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48 commits

Author SHA1 Message Date
aaltshuler
9427fb510e docs(cli): the two config surfaces + the operator file reference
cli-reference.md gains the config-surfaces table (cluster / operator /
flags-env, with omnigraph.yaml marked as the legacy combined file per
RFC-008) and the operator config.yaml reference; audit.md documents the
unified actor chain.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-11 20:32:04 +03:00
aaltshuler
8d7aed065f test(cluster,server): gated object-storage cluster e2e + CI wiring + docs
s3_cluster.rs runs the full control-plane lifecycle against a real
bucket (CI: containerized RustFS; locally the RustFS binary): import →
lock released (pins the drop-time release regression caught on the first
live smoke) → apply (graph roots + catalog on the bucket, nothing local)
→ serving snapshots from both the config dir and the bare URI → schema
evolution → approved delete (prefix removal) → empty-cluster refusal.
The server suite gains the config-free boot test: --cluster s3://… with
zero local files serves a stored query over HTTP.

CI: the rustfs job runs both suites; the classify filter covers the
cluster store/serve modules and the new test files. The server smoke
drops its name filter — every test in the s3 target is bucket-gated, and
a filter matching nothing passes vacuously (which silently ran zero
tests for a while).

Docs: deployment.md gains the Bucket-no-volume shape as the preferred
cloud deployment; cluster.md/server.md document --cluster <uri>;
testing.md maps the new suite.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-11 15:56:40 +03:00
aaltshuler
8dc2f15255 feat(cluster): the storage: root — state, catalog, and graph roots relocatable
cluster.yaml gains an optional storage: URI deciding where everything the
cluster STORES lives: the state ledger, lock, content-addressed catalog,
recovery sidecars, approval artifacts, and the derived graph roots
(<storage>/graphs/<id>.omni). Absent, it defaults to the config directory
itself — the original layout, byte-compatible, so pre-existing clusters and
the whole test suite are untouched. Declared configuration always stays in
the working tree (Terraform's config-local/state-remote split); credentials
are env-only, never in cluster.yaml.

Every command resolves its store from the declared root (a bad root is a
loud invalid_storage_root). Graph-root derivation, the delete executor
(prefix delete via the adapter), the sweep's existence probes, the catalog
payload write/verify/read paths, and the serving snapshot all flow through
ClusterStore — the last raw-fs holdouts for stored state are gone, and the
deny-list gains the rule that keeps it that way.

Tests: default-layout byte-compat, a file:// root relocating the entire
cluster (ledger+catalog+graphs under the new root, nothing under the config
dir, serving snapshot follows), invalid-root validation. 98 in-crate + 9
failpoints + full workspace gate green. The s3:// flavor lands with PR 3's
gated RustFS e2e.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-11 14:28:04 +03:00
aaltshuler
fa6af775c1 feat(cli)!: unified load command; deprecate ingest as an alias
omnigraph load is now the single data-write command:
- works against remote graphs (POSTs the server's /ingest endpoint with the
  same bearer/actor resolution as other remote commands) — previously load
  was the only data command forced to open Lance storage directly
- --from <base> opts into fork-if-missing for --branch (the former ingest
  semantics); without --from a missing branch is an error, never a fork
- --mode is now required: overwrite is destructive, so there is no implicit
  default (the old silent default was overwrite)
- output gains base_branch/branch_created (and table sums on remote loads)

omnigraph ingest stays as a deprecated alias (defaults preserved: --from
main --mode merge) that prints a one-line warning to stderr, matching the
read/change deprecation convention; removal in a later release.

Docs updated in the same change: cli.md, cli-reference.md, policy.md,
audit.md, execution.md (unified load section), AGENTS.md quick-flow,
README.md.

BREAKING CHANGE: scripts running omnigraph load without --mode must now
pass it explicitly (previously defaulted to the destructive overwrite).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-11 04:18:00 +03:00
aaltshuler
90676ef52f feat(server)!: POST /ingest forks only when 'from' is present
Branch creation becomes opt-in by presence of the request's 'from' field.
Previously the handler defaulted from to 'main' and always auto-created a
missing branch — a typo'd branch name silently forked main and landed the
data there, with the client none the wiser. Now a request without 'from'
against a missing branch returns 404 branch-not-found and creates nothing;
with 'from' set, fork-if-missing behaves as before. The BranchCreate
authority is only consulted when a fork will actually happen.

The handler calls the unified load_as directly (the deprecated ingest_as
shim is no longer used in the server). IngestOutput.base_branch becomes
nullable: it echoes the request's 'from' and is null when absent. OpenAPI
regenerated; the CLI's local ingest arm moves to load_file_as + the new
converter shape.

BREAKING CHANGE: clients that relied on implicit fork-from-main with 'from'
omitted must now pass from='main' explicitly. IngestOutput.base_branch is
now nullable.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-11 04:05:29 +03:00
aaltshuler
44b5866516 docs: drop ./ path prefixes; document query discovery
Paths in cluster.yaml and command examples are relative to one explicit
config folder (Terraform-shaped) — the ./ prefixes were noise and are gone
across the user docs (109 instances; ../ links and ./scripts executables
untouched). The cluster docs now present directory discovery as the primary
queries form with the list and map forms documented alongside.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-11 01:33:30 +03:00
Andrew Altshuler
c3ff076e89
Merge pull request #181 from ModernRelay/feat/container-cluster-mode
feat(docker): cluster-mode container + AWS/Railway recipes
2026-06-10 23:57:34 +03:00
aaltshuler
f165145b63 docs(deploy): address review — consistent placeholders, complete ECS command
The ECS day-2 apply gains its required --config flag (the image ships no
omnigraph.yaml, so the CLI cannot locate the cluster dir without it), and
the docker-exec example uses the <you> placeholder convention instead of a
real-looking actor name.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 22:54:26 +03:00
aaltshuler
6b3ae7ac79 docs(deploy): AWS and Railway cluster-mode recipes
The container contract (OMNIGRAPH_CLUSTER + mounted volume + token env),
ECS/Fargate+EFS and Railway-volume walkthroughs, the in-container day-2
loop, and the honest constraints list (volume mandatory, no hot reload,
single-writer apply, shared-volume replicas unvalidated). Operator guide
links the recipes.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 22:45:30 +03:00
aaltshuler
99f7f36864 docs(cluster): the precise omnigraph.yaml contract
The 'Relationship to omnigraph.yaml' section becomes the exact rule set:
cluster commands read the per-operator config for exactly one thing (the
cli.actor default when --as is omitted), a --cluster server reads it for
nothing, and pointing data-plane targets at derived roots is ergonomics,
not coupling. Operator guide and CLI reference updated to match.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 22:30:40 +03:00
aaltshuler
97eb65e921 docs(cluster): operator how-to guide for deploying and managing clusters
New docs/user/cluster.md — the practical companion to cluster-config.md's
reference: zero-to-served walkthrough (validate/import/plan/apply, derived
roots, data loading, --cluster serving), the day-2 edit->plan->apply->restart
loop with a per-change-kind table, drift observation and convergence, the
approval gate for destructive changes, crash/lock/lost-ledger recovery, the
boot-refusal table with remedies, deployment patterns (replicas, backup
unit, CI gating), and the explicit not-yet list (hot reload, S3-hosted
cluster dirs, per-query exposure, pipelines). Linked from the user index,
the agent guide's topic map, and cross-linked from the reference.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 22:10:19 +03:00
aaltshuler
711865e6f1 docs(cluster,server): the Phase 5 mode switch; retire applied-not-serving caveats
The standing caveat ('applied means recorded in the cluster catalog —
nothing more; the server still boots from omnigraph.yaml') retires: cluster
docs gain the 'Serving from the cluster' section (exclusivity, applied-
revision serving, fail-fast readiness, restart-to-pick-up, expose-all
bridge), server.md gains mode-inference rule 0 and the cluster-booted multi
mode, deployment.md the boot-source choice, and the CLI's apply note plus
the cli-reference cluster row (stale back to Stage 3A) now describe the full
convergence surface. RFC-005 flips to Landed with four implementation
deviations recorded.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 17:56:54 +03:00
aaltshuler
6c98560dde docs(cluster): document policy binding metadata (5A)
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 15:30:57 +03:00
aaltshuler
c949a2b717 docs(cluster): document Stage 4C — Phase 4 complete
Approvals + gated graph deletion in the user docs, the approve command in the
CLI reference, RFC-004 flipped to Landed with its three implementation
deviations recorded (row-8 retire-and-repropose, --as instead of --actor/--by,
consumed artifacts rewritten in place rather than moved).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 14:44:12 +03:00
aaltshuler
f217352c93 docs(cluster): document Stage 4B schema apply
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 13:14:20 +03:00
aaltshuler
cb6c67f196 docs(cluster): document Stage 4A graph create
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 05:00:42 +03:00
aaltshuler
15868972ff feat(cluster): verify catalog payload blobs in status and refresh
Closes the Stage 3A product gap where a deleted or corrupted blob under
__cluster/resources/ went unnoticed forever (status reported converged and
apply could not repair it because the digests matched).

verify_catalog_payloads checks every query/policy digest in state against its
content-addressed blob (existence + full sha256 re-hash; graph/schema/unknown
addresses have no payloads and are skipped). status reports findings read-only
(warnings catalog_payload_missing/_mismatch; error catalog_payload_read_error
— an unverifiable catalog must not report healthy). refresh closes the
self-heal loop: missing/mismatched blobs mark the resource drifted and remove
its digest from state so the next plan proposes a create and the next apply
republishes; unreadable blobs keep the digest (no spurious republish), mark
error, and exit non-zero. Verification runs before graph observation so the
recomputed graph composite already excludes removed query digests.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 02:07:08 +03:00
aaltshuler
7f3ecf282a Merge origin/main (#164 axiom-15 docs, #86 TableStorage migration) into feat/cluster-apply-stage3a
Clean auto-merge; also fix the stale 'Stage 2C accepts' line in
cluster-config.md to Stage 3A.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 00:45:44 +03:00
aaltshuler
69b63c33ac Merge remote-tracking branch 'origin/main' into feat/cluster-apply-stage3a 2026-06-10 00:45:03 +03:00
Andrew Altshuler
cec65b8ef8
docs(cluster): axiom 15 — single ownership, mode-switch migration, per-operator layer (#164)
Encode the omnigraph.yaml ↔ cluster.yaml coexistence rules that were implicit
across the specs:

- cluster-axioms.md: new axiom 15 — every fact has exactly one owner at a time;
  coexistence is a mode switch, never a merge; omnigraph.yaml's job description
  shrinks to the permanent per-operator layer. Added review-tension bullet.
- cluster-config-specs.md: "Migration model" subsection (three coexistence
  windows: no-conflict, Phase-5 mode switch, bridges-with-sunsets) and a
  "per-operator layer" completeness table (connection, credential reference,
  active context, ergonomics, personal aliases) with its global-config-dir
  destination per the RFC-002 direction.
- cluster-config-implementation-spec.md: Compatibility Stance #7–#9 (single
  ownership, shrinking role, bridges carry sunsets); Phase 5 boot is an
  exclusive XOR mode switch; fixed the duplicated recoveries/recovery dirs in
  the Phase-1 storage layout.
- docs/user/cluster-config.md: "Relationship to omnigraph.yaml" section in
  current-reality terms (cluster catalog is inspectable, not live).

