950, Lance 7.0 DeleteBuilder::execute_uncommitted),
where a 0-row delete commits no Lance version and the deleted_rows>0 gate becomes
correct by construction.

* fix(engine): a zero-row delete must not advance Lance HEAD

Lance's Dataset::delete commits a new version even when the predicate matches
nothing (build_transaction always emits Operation::Delete), so a node delete
that cascades a delete_where into an incident edge type with no matching edges
advanced that edge table's Lance HEAD while the cascade skipped record_inline
(gated on deleted_rows > 0) — leaving HEAD>manifest drift that wedged the next
strict write and that repair refused as suspicious/unverifiable.

Use Lance 7.0's two-phase DeleteBuilder::execute_uncommitted to read
num_deleted_rows before committing: a no-match delete now advances nothing (no
version, no drift) and the existing deleted_rows>0 gate is correct by
construction. Non-zero deletes commit the staged transaction with
skip_auto_cleanup + affected_rows (parity with the prior inline path).

First step of the staged-delete migration (iss-950); turns the
node_delete_with_no_incident_edges_leaves_no_edge_table_drift regression green.

* feat(engine): stage_delete two-phase primitive (MR-A step 0)

Add TableStore::stage_delete (Lance 7.0 DeleteBuilder::execute_uncommitted),
the two-phase analogue of stage_merge_insert: writes deletion files without
advancing Lance HEAD, returns Option<StagedWrite> (None on 0 rows = true no-op),
carrying the deletion-vector updated_fragments as new_fragments and the
superseded originals as removed_fragment_ids so combine_committed_with_staged
makes the deletion visible to in-query reads.

No affected_rows is threaded: like stage_merge_insert's Operation::Update commit,
the staged delete relies on OmniGraph's per-table write queue + manifest CAS, not
Lance's per-dataset conflict resolver (commit_staged is a single attempt).

Flip the two residual guards to the staged path: staged_writes.rs now asserts
stage_delete does NOT advance HEAD and that a staged delete is read-your-writes
visible (the deletion-vector RYW proof D2 retirement depends on); the
lance_surface_guards delete guard pins execute_uncommitted's UncommittedDelete.

No behavior change yet (callers still use delete_where); Step 1 wires them.

* feat(engine): TableStorage::stage_delete + migrate merge delete path (MR-A step 1a)

Add stage_delete/Option<StagedHandle> to the TableStorage trait (delegates to
TableStore::stage_delete). Migrate the two branch_merge delete sites
(three-way RewriteMerged + adopt delta) from the inline delete_where residual to
stage_delete + commit_staged — identical in shape to the stage_merge_insert +
commit_staged pair above each. HEAD still advances within the merge sequence
(via commit_staged), under the unchanged SidecarKind::BranchMerge Phase-B
confirmation; the _pre_delete/_pre_index failpoints fire by position, unchanged.

merge_truth_table, branching, composite_flow green.

* feat(engine): migrate all delete sites to staged path, retire inline delete (MR-A step 1b/1c)

Routes every delete through the staged write path so delete never advances
Lance HEAD inline — the last inline-commit residual on the mutation path is
gone. `MutationStaging` now accumulates delete predicates (`record_delete`)
alongside pending write batches; at end-of-query `stage_all` combines a
table's predicates into one `(p1) OR (p2) …` `stage_delete` (a deletion-vector
transaction, no HEAD advance) and `commit_all` commits it through the same
`commit_staged` path as inserts/updates. Deletes are now ordinary staged
entries: one sidecar pin at `expected + 1`, no inline special-casing.

Migrated callers (all 5): the 3 mutation.rs sites (delete-node, cascade,
delete-edge) and the 2 merge.rs sites (already on stage_delete in step 1a).
`affected_edges`/`affected` move from post-inline-commit `deleted_rows` to a
committed `count_rows` at record time — exact under D₂, bounded by the cascade
working set. A predicate matching zero rows stages nothing (the staged
equivalent of the old "skip record_inline on 0 deleted rows"), so the zero-row
edge-table drift class stays closed by construction.

Retired scaffolding now that no caller remains:
- `MutationStaging.inline_committed` + `record_inline` → `delete_predicates` +
  `record_delete`; `StagedMutation.inline_committed`/`paths` fields and all the
  `commit_all` inline handling (queue keys, sidecar pins with the
  `record_inline` table_version special-case, the inline recheck loop).
- `open_table_for_mutation`'s post-inline-commit reopen branch (deletes no
  longer advance HEAD mid-query, so a second touch reopens at the pinned
  version like any write).
- `InlineCommitResidual::delete_where` + its `TableStore` impl, the orphaned
  `TableStore::delete_where`, and `DeleteState`. `InlineCommitResidual` now
  carries only `create_vector_index` (Lance #6666 still open).

D₂ stays for now: staged-delete read-your-writes doesn't yet compose into the
pending accumulator (insert-then-delete on one table), so mixed
insert/update/delete in one query is still rejected at parse time. Retiring D₂
is step 2. Doc comments updated to match across exec/, storage_layer, db/.

Tests (all green): writes, consistency, validators, end_to_end, composite_flow,
merge_truth_table, maintenance, recovery, staged_writes, forbidden_apis,
lance_surface_guards, changes, point_in_time (286), plus failpoints (63).

* docs: delete is a staged write, not an inline-commit residual (MR-A step 1)

Update the docs that described `delete` as the inline-commit residual now that
MR-A routes it through `stage_delete`. Always-loaded surfaces (AGENTS.md rule
4 / capability matrix, invariants.md Invariant 4 / truth matrix / known gaps)
plus the dev write-path docs (writes.md, execution.md incl. its mutation
sequence diagram, architecture.md) now state: deletes accumulate as predicates
and stage like inserts/updates, no inline HEAD advance; `InlineCommitResidual`
carries only `create_vector_index` (Lance #6666). The parse-time D₂ rule is
documented as retained — not because delete inline-commits, but because
staged-delete read-your-writes is not yet wired into the pending accumulator
(MR-A step 2). lance.md's 7.0 audit note marked MR-A as landed.

* docs: D₂ is a deliberate boundary, not temporary scaffolding (MR-A close-out)

After MR-A staged the delete path, D₂ (a mutation query is insert/update-only
OR delete-only) was left framed as temporary — "until Lance ships two-phase
delete" / "retire in step 2". Lance shipped that and we used it for the
inline-commit fix; D₂'s original justification is gone. It now stands for a
different, permanent reason: keeping a query to one kind keeps its
read-your-writes unambiguous and each table to one version per query. Retiring
it would buy single-commit mixed atomicity (cheap workaround: split, or a
branch) at the cost of an in-query delete view, pending pruning, edge
id-resolution, and two-commit-per-table ordering in the hot mutation path —
complexity not worth earning. Decision: keep D₂ as a deliberate boundary.

Reframes the now-stale wording everywhere, no logic change:
- The D₂ parse-time error message no longer promises "this restriction lifts
  when Lance exposes a two-phase delete API"; it states the boundary and points
  to a branch+merge for one atomic commit.
- `enforce_no_mixed_destructive_constructive` doc, AGENTS.md, invariants.md
  (Invariant 4 / truth matrix / removed from the known-gaps), writes.md,
  architecture.md, lance.md, and the user mutations doc (which wrongly said
  deletes "commit through a different path" — both stage now).
- Swept remaining stale `delete_where` mentions left from the Step-1 migration:
  the merge.rs "swap when upstream ships" comments (already swapped), the
  forbidden_apis / table_ops residual notes, the staged_writes vector-index
  guard doc (was "same as stage_delete's absence" — stage_delete now exists),
  and test comments/assert messages in recovery/maintenance/writes/failpoints.
  Genuinely-historical records (dated Lance audit, rfc-013, bug-case-fix) left.

Verified: engine builds warning-free; check-agents-md OK; writes/maintenance/
recovery/staged_writes/forbidden_apis all green. Closes MR-A.

* test(engine): overlapping delete predicates must not double-count affected_* (red)

Reproduces a reporting regression from the staged-delete migration flagged in
PR #308 review. Because deletes now stage (instead of inline-committing), two
delete statements in one query both scan the same unchanged committed snapshot;
counting each predicate independently over-reports `affected_*` when they
overlap. The old inline path committed each delete before the next ran, so it
counted distinct.

`delete Person where name = "Alice"` then `delete Person where age > 29` over
the standard fixture (Alice 30, Charlie 35) removes 2 distinct nodes and 3
distinct edges, but the buggy per-statement counting returns 3 nodes / 6 edges.
RED at this commit (asserts left=3, right=2).