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
2026-06-10 00:44:51 +03:00
devin-ai-integration[bot]
2c578a60b2
(feat) convert engine call sites to &dyn TableStorage; demote legacy TableStore methods to pub(crate) (#86)
* MR-854: convert engine call sites to &dyn TableStorage; demote legacy methods

Phase 1b: every db.table_store.X(...) call site converts to
db.storage().X(...), reaching the storage layer through the sealed
TableStorage trait (returns &dyn TableStorage). Opaque SnapshotHandle
and StagedHandle replace bare lance::Dataset and Transaction in the
threaded values.

Phase 9: the inherent inline-commit methods on TableStore
(append_batch, merge_insert_batch{,es}, overwrite_batch,
create_btree_index, create_inverted_index) demote from pub to
pub(crate). Their only remaining direct users are table_store.rs
itself and the bulk loader's LoadMode::{Append, Overwrite, Merge}
concurrent fast-paths in loader::write_batch_to_dataset (no
two-phase shape in Lance 4.0.0 — closes after lance#6658 and #6666).

Docs:
- invariants.md \u00a7VI.23: drop "at the writer-trait surface"
  qualifier; staged primitives are now the only engine surface.
- runs.md: residual matrix shrinks to delete_where and
  create_vector_index (the two upstream-blocked residuals).
- forbidden_apis.rs: replace transitional language with the
  current allow-list shape (table_store.rs + loader concurrent
  fast-path only).

Files touched:
- changes/mod.rs, db/omnigraph.rs (+export/optimize/schema_apply/
  table_ops.rs), exec/{merge,mod,mutation,staging}.rs,
  loader/mod.rs, storage_layer.rs, table_store.rs,
  tests/forbidden_apis.rs, docs/{invariants,runs}.md.

Co-Authored-By: Ragnor Comerford <ragnor.comerford@gmail.com>

* MR-854: replace test-only inline-commit append callers with local Lance helpers

After demoting TableStore::append_batch from pub to pub(crate), the
integration tests in tests/recovery.rs and tests/staged_writes.rs
that previously called store.append_batch(...) directly to simulate
HEAD-ahead-of-manifest drift can no longer access the inherent
method. Replace those calls with small in-test helpers that do a raw
Dataset::append (the same body the inherent method runs).

- tests/helpers/mod.rs gains lance_append_inline (shared helper).
- tests/staged_writes.rs gets a file-local lance_append_inline_local
  (staged_writes.rs does not import helpers::).
- tests/recovery.rs drops the unused TableStore import in the one
  function whose store binding became unused after the conversion.

Co-Authored-By: Ragnor Comerford <ragnor.comerford@gmail.com>

* MR-854: retrigger CI for flaky Test Workspace job

Co-Authored-By: Ragnor Comerford <ragnor.comerford@gmail.com>

* MR-854: convert remaining table_store call sites in export.rs / read_blob

Two leftover `self.table_store.X` / `db.table_store.X` call sites were
missed in the initial sweep — flagged by Devin Review on PR #86. Both
now go through the trait surface:

- `entity_from_snapshot` (db/omnigraph/export.rs): switch from
  `db.table_store.open_snapshot_table` + `db.table_store.scan` to
  `db.storage().open_snapshot_at_table` + `db.storage().scan`.

- `read_blob` (db/omnigraph.rs): replace
  `snapshot.open(table_key)` + `self.table_store.first_row_id_for_filter`
  with `self.storage().open_snapshot_at_table` +
  `self.storage().first_row_id_for_filter`. The follow-up
  `take_blobs` call still needs an `Arc<Dataset>` (it's a Lance blob
  accessor not surfaced through the trait), so we hand off via
  `SnapshotHandle::into_arc()` with a comment.

After this commit, no engine code outside `table_store.rs` reaches the
inherent `TableStore` API — the docs/runs.md and docs/invariants.md
claim is now uniformly true.

Co-Authored-By: Ragnor Comerford <ragnor.comerford@gmail.com>

* MR-854: post-rebase doc fixes (Lance 6.0.1, MR-A framing, into_dataset note)

Reviewer feedback on the rebased PR:

* docs/dev/writes.md residuals matrix: drop demoted methods from the trait-surface table (now `pub(crate)`); keep only the two genuine trait-surface residuals (`delete_where`, `create_vector_index`); reframe under MR-A (Lance v7.x bump) per docs/dev/lance.md.

* tests/forbidden_apis.rs: update transitional allow-list header to (a) drop the truncate_table mislabel (truncate_table is a Lance Dataset method, not a TableStore method — overwrite_batch's internal call), (b) reframe trait-surface residuals under MR-A / Lance #6666.

* crates/omnigraph/src/storage_layer.rs::SnapshotHandle::{into_arc, into_dataset}: add single-ref invariant doc — both consume Arc via try_unwrap-or-clone; sibling SnapshotHandle clones across an await point force a deep Dataset clone.

* Replace lance-4.0.0 version refs with lance-6.0.1 in active source/test/dev-doc comments (storage_layer.rs, table_store.rs, table_ops.rs, schema_apply.rs, merge.rs, recovery.rs, staged_writes.rs, consistency.rs, docs/dev/execution.md, docs/user/query-language.md). Historical refs in docs/releases/v0.4.1.md and the canonical "Lance 4.0.0 → 6.0.1 migration" line in docs/dev/lance.md left intact.

No engine code changes.

* MR-854: update docs/dev/invariants.md Storage trait row + gap entry

Reviewer feedback: the docs reorg landed; the invariant row now lives in
docs/dev/invariants.md with stable headings (no more numbered §VI.23).

Update two pieces to reflect MR-854 completion:

* Status table 'Storage trait' row: was 'full call-site migration ... incomplete';
  now 'engine call sites all route through db.storage() (MR-854); inline-commit
  inherent methods are pub(crate)-demoted; capability/stat surfaces are roadmap'.

* 'Known Gaps' 'Storage abstraction' entry: was 'older inherent TableStore call
  sites and inline residuals remain'; now names the closed scope (MR-854 — call
  sites migrated, methods demoted, loader fast-paths) and the remaining
  trait-surface residuals under MR-A (Lance v7.x bump) and Lance #6666.

Cross-links to docs/dev/lance.md and docs/dev/writes.md so the framing stays
co-located with the canonical Lance surface tracking.

* MR-854: remove dead inline-commit methods from the storage surface

The loader concurrent fast-path (write_batch_to_dataset) is only reached
for LoadMode::Overwrite — Append/Merge route through MutationStaging — so
its Append/Merge arms were unreachable. Collapse it to overwrite-only and
drop the now-unused mode params, which removes the only callers of:

- TableStorage::append_batch + TableStorage::merge_insert_batches (trait)
- TableStore::merge_insert_batch + merge_insert_batches (inherent)

create_btree_index / create_inverted_index had zero callers anywhere
(scalar index builds use the stage_* primitives). Remove both from the
trait and the inherent impl.

Inherent append_batch stays pub(crate): overwrite_batch and recovery
tests use it. Migrate the one trait-append_batch test caller
(seed_person_row) to stage_append + commit_staged. The merge_insert
FirstSeen-workaround rationale moves from the deleted merge_insert_batch
into stage_merge_insert (now the sole merge path). No behavior change.

Also corrects the inaccurate loader residual comment (the prior text
blamed Lance #6658/#6666, which are the delete and vector-index issues,
for keeping overwrite inline; a stage_overwrite primitive already exists
and schema_apply uses it).

* MR-854: seal db.storage() to staged-only; move residuals to InlineCommitResidual

Split the three remaining inline-commit writes (overwrite_batch,
delete_where, create_vector_index) off the TableStorage trait onto a new
sealed InlineCommitResidual trait, reachable only via the explicit
Omnigraph::storage_inline_residual() accessor. db.storage() now exposes
only staged primitives + reads, so engine code cannot couple a write
with a Lance HEAD advance through the default surface — MR-793 acceptance
§1 ("no public method commits as a side effect of writing") now holds by
construction, not by review + naming.

Call sites moved to storage_inline_residual(): loader overwrite
fast-path, the three mutation delete_where paths, the branch-merge
delete, and the vector-index build. Impl bodies are unchanged (same
delegation to the pub(crate) inherent methods); this is a pure surface
reshape with no behavior change.

The residual trait holds two genuinely upstream-blocked methods
(delete_where -> Lance #6658/v7.x, create_vector_index -> Lance #6666)
plus overwrite_batch, kept for the loader's cross-table bulk-overwrite
concurrency until its staged migration lands (tracked follow-up).

* MR-854 docs: describe the staged-only seal; fix stale Lance index URLs

- writes.md / invariants.md / AGENTS.md: the inline-commit residuals now
  live on InlineCommitResidual behind db.storage_inline_residual(), so
  acceptance §1 holds by construction rather than 'option (b)' per-method
  enumeration. Drop the inaccurate 'until Lance exposes
  Operation::Overwrite { fragments }' claim (that op exists; stage_overwrite
  already builds it) and reframe overwrite_batch as a removable legacy
  residual gated on the loader's bulk-overwrite concurrency.
- forbidden_apis.rs: rewrite the allow-list doc for the split surface.
- lance.md: the index spec pages moved from /format/table/index/ to
  /format/index/ in Lance 6.x (the old paths 404). Fix all 13 URLs.

* MR-854: fix stale lance-4.0.0 comment refs flagged in review

Addresses greptile (exec/merge.rs) and aaltshuler's stale-version blocker:
update lance-4.0.0 -> 6.0.1 in the comment/doc refs within this PR's
footprint (exec/merge.rs, exec/mutation.rs, docs/dev/writes.md). Also
corrects exec/merge.rs to cite lance#6666 (not #6658) for
build_index_metadata_from_segments — that is the vector-index segment-commit
API; #6658 is the two-phase delete. (Pre-existing 4.0.0 refs in untouched
files like architecture.md/storage.md are main's incomplete migration
cleanup, left out of scope.)