* fix(engine): dedup overlapping delete predicates when counting affected_*

Count each delete statement against the committed snapshot MINUS the predicates
a prior delete statement on the same table already recorded:
`(pred) AND NOT ((prior1) OR (prior2) …)`. Summed over statements this is
inclusion-exclusion — `Σ |pₙ \ (p₁ ∪ …)| = |p₁ ∪ p₂ ∪ …|` — exactly the distinct
count the combined `(p1) OR (p2)` staged delete removes. Works for nodes and
edges alike with no edge identity needed; the node ID scan uses the same
exclusion so a later statement also doesn't re-cascade already-deleted nodes.
The ORIGINAL predicate is still what gets recorded (the staged delete removes
the union); only the count uses the exclusion. The common single-delete path is
unchanged (`prior` empty → filter is just the base predicate).

New helper `dedup_delete_filter` + `MutationStaging::recorded_delete_predicates`.
Turns the red regression test green (2 nodes / 3 edges); writes (33),
end_to_end, validators, maintenance, recovery, composite_flow, merge_truth_table,
consistency, changes, and failpoints (63) all stay green.

* test(engine): delete dedup must not drop NULL-column rows (red)

Follow-up to the overlapping-delete fix flagged in PR #308 review (Greptile P1):
the `(base) AND NOT (prior)` exclusion breaks under SQL three-valued logic. If a
prior delete predicate references a NULLable column, a later statement's
matching row whose column is NULL makes `prior` evaluate to UNKNOWN, `NOT
UNKNOWN` is UNKNOWN, and the row is filtered out of the scan — even though the
prior delete never matched it. That drops it from `deleted_ids`, skipping its
cascade (orphaned edges) or, if it is the only match, leaving the node
undeleted. A data bug, not just a miscount.

Data: Charlie(age 35), Zoe(age NULL); Knows Zoe→Charlie. `delete Person where
age > 30` then `delete Person where name = "Zoe"`. Under the buggy `NOT`, Zoe's
scan `(name='Zoe') AND NOT (age>30)` is UNKNOWN → Zoe survives. RED at this
commit (Person count left=1, right=0).

* fix(engine): NULL-safe delete dedup — exclude only definitely-matched prior rows

Change `dedup_delete_filter` from `(base) AND NOT (prior)` to
`(base) AND ((prior) IS NOT TRUE)`. `IS NOT TRUE` keeps both FALSE and UNKNOWN
rows, so a prior predicate that evaluates to SQL UNKNOWN (a NULL in a referenced
column) no longer drops a row this statement legitimately matches — only rows a
prior predicate matched as definitely TRUE are excluded from the count/scan. The
distinct-count semantics are unchanged for non-NULL data.

Turns the red NULL-dedup test green (Zoe deleted, her edge cascaded), and the
overlapping-dedup + writes/end_to_end/validators/maintenance/recovery/
composite_flow/consistency suites stay green.

* docs(engine): note dedup_delete_filter's load-bearing dependency on D₂

Self-review follow-up: the overlapping-delete dedup assumes the committed
snapshot is invariant across a query's statements, which holds only because D₂
forbids mixing writes with deletes (so a delete-touched table has no pending
writes). Make that dependency explicit at the function so a future D₂ relaxation
is forced to revisit the dedup. Comment-only.