* fix(storage): stage loader overwrites

* fix(storage): stage empty schema rewrites

---------

Co-authored-by: Devin AI <158243242+devin-ai-integration[bot]@users.noreply.github.com>
Co-authored-by: Ragnor Comerford <ragnor.comerford@gmail.com>
Co-authored-by: Ragnor Comerford <hello@ragnor.co>
2026-06-09 23:03:08 +02:00
aaltshuler
40a21e4e77 docs(cluster): document Stage 3A config-only cluster apply
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-06-09 23:36:33 +03:00
aaltshuler
89b876c797 Add cluster state lock recovery 2026-06-09 22:31:46 +03:00
aaltshuler
d00d42274e Implement cluster refresh and import 2026-06-09 21:17:23 +03:00
Ragnor Comerford
dbfdddc952
feat(engine): indexed graph traversal (#149)
* perf(engine): route Expand node hydration through the id BTREE via structured filter

hydrate_nodes built an `id IN (...)` SQL string applied via Scanner::filter,
which DataFusion evaluates with InListEval (O(N×M)) rather than using the id
BTREE scalar index — measured at 72× the indexed cost on a 100k-node hop
(MR-376). Build the id IN-list as a structured DataFusion Expr, AND it with
the pushable destination filters, and apply via Scanner::filter_expr (the same
path execute_node_scan already uses); Lance then compiles it to
scalar-index-search -> take.

Destination-filter pushability is now decided by ir_filter_to_expr (structured)
instead of ir_filter_to_sql, so list-contains (array_has) pushes down too.
Removes the now-dead string-filter helpers build_lance_filter, ir_filter_to_sql,
and ir_expr_to_sql; literal_to_sql stays (still used by the mutation delete path).

* feat(engine): add TableStore::scan_edges_by_endpoint for indexed neighbor lookup

Static helper returning edge rows that match a set of endpoint keys on src/dst,
projected to [key_col, opposite_col], via a structured `key_col IN (keys)`
filter_expr. Lance routes it through the persisted BTREE on the endpoint column
(index-search -> take), so cost scales with the frontier size rather than |E|.

Unused until execute_expand's indexed mode lands; isolated in its own commit so
the storage-layer primitive is reviewable on its own.

* feat(engine): add BTREE-indexed Expand traversal path

Split execute_expand into a dispatcher over execute_expand_csr (the existing
in-memory CSR BFS, unchanged) and a new execute_expand_indexed that serves each
hop by batching the frontier into one scan_edges_by_endpoint call against the
persisted src/dst BTREE (index-search -> take), then fans out per source row.
Both share expand_hydrate_and_align — the destination hydration + alignment +
hconcat + in-memory non-pushable filters — which now aligns by string id (a
HashMap) instead of a dense row-id vec, so one tail serves both modes.

Mode selection is OMNIGRAPH_TRAVERSAL_MODE for now (default csr); the
frontier-size auto policy and lazy CSR build follow. AntiJoin stays on CSR.

tests/traversal_indexed.rs (its own #[serial] binary, so env writes never race a
reader) asserts the indexed path matches CSR for one-hop, multi-hop, cross-type,
and no-match cases, and that a freshly-appended unindexed edge is still found
(partial index coverage — fast_search=false unindexed-fragment scan).

* feat(engine): frontier-size Expand dispatcher + lazy CSR build

Replace the env-only mode switch with an auto policy: Expand uses the
BTREE-indexed path when the source frontier is small and the hop count bounded
(OMNIGRAPH_EXPAND_INDEXED_MAX_FRONTIER=1024, OMNIGRAPH_EXPAND_INDEXED_MAX_HOPS=6),
else the in-memory CSR. OMNIGRAPH_TRAVERSAL_MODE=indexed|csr still forces a mode.

Make the CSR index lazy: thread a GraphIndexHandle (memoizing OnceCell over a
Cached/Direct/None builder) through execute_query/execute_pipeline/
execute_rrf_query/execute_anti_join instead of a pre-built Option<&GraphIndex>.
A query served entirely by the indexed path with no AntiJoin never pays the
O(|E|) CSR build — the perf win of Tier 3. AntiJoin still realizes the index
(its negation uses CSR has_neighbors).

Net effect: selective traversals (the common case) skip the whole-graph CSR
build and resolve neighbors from the persisted, incrementally-maintained
src/dst BTREE. Existing traversal/aggregation/end_to_end/search suites now run
the indexed path by default and stay green.

Docs: constants.md (new env knobs), query-language.md (Expand dual path),
indexes.md (graph index is lazy + the indexed alternative).

* test(engine): bench indexed vs CSR selective traversal

Add a selective single-source knows{1,2} comparison to bench_expand: per growing
|E|, time the cold query in csr vs indexed mode (fresh db each, so CSR pays its
O(|E|) build) and assert both modes return identical rows — a guard against the
scalar-index physical_rows silent fallback dropping unindexed-fragment rows. The
existing dense hop1/2/3 latency bench is unchanged.

* feat(engine): surface silent scalar-index fallback in indexed traversal (C6)

Add TableStore::key_column_index_coverage — a metadata-only check (no IO) of
whether a `key_col IN (...)` scan will be served by the persisted BTREE or
silently fall back to a full filtered scan, mirroring Lance's own decision:
no BTREE on the column, or any fragment missing physical_rows (which disables
scalar indices for the whole scan, lance dataset/scanner.rs create_filter_plan).
execute_expand_indexed calls it once per traversal and tracing::warn!s on
Degraded, so the perf cliff is observable instead of hidden behind a bench oracle.

Detection-only: results are correct either way (the scan returns all rows). Closes
the "no silent failures" gap the traversal best-practice audit flagged as the top
deviation, and adds an IndexCoverage value a future cost-based planner can consume.

* perf(engine): dense-id BFS on the indexed traversal path (C3)

execute_expand_indexed ran its per-source BFS in string space
(Vec<HashSet<String>>, HashMap<String,Vec<String>>, ~4 String clones per neighbor
occurrence). Intern node ids to u32 once via a per-traversal TypeIndex (no
GraphIndex/CSR build — laziness preserved) and run visited/seen/frontier/
neighbor-map in dense u32 space, mirroring the CSR path; de-intern only for the
per-hop IN-list and the emitted dst ids handed to the hydrate+align tail.

Behavior-preserving — the traversal_indexed CSR-vs-indexed equivalence tests are
the guard (results are identical, the key type just changes String -> u32).

* refactor(engine): thread the opened edge dataset into indexed Expand

Hoist the edge-dataset open and the C6 index-coverage warning out of
execute_expand_indexed into execute_expand, threading the opened dataset in
as a parameter so it is opened exactly once. Extract the endpoint-column
mapping (endpoint_columns) and the coverage warning (warn_on_degraded_coverage)
as helpers.

Behavior-preserving: same dataset, same warning, same dispatch decision. This
only relocates the open so the upcoming cost-based chooser can consult index
coverage before dispatch without opening the dataset twice.

* feat(engine): cost-based Expand dispatch chooser (C5)

Replace the fixed frontier<=1024 && hops<=6 dispatch threshold with a pure,
IO-free cost model. choose_expand_mode compares the indexed path's
frontier-relative work (hops * frontier * fanout, or hops * |E| when BTREE
coverage is degraded) against the cost of building the whole-graph CSR
(BUILD_FACTOR * |E|), from cheap manifest row counts. Under good coverage this
reduces to a selectivity ratio independent of |E|, preserving the flat-in-|E|
indexed win for selective traversals while routing dense / deep / high-fanout
or degraded-and-expensive traversals to CSR.

execute_expand decides cardinality-first and only opens the edge dataset to
confirm coverage when it leans indexed (no open on a clearly-CSR traversal).
The two env knobs become hard ceilings layered on the model; the
OMNIGRAPH_TRAVERSAL_MODE override still forces a path; the chosen mode is
traced. Results are unchanged across modes — only the path differs.

Adds inline crossover unit tests and extends the traversal_indexed both_modes
harness with an auto pass asserting the chooser is result-preserving across
every traversal shape. Documents the new flag semantics in
docs/user/{constants,query-language}.md.

* test(engine): pin Lance scalar-index coverage + system-column/deletion-metadata surface

Add three Lance surface guards de-risking a future persisted-adjacency cache:
- a compile-only guard pinning the fragment physical_rows + index-detail
  surface that key_column_index_coverage mirrors (the C6 fallback);
- a runtime probe confirming a scalar BTREE on the system column
  _row_last_updated_at_version is not buildable via the normal create-index
  path (the column is not in the user schema), so a version-column range delta
  is not viable as drafted;
- a runtime probe confirming per-fragment deletion metadata
  (deletion_file.num_deleted_rows) is available as cheap O(fragments) metadata,
  the primitive a fragment-coverage delete model would rely on.

The probes turn the two largest substrate assumptions into green/red CI facts
before any cache work begins.

* test(engine): regression for cross-type id-collision in indexed traversal

A node id is unique only within a type, so a Person and a Company can share an
id string. A variable-length traversal over a cross-type edge (WorksAt) must
structurally stop after one hop. This test builds a graph where 'shared' is both
a Person and a Company id and asserts worksAt{1,2} returns only the one-hop
company. It fails today: the indexed path's single string interner de-interns
the hop-1 Company id back to the colliding Person id and runs a hop-2 scan that
matches that Person's edges, emitting a spurious second-hop company (indexed
["other","shared"] vs csr ["shared"]).

* fix(engine): structurally cap cross-type Expand at one hop

A cross-type edge cannot chain (e.g. a Company is not a WorksAt source), so a
variable-length traversal over one is structurally single-hop. Both traversal
paths now enforce this by capping max hops at 1 when from_type != to_type,
instead of relying on the hop-2 scan returning empty.

That reliance was a correctness hole on the indexed path: it interns every
endpoint string into one dense id space, so a cross-type id-string collision (a
Person and a Company sharing an id) let hop 2 de-intern a destination id back to
the colliding source-type id and match its edges, emitting rows the CSR path
never produces. With the cap the cross-type second-hop scan never runs, so the
shared interner can no longer alias across types. Turns the regression test
green (indexed == csr == ["shared"]).

* perf(engine): set-oriented filtered anti-join, remove per-row dispatch

execute_anti_join's filtered slow path sliced the outer batch to one row at a
time and re-ran the inner pipeline per row, so each 1-row inner Expand dispatched
to the indexed path — one Lance scan per outer row, while the CSR realized up
front sat unused.

Replace it with a set-oriented anti-semi-join: tag each outer row with a
synthetic index column, run the inner pipeline once over the whole frontier (the
tag survives Expand's hconcat and Filter's row-drop), then exclude outer rows
whose tag survived. The inner Expand now runs as a single set-at-a-time traversal
over the full frontier; config is read once per operator, not per row (the env
nit is mooted). A produced-but-untagged inner batch fails loudly rather than
silently keeping every row. Results are unchanged (the predicated-negation tests
exercise the path over a multi-row outer with dst-filters).

* test(engine): drop flaky wall-clock budget from the merge truth table

The 30s wall-clock assertion in merge_pair_truth_table flakes under parallel
test load: it tripped at ~31s in the full --test-threads=4 gate while passing at
~20s in isolation. A fixed time budget in a correctness test depends on machine
and parallelism, not correctness; elapsed is still logged for visibility, and a
real merge-perf regression belongs in a bench. The cell-count correctness
assertions (81 / 36 / 45) are unchanged.