* Preserve staged write commit metadata
2026-06-27 16:48:41 +02:00

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# Architecture
OmniGraph is a typed property-graph engine built as a coordination layer over many Lance datasets, with Git-style branches and commits across the whole graph, multi-modal querying (vector + FTS + BM25 + RRF + graph traversal) in one runtime, an HTTP server with Cedar policy, and a CLI driven by a per-operator `~/.omnigraph/config.yaml` plus team-owned cluster directories.
## Reading guide
Three views, increasing zoom:
1. **System context** — what OmniGraph is and what it touches.
2. **Layer view** — the eight-layer stack inside one OmniGraph process.
3. **Component zoom-ins** — what's inside each layer.
For runtime flows (read query, mutation), see [`docs/dev/execution.md`](execution.md). For the on-disk layout of a graph, see [`docs/user/storage.md`](../user/concepts/storage.md).
L1 (orange in the diagrams) is what we inherit from Lance; L2 (blue) is what OmniGraph adds. The L1/L2 framing is also called out in prose at the bottom of this doc.
## System context
```mermaid
flowchart LR
classDef external fill:#fef3e8,stroke:#c46900,color:#000
classDef omnigraph fill:#e8f4fd,stroke:#1e6aa8,color:#000
classDef store fill:#f0f0f0,stroke:#555,color:#000
cli[CLI users]:::external
http[HTTP clients<br/>and SDKs]:::external
agents[Agents]:::external
embed[Embedding providers<br/>OpenAI / Gemini]:::external
og[OmniGraph<br/>kernel]:::omnigraph
cedar[Cedar policy<br/>engine]:::external
s3[Object store<br/>local FS / S3 / RustFS]:::store
cli --> og
http --> og
agents --> og
og --> embed
og --> cedar
og --> s3
```
OmniGraph runs as a single process (one binary, multiple crates). External dependencies are the embedding APIs (called during ingest and at query-time normalization), Cedar (called for every privileged action), and an object store (everything OmniGraph persists lands here).
## Layer view
Inside the OmniGraph process, work flows through these layers:
```mermaid
flowchart TB
classDef l2 fill:#e8f4fd,stroke:#1e6aa8,color:#000
classDef l1 fill:#fef3e8,stroke:#c46900,color:#000
subgraph CLIs[CLI and HTTP server]
cli[omnigraph CLI]:::l2
srv[omnigraph-server<br/>Axum + Cedar]:::l2
end
subgraph compiler[omnigraph-compiler]
front[parse → AST → typecheck → catalog → IR]:::l2
end
subgraph engine[omnigraph engine]
plan[exec query and mutation]:::l2
gi[graph index CSR/CSC<br/>RuntimeCache LRU 8]:::l2
coord[coordinator<br/>ManifestCoordinator · CommitGraph]:::l2
end
subgraph storage[storage trait — wraps Lance]
ts[table_store · storage.rs<br/>direct lance::Dataset today]:::l2
end
subgraph lance_layer[Lance 4.x — substrate]
lance[per-dataset versions, fragments<br/>BTREE · Inverted FTS · IVF/HNSW vector<br/>merge_insert · compact_files · cleanup_old_versions]:::l1
end
subgraph object_store[Object store]
os[local FS · S3 · RustFS · MinIO]:::l1
end
CLIs -- "string + params" --> compiler
compiler -- IROp --> engine
engine -- "scan / write request" --> storage
storage -- "Stream of RecordBatch" --> engine
storage -- "Lance API calls" --> lance_layer
lance_layer -- bytes --> object_store
```
The storage seam is partly aspirational. `TableStorage` exists as the sealed staged-write trait, but capability/stat surfaces and full call-site migration are still roadmap. The diagram shows the intended boundary.
## Component zoom-ins
### Compiler — `omnigraph-compiler`
```mermaid
flowchart LR
classDef l2 fill:#e8f4fd,stroke:#1e6aa8,color:#000
src[".gq source"]:::l2
p[parser Pest<br/>query.pest · schema.pest]:::l2
ast[AST<br/>QueryDecl · Mutation · Schema]:::l2
cat[catalog<br/>NodeType · EdgeType · Interface]:::l2
tc[typecheck<br/>typecheck_query]:::l2
low[lower<br/>lower_query]:::l2
ir[IROp pipeline<br/>NodeScan · Expand · Filter · AntiJoin]:::l2
src --> p --> ast --> tc
cat --> tc
tc --> low --> ir
```
The compiler crate has zero Lance dependency. It owns the schema language, the query language, and the AST → IR lowering.
Code paths:
- Parser: `crates/omnigraph-compiler/src/query/parser.rs`, `crates/omnigraph-compiler/src/query/query.pest`
- Typecheck: `crates/omnigraph-compiler/src/query/typecheck.rs:83` (`typecheck_query`)
- Lower: `crates/omnigraph-compiler/src/ir/lower.rs:11` (`lower_query`)
- Catalog: `crates/omnigraph-compiler/src/catalog/`
### Engine — `omnigraph` crate
```mermaid
flowchart TB