* fix(engine): total deterministic ORDER via entity-key tie-break + NULL contract

apply_ordering used an unstable lexsort with no tie-break, so rows with equal
user-sort keys came out in a run-dependent order (the input order depends on
scan parallelism / upstream hashing) — making ORDER ... LIMIT non-deterministic,
a latent deny-list violation (no nondeterministic result ordering).

Append the bound entities' key columns (<var>.id, unique per row) in canonical
name-sorted order as ascending tie-breaks, giving a total, reproducible order
(and a deterministic top-N when ties straddle the LIMIT cutoff). NULL placement
(nulls_first = !descending) is unchanged and now documented as the contract.

New tests/ordering.rs locks descending, multi-key precedence, the deterministic
key tie-break (data loaded in a different order than the expected output, so it
proves the tie sorts by key not by load order), and NULL placement under ASC/DESC.
docs/user/query-language.md documents the total-order + NULL contract.

* test(engine): property-based query-correctness invariants over generated graphs

Adds a proptest harness (new dev-dep) that generates small graphs whose Person
and Company keys are drawn from a shared 5-key alphabet, so cross-type id
collisions, cycles, and self-loops arise by search rather than from one
hand-built fixture. Three invariants:

- prop_expand_indexed_eq_csr: csr == indexed == auto over knows{1,3} (same-type,
  cycles) and worksAt{1,2} (cross-type, collision-prone) from every start.
- prop_results_subset_of_existing_nodes: no phantom rows (catches over-emission
  even if both modes are wrong identically).
- prop_antijoin_partitions_persons: not{worksAt} and its complement are disjoint
  and cover all persons.

Verified the guard bites: neutering the cross-type hop cap makes
prop_expand_indexed_eq_csr fail and proptest shrinks it to persons["c","e"] /
companies["b","c"] — the cross-type collision class the hand-built fixture
only sampled once. Tests are sync + #[serial] (per-case runtime; the mode test
writes OMNIGRAPH_TRAVERSAL_MODE).

* test(engine): cover cycle/self-loop termination + nested anti-join (C5 edge cases)

- variable_hops_terminate_and_dedup_on_cycle: a 3-cycle a->b->c->a traversed with
  knows{1,5} (ceiling above the cycle length) terminates and emits each node once
  (the c->a back-edge hits the seeded source); both_modes confirms indexed == csr.
  Uses a bounded range deliberately — unbounded {1,} is a typecheck error, not a
  runtime path.
- variable_hops_handle_self_loop: a->a self-loop does not loop forever and does
  not re-emit the seeded source.
- nested_anti_join_double_negation: not { worksAt; not { name = Acme } } recurses
  through execute_pipeline, yielding [Alice,Charlie,Diana] (people with no non-Acme
  employer) — distinct from plain unemployed [Charlie,Diana].

* test(engine): execution goldens for typed-literal filters (C4 gap #4)

New literal_filters.rs covers filtering by F64/F32/Bool/Date/DateTime LITERALS
across both arms: standalone comparisons ($m.score > 1.5, $m.ratio <= 0.25,
$m.active = true, $m.born >= date(...), $m.seen < datetime(...)) exercise the
in-memory comparison path, and inline bindings (Metric { active: true },
Metric { score: 3.0 }) exercise Lance filter_expr pushdown. Seeds partition each
predicate so a dropped/miscast filter returns all rows. (Param-bound scalars and
list-column contains are covered elsewhere.)

* test(engine): full rank-order goldens for nearest + bm25 (gap #2)

Existing search tests stopped at top-1 (nearest) or non-empty (bm25), so a
regression corrupting ranks 2..k or reversing the sort direction passed CI
silently. Pin the FULL ordered slug list: nearest([0.1,0.2,0.3,0.4]) ->
[ml-intro, nlp-guide, rl-intro] (ml-intro exact at dist 0, rest by ascending
L2); bm25(Learning) -> [rl-intro, ml-intro, dl-basics] (descending score).
nearest/bm25 skip apply_ordering (is_search_ordered) and return Lance native
order, so result_slugs row order == rank order; values resolved by running and
confirmed stable across runs.

* test(engine): search fuzzy/match_text characterization + RRF non-default pairings

- match_text_matches_exact_set_excludes_unrelated: match_text(body,'neural') ==
  [dl-basics] exactly (not just contains).
- fuzzy_does_not_match_under_default_tokenizer: characterizes that fuzzy() is
  inert with the default tokenizer here (search/match_text work, fuzzy returns
  nothing); turns red — to be promoted to a real golden — if fuzzy starts matching.
- rrf_fuses_two_fts_fields / rrf_fuses_two_vector_queries: RRF fuses arms other
  than the default nearest+bm25 (bm25 title+body; two vector queries), proving
  primary_var resolves and fusion runs. New fixtures/search.gq queries +
  two_vector_params helper. Orders resolved by running, confirmed stable.

* test(engine): anti-join fast-vs-slow path equivalence harness

anti_join_fast_and_slow_paths_agree: the CSR has_neighbors fast path
(not { $p worksAt $_ }) and the set-oriented inner-pipeline replay (same
negation forced slow by an always-true $c.name != "" dst filter) must produce
the same result ([Charlie, Diana]). Closes the second real engine fork explicitly.

* test(engine): regression for nested slow-path anti-join tag collision

A nested not { ... not { ... } } where both levels hit the set-oriented slow
path collides on the fixed __antijoin_outer_row correlation column: the inner
call appends a duplicate, and column_by_name reads the OUTER tag. Fan-out (p1
works at two companies) makes inner row indices diverge from outer tags, so the
bug returns the wrong person set. Fails on current code (left ["p2","p4"] vs
right ["p3","p4"]).

* fix(engine): collision-free anti-join correlation tag for nested negation

The set-oriented anti-join tagged the outer batch with a fixed column name and
read it back by name. Under a nested slow-path anti-join the enclosing tag rides
through the inner pipeline, so the inner call produced a duplicate field; Arrow
permits duplicate names and column_by_name returns the first, so the inner
negation mis-correlated against the outer row indices.

Choose a tag name not already present in the batch (suffix-incremented), so each
nesting level reads its own correlation column. Turns the fan-out regression
green; the existing nested/fast-vs-slow/proptest anti-join invariants still pass.

* fix(engine): cap cross-type hops in the Expand cost model

gather_cost_inputs fed the requested max_hops into choose_expand_mode even though
execute_expand_indexed runs at most one hop for a cross-type edge. So a cross-type
variable-length expand (e.g. worksAt{1,5}) had its indexed cost scaled by 5 while
only one hop runs, skewing the chooser toward CSR (an unnecessary whole-graph
build) near the crossover. Results were unaffected (modes are equivalent); this
is a plan-accuracy fix.

Add cost_effective_hops(requested, same_type) — caps to 1 for cross-type — and
apply it in gather_cost_inputs so the estimate matches what executes. Unit test
covers the cap and the crossover consequence (capped 1 hop stays indexed where
the requested 5 would have flipped to CSR).

* perf(engine): realize anti-join CSR lazily + reuse a warm CSR in the chooser

Two CSR build/reuse fixes flagged on the set-oriented anti-join work (results
unchanged — plan/perf accuracy):

- execute_anti_join called graph_index.get() (the O(|E|) whole-graph CSR build)
  unconditionally, but only the bulk fast path consumes it; a filtered/nested
  slow-path anti-join's inner Expand picks its own access path. Gate the build on
  a pure shape predicate (bulk_anti_join_applies) so a selective anti-join over a
  large graph no longer pays a build it won't use.
- gather_cost_inputs hardcoded csr_cached=false, so once an earlier op realized
  the CSR, later Expands still cost it as a cold build and could pick per-hop
  indexed scans over reusing the warm in-memory CSR. Add GraphIndexHandle::
  is_built() and thread it through so the chooser reuses a materialized CSR.

Anti-join, cross-type, proptest-equivalence, and chooser unit tests stay green.

* test(engine): RAII traversal-mode guard in proptest equivalence

prop_expand_indexed_eq_csr set/cleared OMNIGRAPH_TRAVERSAL_MODE manually; a panic
between set and clear (e.g. a query unwrap on a generated case) would leak the
forced mode into proptest's shrink/subsequent cases and mask the divergence under
test. Replace with a ModeGuard that clears on drop (including on unwind), scoping
the forced mode to a single query.

* test(engine): regression for multi-hop anti-join hop bounds

The bulk anti-join fast path answers via has_neighbors (one-hop existence), so
not { $p knows{2,2} $x } wrongly drops a node with a 1-hop neighbor but no
2-hop path. On a->b (sink) and c->d->e, only c has a 2-hop path; the query should
keep [a,b,d,e]. Fails on current code (left ["b","e"] — only the sinks).

* fix(engine): restrict anti-join bulk fast path to one-hop expands

bulk_anti_join_applies accepted any single Expand, but try_bulk_anti_join_mask
decides via the CSR has_neighbors one-hop existence check — wrong for multi-hop
negations. Require min_hops==1 && max_hops==1 in the predicate; anything else
falls to the slow path, whose inner Expand runs the real bounded traversal.
Turns the multi-hop regression green; one-hop anti-joins unchanged.

* fix(engine): IndexCoverage reports Degraded for uncovered fragments

key_column_index_coverage checked BTREE-exists + physical_rows but not that the
index actually covers the current fragments. Since edge-index creation is skipped
once a BTREE exists, fragments appended later stay unindexed while coverage still
reported Indexed — so the cost chooser priced a partly-full scan as fully indexed.

Compare the BTREE's fragment_bitmap (public on lance_table IndexMetadata) against
the dataset's current fragment ids; report Degraded when any are uncovered. A None
bitmap means Lance can't report coverage — don't over-degrade. Results are
unaffected (the scan returns unindexed-fragment rows either way); this corrects
the cost signal.

Test: a freshly-loaded edge BTREE is Indexed; after appending an edge the new
fragment is uncovered → Degraded. Surface guard pins IndexMetadata.fragment_bitmap.