classDef l2 fill:#e8f4fd,stroke:#1e6aa8,color:#000
subgraph exec[exec module]
eq[query · execute_query<br/>query.rs:347]:::l2
em[mutation · mutate<br/>mutation.rs:511]:::l2
ld[loader · ingest<br/>loader/mod.rs:74]:::l2
end
subgraph state[graph state]
coord[GraphCoordinator]:::l2
mr[ManifestCoordinator<br/>db/manifest.rs]:::l2
cg[CommitGraph<br/>projection of __manifest graph_commit/graph_head rows]:::l2
stg[MutationStaging<br/>per-query in-memory accumulator<br/>exec/staging.rs]:::l2
end
subgraph idx[graph index]
gi[GraphIndex<br/>CSR/CSC built per query]:::l2
rc[RuntimeCache LRU=8]:::l2
end
subgraph io[Lance I/O]
ts[table_store]:::l2
st[storage adapter<br/>storage.rs]:::l2
end
eq --> gi
eq --> ts
em --> stg
em --> ts
ld --> stg
ld --> ts
eq --> mr
em --> mr
coord --> mr
coord --> cg
ts --> st
```
The engine binds the compiler IR to Lance. It owns multi-dataset coordination, the graph topology index, the per-query staging accumulator, and the snapshot/manifest read path.
Code paths:
- Read entry: `Omnigraph::query` at `crates/omnigraph/src/exec/query.rs:7`
- Mutation entry: `Omnigraph::mutate` at `crates/omnigraph/src/exec/mutation.rs:511`
- Manifest commit: `ManifestCoordinator::commit` at `crates/omnigraph/src/db/manifest.rs:280`
- Graph index: `crates/omnigraph/src/graph_index/`
- Loader: `Omnigraph::ingest` at `crates/omnigraph/src/loader/mod.rs:74`
### Mutation atomicity — in-memory accumulator (MR-794)
Inserts and updates inside `mutate_as` and the bulk loader's
Append/Merge modes go through `MutationStaging`
([`crates/omnigraph/src/exec/staging.rs`](../../crates/omnigraph/src/exec/staging.rs)),
a per-query in-memory accumulator. No Lance HEAD advance happens during
op execution; one `stage_*` + `commit_staged` per touched table runs
at end-of-query, then the publisher commits the manifest atomically.
```
op-1 (insert/update) → push RecordBatch → MutationStaging.pending[table]
op-2 (insert/update) → read committed via Lance + pending via DataFusion
MemTable (read-your-writes) → push batch
op-N → push batch
─── end of query ───────────────────────────────────────
finalize: per pending table:
concat batches → stage_append OR stage_merge_insert OR stage_overwrite
→ commit_staged
publisher: ManifestBatchPublisher::publish (one cross-table CAS)
```
A failed op leaves Lance HEAD untouched on the staged tables: the next
mutation proceeds normally with no drift to reconcile. Concrete
contracts:
- `D₂` parse-time rule: a query is either insert/update-only or
delete-only. Mixed → reject. Deletes now stage like inserts/updates
(MR-A: `stage_delete` via Lance 7.0 `DeleteBuilder::execute_uncommitted`),
so they no longer advance HEAD inline; D₂ is a deliberate boundary
(constructive XOR destructive per query) that keeps in-query read-your-writes
unambiguous — compose mixed operations via separate mutations or a branch.
- `LoadMode::Overwrite` uses Lance `Operation::Overwrite` through the
same staged path. Loader validation runs against the replacement
in-memory batches before any `commit_staged`, and the publish window is
covered by `SidecarKind::Load` recovery.
- Read sites consume `TableStore::scan_with_pending`, which Lance-scans
the committed snapshot at the captured `expected_version` and unions
with a DataFusion `MemTable` over the pending batches.
This pattern realizes read-your-writes within a multi-statement mutation
and keeps failure scope bounded for inserts/updates by construction at
the writer layer. See [docs/dev/invariants.md](invariants.md) and
[docs/dev/writes.md](writes.md) for the publisher CAS contract this builds on.
### Storage trait — today vs. roadmap
```mermaid
flowchart LR
classDef now fill:#e8f4fd,stroke:#1e6aa8,color:#000
classDef future fill:#fff,stroke:#888,stroke-dasharray:5 5,color:#444
subgraph today[Today]
d1[table_store<br/>opens lance::Dataset directly]:::now
d2[storage.rs<br/>S3 / file URI plumbing]:::now
end
subgraph roadmap[Roadmap - storage capabilities]
t[trait Dataset<br/>schema · stats · placement<br/>capabilities · scan · write]:::future
impl1[LanceStorage]:::future
impl2[future test impl]:::future
end
today -.-> roadmap
t --> impl1
t --> impl2
```
The staged-write trait exists today as `TableStorage`, implemented by `TableStore`. Full engine migration plus capability and statistics surfaces remain roadmap, so the planner cannot yet reason about all pushdown opportunities through a documented trait surface.