* docs: clarify the Expand frontier ceiling bounds the initial dispatch frontier

The cap is applied at dispatch on the initial frontier; per-hop fan-out
(union_dense) is not hard-capped. Correct the constants.md and query-language.md
claims: the ceilings bound the initial-dispatch frontier/hops, the cost model
estimates total indexed work as ~hops*frontier*fanout (pricing dense fan-out
toward CSR), and per-hop work is not a hard bound. Drops the overstated 'hard
caps bound indexed work' / 'cost ∝ frontier' wording.
2026-06-09 18:09:13 +02:00
aaltshuler
2f19656c0e fix(cluster): tighten state lock observations 2026-06-09 18:30:33 +03:00
aaltshuler
b046515e1c Merge origin/main into cluster-config-docs 2026-06-09 18:11:12 +03:00
Ragnor Comerford
d0e39e677e
fix(maintenance): route uncovered drift through repair (#156)
* docs(invariants): note the non-atomic manifest->commit-graph publish gap

Every graph publish commits __manifest then appends _graph_commits as two
separate writes; a crash between them leaves the manifest ahead of the commit
DAG. Live reads + durability are unaffected (reads resolve via the manifest) and
recovery does not repair it; impact is bounded to commit history / time-travel
by commit id / merge-base completeness. Pre-existing across all publishes, not
the optimize reconcile specifically. Documented as a Known Gap; the fix is a
commit-graph reconcilable from the manifest, not a recovery sidecar.

* fix(maintenance): route uncovered drift through repair

* fix(maintenance): harden repair review feedback
2026-06-09 14:42:54 +02:00
aaltshuler
a7956ea5a9 Add cluster JSON state ledger status 2026-06-08 21:09:23 +03:00
aaltshuler
043b02e617 feat(cluster): add read-only validate and plan 2026-06-08 20:07:39 +03:00
Ragnor Comerford
e62d9166fb
fix: optimize publishes compaction; recovery roll-back converges manifest (#141)
* test(optimize): cover manifest publish + HEAD-drift reconcile

Red against the pre-fix optimize, which ran compact_files without
publishing the compacted version to __manifest:

- maintenance: optimize must publish so the manifest table_version
  tracks the compacted Lance HEAD and a later schema apply succeeds;
  and must reconcile a pre-existing manifest-behind-HEAD drift (forged
  via raw Lance compaction) so strict writes commit again.
- end_to_end + composite_flow: post-optimize query / strict update /
  reopen in the full lifecycle (the canonical flow previously omitted
  post-optimize writes as a documented "known limitation").
- failpoints: a crash between compaction and the manifest publish rolls
  forward on next open.

* fix(optimize): publish compaction to manifest and reconcile HEAD drift

optimize ran Lance compact_files without publishing the new version to
__manifest, so the manifest table_version lagged the Lance HEAD: reads
stayed pinned to the pre-compaction version, and the next schema apply or
strict update/delete failed its HEAD-vs-manifest precondition with
"stale view ... refresh and retry" (open-time recovery rollback inflated
the gap on retry).

optimize now publishes each compacted table's version under the
per-(table, main) write queue, guarded by a manifest CAS and a
SidecarKind::Optimize recovery sidecar (loose-match; roll-forward is safe
because compaction is content-preserving). When a table has nothing left
to compact but its Lance HEAD is already ahead of the manifest pin
(pre-fix drift, or a recovery restore commit), optimize reconciles the
manifest forward to HEAD (metadata-only, no sidecar). Caches and the
CSR/CSC graph index are invalidated after a publish.

Docs updated (maintenance, storage, branches-commits, writes, testing).

* test(recovery): rollback convergence + optimize-defer regressions

Red against the current code, landed before the fix:
- recovery: after the open-time sweep rolls a sidecar back, the manifest
  must track Lance HEAD (no residual drift) so a follow-up schema apply
  succeeds — the original "+1 per retry" loop. Today roll-back restores
  without publishing, so the manifest lags HEAD and the apply fails its
  HEAD-vs-manifest precondition.
- maintenance: optimize must refuse while a recovery sidecar is pending —
  operating on an unrecovered graph could publish a partial write the
  sweep would roll back.

Also removes optimize_reconciles_preexisting_manifest_head_drift: the
ad-hoc drift reconcile it covered is replaced by recovery-side convergence.

* fix(recovery): converge manifest on roll-back; optimize defers on pending recovery

Root of PR #141's review findings and the original "+1 per retry" loop:
a Lance HEAD ahead of the manifest was ambiguous (benign content-preserving
drift vs. a partial write a sidecar will roll back), and optimize's reconcile
guessed it benign. Close the class instead of guessing:

- Recovery roll-back now PUBLISHES the restored version (via a
  push_table_update_at_head helper shared with roll-forward), so the manifest
  tracks the Lance HEAD after recovery — symmetric with roll-forward. This
  fixes the +1 loop (after one roll-back the retry's HEAD-vs-manifest
  precondition passes) and removes the only remaining source of orphaned
  drift. The audit still records the logical rolled-back-to version; the
  manifest is published at the restore commit (identical content).
- optimize drops the ad-hoc drift reconcile and instead REFUSES when a
  __recovery sidecar is pending, so it only ever operates on a recovered
  graph (manifest == HEAD); its compaction publish can no longer commit a
  partial write. With the reconcile gone, the blob-skip-vs-reconcile gap is
  moot.

Updates the rollback recovery-test helper (manifest == HEAD after roll-back),
the failpoints assertions, and the user/dev docs.

* test(recovery): fix rollback assertion for manifest convergence

The roll-back-publishes change makes the manifest version advance after a
SchemaApply roll-back (to the old-schema content), so the
schema_apply_without_schema_staging_rolls_back_on_next_open assertion must
be `version > pre`, not `version == pre`. This update was dropped during
the commit churn and surfaced as a CI Test Workspace failure; the
old-schema-preserved intent stays covered by count_rows + _schema.pg + the
RolledBack convergence invariant.
2026-06-08 02:50:12 +03:00
Ragnor Comerford
54842808db
feat(engine): sweep & remove legacy __run__ branch guard (MR-770) (#132)
* feat(engine): sweep legacy __run__ branches via v2→v3 manifest migration

Pre-v0.4.0 graphs can carry stale `__run__<id>` staging branches on the
`__manifest` dataset, left by the Run state machine removed in MR-771. Lance's
`list_branches` still enumerates them, so they leak into `branch_list()` and
count as blocking branches at schema-apply time.

Add a one-time `migrate_v2_to_v3` arm to the internal-schema dispatcher: on the
first read-write open it enumerates `__manifest` branches, deletes every
`__run__*` ref, and bumps the stamp to 3. Idempotent under retry (re-enumerates
fresh each run). The `"__run__"` prefix is inlined so the migration does not
depend on the run_registry guard that MR-770 removes next.

This is the prerequisite sweep; the guard removal follows in the next commit.

* refactor(engine): remove the legacy __run__ branch guard (MR-770)

With the v2→v3 migration sweeping stale `__run__*` branches off `__manifest`
on first read-write open, the defense-in-depth `is_internal_run_branch` guard
is no longer needed.

- delete `db/run_registry.rs`; drop the module + re-export from `db/mod.rs`
- collapse `is_internal_system_branch` to the schema-apply-lock check only
- `ensure_public_branch_ref`: drop the run-ref rejection; `__run__*` is now an
  ordinary branch name
- `branch_merge`: reject `is_internal_system_branch` (was run-only) so the
  schema-apply lock is rejected consistently with create/delete — a small,
  deliberate tightening
- update the inline schema-apply test + the writes integration tests
  (`public_branch_apis_reject_internal_run_refs` →
  `public_branch_apis_reject_internal_system_refs`, which also asserts
  `__run__*` now creates successfully)
- docs: flip the "pending production sweep / defense-in-depth" notes to
  "auto-swept by the v2→v3 migration"; document the read-only-open limitation

Known residual: the inert `_graph_runs.lance` / `_graph_run_actors.lance` bytes
remain until a `StorageAdapter::delete_prefix` primitive lands.

* fix(engine): run __run__ sweep at Omnigraph::open, not only on publish

Review (PR #132) caught a regression: removing __run__ from
`is_internal_system_branch` exposed legacy `__run__*` branches to the
schema-apply blocking-branch checks (schema_apply.rs:104 and :778) and to
`branch_list()`, but the v2→v3 sweep ran only inside the publisher's
`load_publish_state`. On a pre-v0.4.0 graph whose first write is a schema
apply, the blocking-branch check fires before any publish, so apply failed
with "found non-main branches: __run__…". The same lazy timing also created a
reverse hazard: a user-created `__run__*` branch on a still-v2 graph could be
deleted by the first publish's sweep.

Fix: run the internal-schema migration in `Omnigraph::open(ReadWrite)` (new
`manifest::migrate_on_open`), before the coordinator reads branch state. The
sweep now lands before any branch-observing code, and a graph is stamped v3 at
open — so the one-time sweep can never catch a legitimately-created branch.
Both checks and `branch_list` see the swept graph; correct by construction for
every write path.

Accepted residual: a read-only open of an unmigrated legacy graph still lists
`__run__*` (read-only opens must not write, so they can't sweep). Documented.

Regression test `legacy_run_branch_is_swept_on_open_and_does_not_block_schema_apply`
confirmed RED before the fix (panicked on the branch_list leak assertion) and
GREEN after. Also updates the stale schema_apply.rs comment, the writes.md
"Migration code" section, and adds the v3 row to storage.md's migration table.

* test(engine): sweep multiple legacy __run__ branches; doc nit

Strengthen the v2→v3 migration test to synthesize three `__run__*` branches
(a real legacy graph accumulates one per run) so the migration's delete loop
is exercised on a single reused dataset handle, not just a single branch.
Confirms multi-branch deletion is safe.

Also drop a stale "active runs" reference from the branch_delete doc line.

* fix(engine): force-delete in __run__ sweep for concurrency safety

`migrate_v2_to_v3` ran `Dataset::delete_branch` (= `branches().delete(.., false)`),
which errors "BranchContents not found" if the branch is already gone. Since the
sweep now runs in `Omnigraph::open(ReadWrite)`, two processes opening the same
legacy v2 graph concurrently would race: one wins each delete, the other's open
fails. The migration only claimed idempotency under *sequential* retry.

Switch to `Dataset::force_delete_branch` (= `delete(.., true)`), Lance's
documented path for cleaning up zombie branches, which tolerates an
already-absent branch. The sweep is now idempotent under concurrent runners and
robust to partial/zombie state. Found in self-review; no behavior change for the
common single-open path.

* docs(release): note MR-770 __run__ cleanup in v0.6.1

* docs(branches): reconcile branch cleanup semantics
2026-06-07 18:33:14 +03:00
Ragnor Comerford
d54bccb940
fix(optimize): skip blob-bearing tables to avoid Lance compaction crash (#138)
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* test(optimize): pin Lance blob-column compaction failure as a surface guard

Lance compact_files mis-decodes blob-v2 columns under its forced BlobHandling::AllBinary read ("more fields in the schema than provided column indices"), failing even a pristine uniform-V2_2 multi-fragment blob table; reads use descriptor handling and are unaffected.

Guard 10 reproduces this and is self-retiring: it turns red on the Lance bump that fixes the bug, forcing LANCE_SUPPORTS_BLOB_COMPACTION to flip.

* fix(optimize): skip blob-bearing tables instead of crashing compaction

omnigraph optimize aborted the whole sweep when any node/edge table had a Blob property: Lance compact_files cannot decode blob-v2 columns under AllBinary (the column-index error pinned by the surface guard). Skip blob-bearing tables behind a LANCE_SUPPORTS_BLOB_COMPACTION gate and report them via TableOptimizeStats.skipped / SkipReason (surfaced in the CLI and a tracing::warn) instead of erroring, which also isolates the failure so the other tables still compact.

Reads/writes are unaffected; only fragment/space reclamation on blob tables is deferred until the upstream Lance fix. Adds a maintenance.rs regression test (validated red with the column-index symptom before the fix, green after), a concise v0.6.1 release note, and updates docs (maintenance, cli-reference, AGENTS capability matrix, invariants Known Gaps, lance.md audit, constants).

* refactor(optimize): make TableOptimizeStats and SkipReason non_exhaustive

Both are returned result types, never built by callers, so #[non_exhaustive] makes this the last field/variant addition that can break downstream literal construction and keeps future ones non-breaking (review feedback on the public-field addition). The v0.6.1 Compatibility Notes call out the source-level change.

Also drops the now-stale "RED today / GREEN after the fix lands" narration in the optimize_skips_blob_table_and_reports_skip test (historical regression context now that the fix is in this branch), and folds in the expanded v0.6.1 release note.

* chore(release): bump workspace to v0.6.1

Coherent version bump to accompany the v0.6.1 release note: all five crate manifests + path-dependency constraints, Cargo.lock, the AGENTS.md surveyed-version line, and openapi.json info.version move 0.6.0 -> 0.6.1. Matches the established release pattern (#118 landed the v0.6.0 note + bump together) and resolves the Codex/Devin review flag that a v0.6.1 note without a bump leaves CARGO_PKG_VERSION reporting 0.6.0 and mixed package versions.
2026-06-02 17:12:00 +02:00
Ragnor Comerford
3c2b1b8051
Stored-query registry foundation + config/CLI RFC-002 (#128)
* MR-969: add stored-query registry config surface

Introduce the `queries:` block in omnigraph.yaml — an inline
`name -> entry` map of stored queries, per-graph
(`graphs.<id>.queries`) and top-level for single-graph mode, mirroring
how `policy` is wired in both modes. Each entry points at a `.gq` file
and carries optional MCP exposure settings (`expose`, `tool_name`),
defaulting to not-exposed.

Additive: absent `queries:` leaves current behavior unchanged.

- QueryEntry { file, mcp: McpSettings { expose, tool_name } }
- `queries` field on TargetConfig + OmnigraphConfig (serde default)
- query_entries() / target_query_entries() accessors
- resolve_query_file() — base_dir-relative `.gq` path resolution
- round-trip + absent-block tests

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* Add stored-query registry loader and GraphHandle wiring

Add a `queries` module: QueryRegistry loads each declared `.gq` entry,
parses it, and selects the query whose symbol matches the manifest key,
asserting the two agree (key == `query <name>` symbol). Identity is the
query name; a key/symbol mismatch is a load-time error. Errors are
collected, not fail-fast, so a bad registry surfaces every broken entry
at once. Schema type-checking is deliberately left to a separate pass so
the loader stays callable without an open engine.

Thread an `Option<Arc<QueryRegistry>>` through GraphHandle alongside the
per-graph policy; the URI-canonicalizing clone propagates it. Production
openers default to None for now — the boot path loads and attaches the
registry in a later change.

- QueryRegistry::{from_specs, load, lookup, iter}; StoredQuery::is_mutation
- GraphHandle.queries field, propagated on canonical clone
- registry unit tests: identity match/mismatch, multi-query selection,
  per-entry parse errors, error collection, mutation classification

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: add RFC-002 config & CLI architecture

Layered config (user-global ~/.config/omnigraph/ + per-project), a
unifying `target` abstraction resolving to (locus, graph, sub-state,
credential) with embedded-URI XOR remote-server loci, multi-server ×
multi-graph client targeting, credentials by-reference, and the
file-naming decision: project and server config are one artifact
(`omnigraph.yaml`); the only differently-named file is the user-global
`config.yaml`, split by scope not role. Includes the 12-factor bind
portability rule (prefer --bind/OMNIGRAPH_BIND over a committed
server.bind) and the defined-locally / invoked-remotely model for
stored queries. Derived from first principles working backwards from
what the engine enables; validated against kube/Helix/git/compose.

Linked from docs/dev/index.md. Proposed; phased rollout for the
MR-973/974/981 family.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* Add check() to validate stored queries against the live schema

A pure check(registry, catalog) that type-checks every stored query via
the same typecheck_query_decl the engine runs for inline queries — no
parallel implementation. Failures are collected, not fail-fast, so an
operator sees every broken query (e.g. a type/property a migration
renamed or removed) in one pass. Breakages are fatal (the boot path will
refuse to start); warnings are advisory.

Pure over (registry, catalog) so it is callable both at boot (engine
catalog) and offline from the CLI without an open engine.

Advisory lint: an mcp.expose:true query that declares a Vector(N)
parameter warns — an LLM cannot supply a raw embedding vector; such a
query should take a String parameter and embed server-side. Warns
rather than rejects, since service-to-service callers may pass vectors.

- CheckReport { breakages, warnings }; has_breakages / is_clean
- tests: valid query, unknown type, unknown property, collect-not-fail-fast,
  vector-param-exposed warns, unexposed silent

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* Drop internal plan-label refs from stored-query config comments

Doc comments referenced sequencing labels ("C2") that mean nothing to a
reader; reword to describe the behavior directly. Comment-only.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: reconcile aliases with the role model in RFC-002

Place the existing client-only `aliases:` block in the client/server
role split: aliases are client-role (CLI, embedded, ungated) and may
live in both user-global and project config; `queries:` is server-role
(deployment manifest only). They overlap as "name -> .gq"; `queries:` is
the superset, and the end-state subsumes aliases (definition -> queries,
target/branch/format -> client invocation context, positional args ->
CLI sugar). v1 keeps aliases unchanged.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: make RFC-002 config global-first, project-optional

The global user config is the primary, self-sufficient default; the
CLI works from any directory with no project file (the kubectl/aws/gh
posture), a deliberate flip from today's project-anchored behavior.
The project omnigraph.yaml becomes an optional repo-scoped override and
the deployment manifest. Uniform schema, both layers optional; global
can hold any section including a personal server's graphs/queries.
Additive: project still overrides global; the flip adds a fallback
layer below the project file rather than removing it.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: justify XDG ~/.config/omnigraph over legacy ~/.omnigraph in RFC-002

Make the rationale explicit: XDG-first because OmniGraph is a client
that will cache remote catalogs and keep session state alongside
secrets, and XDG separates config / cache / state into distinct dirs
(clear cache without touching creds; backups skip cache) whereas a
single ~/.omnigraph/ mixes them. Honor ~/.omnigraph/ as a fallback for
the peer-group (aws/kube/docker/helix) expectation. Add XDG_CACHE_HOME
/ XDG_STATE_HOME to the override precedence.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: build RFC-002 credentials on the existing env-file mechanism

OmniGraph already has credentials-by-reference: bearer_token_env names
the env var, and auth.env_file is a git-ignored dotenv the CLI
auto-loads (real env vars win), resolved via resolve_remote_bearer_token.
The RFC's proposed credentials.yaml + token_env were redundant parallel
inventions. Reconcile: reuse bearer_token_env (extend to
servers.<name>) and auth.env_file (add a global ~/.config/omnigraph/.env
layered under the project .env.omni); OS keychain is an additive future
resolver. No new credentials.yaml. Updated summary, non-goals,
background, file-naming, credentials, example, login, migration, rollout.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: use single ~/.omnigraph dir (Helix-style), not XDG, in RFC-002

Reverse the earlier XDG-first call. The prior argument rested on a false
dichotomy (single-dir => mixed config/cache/state); in fact the peer
tools (aws, kube, helix) achieve separation via SUBDIRECTORIES inside
one ~/.tool/ dir (~/.aws/sso/cache/, ~/.kube/cache/), getting cache
hygiene AND one discoverable place. So everything goes under
~/.omnigraph/: config.yaml, credentials (dotenv, 0600), cache/, state/.
Lower cognitive load, matches what DB/cloud-CLI users expect, matches
Helix. OMNIGRAPH_HOME overrides; $XDG_CONFIG_HOME optionally honored but
~/.omnigraph/ is canonical. Updated all paths, the rationale paragraph,
the file-naming table (added a cache/state row), and env precedence.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: reconcile RFC-002 with shipped/planned CLI tickets

Align with reality found in existing tickets:
- Noun is graph/graphs, not target/targets (MR-603 done renamed the
  config key targets->graphs, flag --graph). Use graphs:/--graph; an
  entry is embedded (uri) XOR remote (server + remote graph name).
- ~/.omnigraph/ confirmed by MR-581 (og template pull, done) which
  already quick-starts templates there.
- Templates already exist (MR-581/MR-531) — not invented here.
- The init family is already specced (init, quickstart MR-973, serve
  MR-970, prune MR-972, mcp install MR-974, agent-mode MR-981); this
  RFC only adds the user route (~/.omnigraph/config.yaml + login).
- aliases: -> operations: planned (MR-839).
- bearer_token_env gap tracked in MR-971.
- query lint/check already exist (MR-639) — registry validator must not
  collide with the singular `query check`.
Add a Reconciliation section; fix the canonical example to graphs:/--graph.
Also: merge semantics refined (deep-merge settings, replace named
entries, replace lists, config view --resolved --show-origin).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: correct stale-ticket claims and fold init/bootstrap design into RFC-002

Verify against code, not ticket statuses (MR-581 is marked done but is
stale/unbuilt): no ~/.omnigraph usage, no template/serve/quickstart/
prune/login commands exist; config still uses aliases: (no operations:).
So ~/.omnigraph/ stands on peer-convention merits alone, and templates
are a design question, not a foothold. Add §7.5: the three-tier init
model (user route = login + ~/.omnigraph/config.yaml; thin project init;
fat quickstart + templates) with first-principles positions (split
init/login, in-place refuse-if-exists, interactive vs --auto/agent-mode,
--template flag, secrets-on-scaffold gitignore rule). This RFC owns only
the user route; the rest are sibling tickets (MR-973/970/972/974/981).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs: breadboard + slice Shape A in RFC-002

Add the implementation breadboard (places P1-P5, affordances N1-N14 with
NEW markers, mermaid) and five vertical slices for the selected config/
CLI/init shape: V1 global layer + merge engine + config view; V2 remote
graphs + HTTP-client path + credential resolution; V3 omnigraph login;
V4 init-hardening + quickstart + templates (rides MR-970); V5 agent-mode
(MR-981). Rollout reordered to the slice sequence; spikes X1-X4 gate
their owning slice. V1-V2 close the substantive client->server gap.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* Add InvokeQuery Cedar action (coarse, graph-scoped)

A per-graph, branch-scoped action that gates invoking a server-side
stored query by name. Coarse for now: an `invoke_query` allow rule
permits any stored query on the graph; a future, additive refinement
adds an optional per-query-name scope without changing rules written
against the coarse action. Enforcement is at the HTTP boundary; the
engine `_as` writers still enforce read/change per the query body, so a
stored mutation is double-gated (invoke_query to reach the tool, change
for the write). No call site yet — the invocation handler wires it in a
later change (same pattern as Admin/GraphList added ahead of consumers).