### Index lifecycle — today vs. roadmap
```mermaid
flowchart LR
classDef now fill:#e8f4fd,stroke:#1e6aa8,color:#000
classDef future fill:#fff,stroke:#888,stroke-dasharray:5 5,color:#444
subgraph today[Today]
ei[ensure_indices<br/>omnigraph.rs:445]:::now
manual[called manually<br/>or from optimize]:::now
end
subgraph roadmap[Roadmap - manifest reconciler]
rec[Reconciler<br/>observes manifest]:::future
diff[coverage diff<br/>fragments fragment_bitmap]:::future
wp[worker pool<br/>builds index segments]:::future
end
manual --> ei
today -.-> roadmap
rec --> diff --> wp
```
Today, indexes are built explicitly via `ensure_indices`. Reads degrade gracefully when index coverage is partial — Lance's scanner unions indexed and scan paths automatically. The roadmap reconciler observes manifest state and converges coverage in the background.
### Server / CLI
```mermaid
flowchart LR
classDef l2 fill:#e8f4fd,stroke:#1e6aa8,color:#000
cli[omnigraph CLI<br/>command families]:::l2
srv_in[Axum HTTP<br/>REST + OpenAPI]:::l2
auth[Bearer auth<br/>SHA-256 hashed tokens]:::l2
pol[Cedar policy gate<br/>per request]:::l2
wl[WorkloadController<br/>per-actor admission]:::l2
eng[engine API<br/>Arc&lt;Omnigraph&gt;]:::l2
wq[WriteQueueManager<br/>per-(table, branch)]:::l2
cli -.-> eng
srv_in --> auth --> pol --> wl --> eng
eng --> wq
```
The server applies Cedar policy at the HTTP boundary today. The roadmap, called out in [docs/dev/invariants.md](invariants.md) as a known gap, is to push policy into the planner as predicates. After Cedar, mutating handlers go through `WorkloadController` (per-actor admission cap + byte budget; PR 2 / MR-686) before reaching the engine. The engine itself holds an `Arc<WriteQueueManager>` so concurrent mutations on the same `(table, branch)` serialize at the queue, while disjoint keys run in parallel — see [docs/user/server.md](../user/operations/server.md) "Per-actor admission control" and [docs/dev/writes.md](writes.md). The CLI bypasses the HTTP layer (and admission) and calls the engine API directly.
Code paths:
- Server entry: `crates/omnigraph-server/src/lib.rs`
- Auth: `crates/omnigraph-server/src/auth.rs`
- Policy: `crates/omnigraph-server/src/policy.rs`
- CLI: `crates/omnigraph-cli/src/main.rs`
## L1 / L2 framing
Throughout the docs, capabilities are split into:
- **L1 — Inherited from Lance**: what OmniGraph gets "for free" by sitting on top of the Lance dataset format (columnar Arrow storage, per-dataset versions and branches, index types, `merge_insert`, `compact_files` / `cleanup_old_versions`).
- **L2 — Added by OmniGraph**: typing (schema language), graph semantics, multi-dataset coordination via `__manifest`, graph-level branches and commits, the `.gq` query language and IR, the topology index, the HTTP server, Cedar policy, the CLI.
## Concurrency model
- **MVCC**: every Lance write bumps a per-dataset version; the OmniGraph manifest version coordinates which sub-table versions are visible together.
- **Snapshot isolation**: a query holds one `Snapshot` for its lifetime; concurrent writes don't leak in.
- **Cross-branch isolation**: copy-on-write means readers and writers on different branches don't block each other.
- **Per-query staging**: `mutate_as` and `load` (Append/Merge) accumulate insert/update batches in an in-memory `MutationStaging`; one `stage_*` + `commit_staged` per touched table runs at end-of-query, then the publisher commits the manifest atomically. A mid-query failure leaves Lance HEAD untouched on staged tables. (MR-794; pre-v0.4.0 used a `__run__<id>` staging branch + Run state machine, removed in MR-771.)
- **Schema-apply lock**: `__schema_apply_lock__` system branch serializes schema migrations.
- **Fail-points** (`failpoints` cargo feature): `failpoints::maybe_fail("operation.step")?` in `branch_create`, publish, etc., for deterministic failure injection in tests.
## Workspace crates
- `omnigraph-compiler` — schema and query grammars, catalog, IR, lowering, type checker, lint, migration planner, OpenAI-style embedding client.
- `omnigraph` (engine, published as `omnigraph-engine` on crates.io since v0.2.2) — the Lance-backed runtime: manifest, commit graph, snapshot, exec (incl. per-query `MutationStaging` accumulator), merge, loader, Gemini embedding client.
- `omnigraph-cli` — the `omnigraph` binary.
- `omnigraph-server` — the `omnigraph-server` binary (Axum HTTP server).