- variant + as_str/resource_kind(Graph)/FromStr/uses_branch_scope
- Cedar schema: invoke_query appliesTo Graph
- tests: per-graph allow/deny, branch-scope accepted

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* Load and type-check stored queries at server boot, refusing breakage

At startup the server now loads each graph's stored-query registry,
type-checks every query against that graph's live schema, and refuses to
boot if any query references a type/property the schema doesn't have
(same posture as bad policy YAML) — so schema drift surfaces at the
deploy boundary, not silently at invocation. Non-blocking warnings are
logged. The validated registry is attached to the GraphHandle (the two
production sites previously held `queries: None`).

Loading (parse + key==symbol identity) happens at settings-build time
where the config is in scope; the schema type-check happens after each
engine opens (single mode in `open_single_with_queries`, multi mode in
`open_single_graph`). `open_with_bearer_tokens_and_policy` delegates
with an empty registry so its 18 test callers are unchanged; the public
`new_*` constructors are unchanged (only the private build path threads
the registry).

- ServerConfigMode::Single / GraphStartupConfig carry the loaded registry
- boot tests: valid registry boots; type-broken query refuses boot + names it

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* Add `omnigraph queries validate` and `queries list` CLI

`queries validate` type-checks the stored-query registry against the
live schema offline — it opens the selected graph, runs the same
check() the server runs at boot, prints breakages/warnings (human or
--json), and exits non-zero on any breakage — so an operator can catch
a query broken by a schema change without restarting the server.
`queries list` prints each registered query's name, MCP exposure, and
typed params.

Named `validate` (not `check`) to avoid overlap with the existing
`omnigraph lint` — `query check`/`query lint` are already deprecated
argv-shims to `lint`. Registry entries resolve like the server: a named
graph uses its per-graph `queries:`; otherwise the top-level one.

- Queries subcommand group; reuses QueryRegistry::load + check from
  omnigraph-server; local-only (needs the schema), mirrors lint
- tests: clean registry exits 0, broken query exits non-zero + names it,
  list shows the query and its typed params

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* Route registry selection through one shared query_entries_for

The "which queries: block applies for graph X" rule existed twice — the
server boot path and the CLI's registry_entries — and had already drifted:
the CLI carried an unreachable unwrap_or_else fallback the server lacked.

Add OmnigraphConfig::query_entries_for(graph: Option<&str>) as the single
definition (named graph -> its per-graph block; otherwise top-level) and
route all three sites through it: server single mode, server multi-graph
loop, and the CLI. The CLI's dead fallback arm is deleted; CLI and server
now resolve identically by construction.

No behavior change. Extends the config round-trip test to pin the selector,
including the unknown-name -> top-level fallback the deleted CLI arm covered.

* Funnel registry validation through one validate_and_attach gate

The check -> refuse-on-breakage -> log-warnings -> empty->None block was
copy-pasted across both open paths (single mode and the multi-graph
per-graph open), differing only by the graph label. A third opener could
attach a registry that was never schema-checked.

Extract validate_and_attach(queries, catalog, label) -> Option<Arc<..>> as
the single gate both paths call, so attaching an unchecked registry is no
longer expressible. The catalog handle is an owned Arc, so calling it
before the multi-mode policy match (which rebinds db) is borrow-clean.

No behavior change. Adds a direct unit test of the helper (empty / clean /
breakage incl. the graph label in the message) — covering the multi-graph
path's logic, which previously had no boot-refusal coverage.

* Resolve param types structurally in the MCP vector lint

The exposed-query advisory detected vector params with
type_name.starts_with("Vector(") — a second copy of the compiler's own
ScalarType::from_str_name vector parsing that could drift from it.

Key the lint off PropType::from_param_type_name + ScalarType::Vector(_)
instead, the one canonical resolver the type system already uses. Any
future param-suppliability lint now reads the structured type rather than
scanning the surface string.

Behavior-preserving: the grammar forbids list-of-vector params
(list_type = "[" base_type "]", and base_type excludes Vector), so the only
input where the structured and string checks could differ is unparseable.
Adds a guard test that an exposed String param does not false-trigger the
warning.

* Refuse duplicate MCP tool names across exposed stored queries

The effective MCP tool name (explicit tool_name, else the query name) is a
second identity namespace beside the registry key, but nothing enforced it
unique — two exposed queries could claim one catalog key, and each consumer
re-derived the name ad hoc.

Add StoredQuery::effective_tool_name() as the one definition, and a
load-time uniqueness pass in from_specs over exposed queries: a collision is
a collected LoadError naming the loser and the winner. Scoped to exposed
queries (unexposed have no MCP tool); deterministic over the BTreeMap so the
first-declared wins and the error order is stable.

New (rare) refusal: a config with colliding exposed tool names now fails
`omnigraph queries validate` offline and refuses server boot, the same
posture as a malformed registry. Release-note-worthy.

Test-first: duplicate_exposed_tool_name_is_a_load_error (red before the
pass, green after) + a CLI offline test; the unexposed sibling pins the
exposed-only scope; effective_tool_name asserts folded into the load test.

* docs: document the queries registry, CLI, and invoke_query action

The stored-query surface shipped without user docs. Add it, per the same-PR
maintenance contract:

- policy.md: invoke_query as per-graph action #10 (branch-scoped), with the
  double-gating note; renumber graph_list; add it to the branch_scope list.
- cli-reference.md: the `queries validate | list` command, and the
  `queries:` config block (per-graph + top-level) with mcp.expose/tool_name
  and the tool-name uniqueness rule.
- server.md: boot-time stored-query type-check (refuse on breakage), noting
  invocation over HTTP/MCP is not yet exposed.

* Add POST /queries/{name} stored-query invocation handler

Invoke a curated server-side stored query by name: source + name come from
the per-graph queries: registry, the client sends only runtime inputs
(params, branch, snapshot). Gated by the invoke_query Cedar action at the
boundary; the handler delegates to the existing run_query/run_mutate, whose
inner Read/Change enforce still runs — so a stored mutation is double-gated
(invoke_query to reach the tool, change for the write).

- InvokeStoredQueryRequest + an untagged InvokeStoredQueryResponse
  { Read(ReadOutput), Change(ChangeOutput) } → one Json<_> return type and a
  oneOf 200 schema (a correct contract, not a wrong-but-simple one).
- Route lives in per_graph_protected → single-mode /queries/{name} and
  multi-mode /graphs/{id}/queries/{name} for free.
- Deny == unknown: an invoke_query denial and a missing query both return the
  same 404, so the catalog can't be probed by an unauthorized caller.
- OpenAPI regenerated; tests cover read, mutation double-gate (403 vs 200),
  bad-param 400, and the identical-404 deny path.

Completes the MR-969 V1 invocation slice (registry + /queries/{name} + invoke_query).

* docs: stored-query invocation endpoint; flip the not-yet-exposed caveat

Now that POST /queries/{name} ships (C7), document it: add the endpoint to
server.md's inventory + an invocation section (body, untagged read/mutate
envelope, invoke_query gate, double-gated mutations, deny == 404), and flip
the startup note that said invocation was not yet exposed. In policy.md,
replace "no invocation call site yet" on the invoke_query action with a
pointer to the endpoint.

* Scope the stored-query 404-hiding claim to non-invoke_query callers

Review found the deny==404 catalog-hiding was overstated as a contract: it
holds only at the outer invoke_query gate. A caller that HOLDS invoke_query
but lacks read/change gets the inner gate's 403 for an existing query vs 404
for an unknown one — so existence is visible to grant-holders by design (the
intended double-gate). The handler docstring, OpenAPI 404 description, and
server.md all claimed the 404 was airtight against any denied actor.

Correct the wording in all three (no behavior change) and add the missing
symmetric test (invoke_query but no read -> 403 for an existing query, 404
for unknown) so the actual contract is pinned. Also document that in
default-deny mode (tokens, no policy) every invocation 404s until an
invoke_query rule is configured.

Nits: the from_specs collision comment said "first declared wins" but it is
lexicographically-first by name (BTreeMap); the effective_tool_name docstring
overclaimed the CLI display routes through it (it resolves the rule on its
own output DTO).

* Default mcp.expose to true (the manifest entry is the opt-in)

expose controls MCP-catalog membership only — it is not an authorization
gate (invocation is gated by invoke_query regardless). So requiring a
per-query mcp.expose: true was friction with no safety benefit: a
non-exposed query is still HTTP-invocable by name. Flip the default so
declaring a query in the manifest exposes it to the agent tool catalog by
default; expose: false is the escape hatch for service-only queries.

Both the absent-mcp path (Default impl) and the present-but-no-expose path
(serde default fn) now yield true. Doc comments + cli-reference updated; the
config round-trip test asserts the new default.

* Add GET /queries stored-query catalog endpoint

List a graph's mcp.expose stored queries as a typed tool catalog so a client
(the MCP server) can register them as tools without fetching .gq source.
Each entry carries name, MCP tool_name, description/instruction, a
read/mutate flag, and decomposed typed params (kind enum: string|bool|int|
bigint|float|date|datetime|blob|vector|list, plus item_kind for lists and
vector_dim) — so the consumer builds an input schema with a closed match and
never re-parses omnigraph type spelling. I64/U64 are bigint (string on the
wire): a JSON number loses precision past 2^53 and the engine already accepts
decimal strings.

Read-gated (works in default-deny; the catalog is graph-wide, authorized
against main). NOT Cedar-filtered per query yet — a reader can list a query
whose invoke_query they lack (documented gap until per-query authz lands);
invocation stays invoke_query-gated + deny==404.

- api: QueriesCatalogOutput / QueryCatalogEntry / ParamDescriptor / ParamKind
  + query_catalog_entry (reuses PropType::from_param_type_name; scalar_kind is
  exhaustive, so a new ScalarType is a compile error here until catalogued).
- GET /queries route in per_graph_protected (→ /graphs/{id}/queries in multi
  mode); OpenAPI regenerated; path allowlists updated.
- Tests: projection unit (every kind, list, vector, nullable, mutation,
  empty) + handler (exposed-only filter, read-gate probe-oracle, empty
  registry).

* docs: GET /queries stored-query catalog endpoint

Document the catalog: the endpoint table row (GET /queries, read-gated), a
catalog section (typed-param kind enum, bigint/date/datetime/blob-as-string,
graph-wide/branch-independent, mcp.expose default true, the read-gated
probe-oracle gap), and flip the startup note now that the catalog ships.

* Collect file-I/O and parse errors in QueryRegistry::load in one pass

load() early-returned on any unreadable .gq file, masking parse / identity /
tool-name-collision errors in the OTHER (readable) files — so an operator
fixed the missing file, restarted, and only then saw the next broken query.
Now it collects I/O errors but still runs from_specs on the readable specs
and returns the union, so every broken entry surfaces at once (matching the
collected-errors contract the rest of the registry already follows).

Safe: from_specs' tool-name collision check runs over loaded queries only, so
dropping an I/O-failed entry can only under-report a collision, never invent
one. I/O errors are ordered first (BTreeMap key order), then spec errors.

Adds a load-level test (tempdir: a valid, a missing, and a parse-broken .gq)
asserting all three surface in one Err — confirmed red before the fix.

* Make invoke_query graph-scoped (one branch authority)

invoke_query gates reaching the curated stored-query surface — a graph-level
capability. Per-branch/snapshot access is already enforced by the inner
read/change gate in run_query/run_mutate (authorized against the resolved
branch), so branch-scoping the outer gate was redundant AND wrong for snapshot
reads (it defaulted to main). Drop the branch dimension: remove InvokeQuery
from uses_branch_scope (it joins admin as graph-scoped) and authorize the
boundary gate with branch: None.

Lossless: an actor confined to branch X by their read/change rules can still
only invoke a stored query that touches X. A rule that sets branch_scope on
invoke_query is now rejected by validate() — write invoke_query in its own
rule.

Ripple (atomic): restructure the server invoke fixture so invoke_query sits in
its own branch_scope-free rule; invert invoke_query_is_branch_scoped ->
invoke_query_rejects_branch_scope; the per-graph authorize test uses
branch: None; docs (policy.md, server.md, the InvokeQuery doc). No wire/OpenAPI
change.

* Resolve graph config by identity, not server mode

Which policy/queries block applies for a graph was decided three different,
mode-dependent ways: single-mode boot used top-level even for a named graph;
multi-mode used per-graph (and silently ignored a top-level queries block); the
CLI used per-graph for a named target. So `queries validate --target prod`
could check a different registry than the single-mode server loaded, and a
named graph's per-graph policy/queries were silently shadowed.

Make config a function of graph IDENTITY: a graph served by NAME
(--target/server.graph, a graphs: entry) uses its own graphs.<name>.{policy,
queries}; a bare URI is anonymous and uses top-level. One rule, applied by
single-mode boot, multi-mode boot, and the CLI — so they can't diverge and the
CLI predicts the server exactly.

No silent ignore: serving a named graph while a top-level policy/queries block
is populated now refuses boot, naming the block (the multi-mode top-level-policy
bail, extended to queries and to single-mode-named). The CLI's `queries
validate` derives the schema URI and the registry from ONE selection, and a
positional URI forces anonymous (ignoring cli.graph) so the two can't come from
different graphs.

BREAKING (released behavior): single mode by name (--target/server.graph) with
top-level policy/queries previously used top-level; it now uses the per-graph
block and refuses boot if top-level is also populated. Bare-URI single mode is
unchanged. Loud, with migration text pointing at graphs.<name>.

- config: resolve_policy_file_for (policy sibling of query_entries_for, no
  top-level fallback) + populated_top_level_blocks for the coherence check.
- characterization tests (single-mode named -> per-graph; named + top-level ->
  bail; multi-mode top-level queries -> bail; CLI positional-URI -> top-level).
- docs: policy.md, server.md, cli-reference.md.

* docs: RFC-002 credentials keyed by server name (keychain/profile/env)

Reworks the RFC's credentials model: secrets are keyed by server name — OS
keychain `omnigraph:<server>` (preferred) -> a `[<server>]` profile in
`~/.omnigraph/credentials` -> `OMNIGRAPH_TOKEN[_<SERVER>]` env (CI), the
AWS/gh/kube model. `servers.<name>` is endpoint-only by default but may carry
an explicit, secret-free `auth: { token: { env|file|command|keychain } }`
source. The shipped `bearer_token_env` + `.env.omni` dotenv remain a legacy
compat path; no `credentials.yaml`.

* docs: RFC-002 — typed graph locator (storage/server/graph_id), not a uri string

Add §1.1: the resolved graph address is a typed GraphLocator
(Embedded{storage} | Remote{server, graph_id}), not a flat uri: String.
Diagnoses the string model's cost in the code today (~16 is_remote_uri forks,
TargetConfig can't express multi-server x multi-graph, the CLI bails on remote,
the ts SDK models baseUrl+graphId separately) and settles the YAML naming so
the key names the locus:

- storage: (embedded) — shipped uri: is a deprecated alias
- server: + graph_id: (remote) — graph_id defaults to the entry key
- storage xor server, reject both/neither (no silent ambiguity)

Kills the graphs:/graph: collision and the uri:-might-be-a-server ambiguity.
Updates the §1/§8 examples and the entry-shape notes to the new naming.

* Test: queries list must reject an unknown --target

queries list opens no graph URI, so unknown-graph validation does not ride
along on resolve_target_uri the way it does for every other command. The new
test reproduces the gap: with an unknown --target the command currently exits 0
and prints the (empty) top-level registry instead of erroring like the
URI-resolving commands do. Fails against current code; the fix follows.

* Validate the graph selection in queries list

Graph-existence validation was a side effect of URI resolution: every
URI-resolving command rejects an unknown --target via resolve_target_uri, but
queries list opens no URI, so query_entries_for(Some(unknown)) silently fell
back to the top-level registry and showed the wrong (or empty) catalog.

Make membership a property of the selection: add the fallible
resolve_graph_selection alongside the infallible query_entries_for (a known
name passes through, an unknown name errors with the same message as
resolve_target_uri, None stays anonymous), and validate the selection in
execute_queries_list. query_entries_for is unchanged — server boot's bare-URI
path still needs its None -> top-level arm.

* Surface policy-engine errors from stored-query invoke

The invoke handler mapped every authorize_request failure to 404 ('stored
query not found'), which collapsed the authorization decision (deny -> 403)
together with operational failures (no actor -> 401, Cedar evaluation error ->
500). A real policy-engine 500 was hidden as a missing query.

Separate the two concerns instead of sniffing the masked status. Extract
authorize() returning an Authz { Allowed, Denied(msg) } decision and reserve
Err for operational failures only; authorize_request becomes a thin wrapper
that maps Denied -> 403, so the 16 deny-as-403 callers are unchanged. The
invoke handler now matches the decision directly: a denial stays 404 (deny ==
missing, so the catalog can't be probed without the grant), while a 401/500
propagates with its true status.

500 is now a reachable outcome on POST /queries/{name}; document it in the
endpoint responses and regenerate openapi.json.

* Extract the named-graph/top-level coherence rule into one helper

The rule 'a named graph uses its own graphs.<name> block, so a populated
top-level block is a config error' lived inline in single-mode server boot.
Extract it to OmnigraphConfig::ensure_top_level_blocks_honored so the same
definition can be shared by the CLI selection gate (next commit) and the two
can't drift. Boot calls the helper; the message is reworded context-neutral
(drops 'serving') so it reads correctly from both boot and the CLI.

Behavior-preserving: multi-graph mode keeps its own unconditional check, and
single_mode_named_graph_rejects_top_level_blocks still passes.

* Test: queries validate/list must reject a named graph with a top-level block

Server boot refuses a config where a graph is selected by name yet a top-level
queries:/policy.file block is populated (the block would be silently ignored).
The CLI's queries validate/list resolve the same named selection but skip that
coherence check, so they give a false green / list the per-graph block. The new
test reproduces it: validate prints OK and list succeeds where boot would
refuse. Fails against current code; the fix follows.

* Enforce top-level coherence in the single CLI selection gate

queries validate validated graph membership only as a side effect of URI
resolution and queries list only via resolve_graph_selection's membership
check; neither applied the named-graph/top-level coherence rule server boot
enforces, so both gave a false green on a config boot refuses.

Fold ensure_top_level_blocks_honored into resolve_graph_selection so it is the
single gate that returns only valid + server-coherent selections, and route
resolve_selected_graph (queries validate) through it; queries list already
calls the gate. A named graph with a populated top-level block now errors in
both commands, matching boot. A positional URI stays anonymous (top-level
honored), so queries_validate_positional_uri_ignores_default_graph is
unaffected.

* docs: RFC-003 — MCP server surface for omnigraph-server

Detailed MCP-transport design for the stored-query/MCP work, building on the
shipped #128 registry. Corrects the draft against the branch head: the coarse
invoke_query gate + 404 denial-masking are already wired (server_invoke_query),
so per-query invoke_query scope (PolicyRequest has no query-name dimension yet)
is the real prerequisite; positions the doc as superseding rfc-001's MCP
transport (/mcp/tools+/mcp/invoke) and reconciles the shipped mcp.expose YAML
form and the schema-introspection non-goal; grounds the parity surface in the
actual omnigraph-ts package (13 tools with read/change ids, 2 resources).

* docs(config): clarify graph config boundaries

* fix(config): enforce graph-scoped policies and query validation

* fix(cli): require graph selection for scoped query registries

* fix(server): preserve named graph id in single mode policy

* fix(cli): share graph identity for policy resolution

* test(cli): cover policy tooling server graph selection

* fix(cli): honor server graph for policy tooling

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-06-01 22:50:31 +02:00
Ragnor Comerford
353c0c876a
fix(branch): make branch delete correct under partial failure (#137)
* test(lance): pin force_delete_branch surface guard

Pin the Lance 6.0.1 force_delete_branch behavior the branch-delete
single-authority redesign relies on: plain delete_branch errors on a
missing ref, force_delete_branch removes an existing forked branch, and
the local-store quirk where force_delete on a fully-absent branch still
errors (worked around by the upcoming TableStore::force_delete_branch).

Re-pin the docs/dev/lance.md alignment stanza (9 guards; 4 runtime).

* feat(storage): add force branch-delete to TableStore + CommitGraph

Add TableStore::force_delete_branch and CommitGraph::force_delete_branch
(idempotent: tolerate an already-absent branch via Lance RefNotFound /
NotFound), plus CommitGraph::list_branches for the cleanup reconciler to
diff against the manifest authority. RefConflict (referencing
descendants) is still surfaced. Unused until the branch-delete rewire.

* test(maintenance): red — cleanup reconciles orphaned branch forks

Forge a Lance branch on the Person table that the manifest never
references (a zombie fork from an incomplete prior delete) and assert
cleanup reclaims it while leaving main intact. Fails today: cleanup does
not yet reconcile orphaned forks. Goes green with the next commit.

* fix(maintenance): reconcile orphaned branch forks in cleanup

Add reconcile_orphaned_branches: force_delete_branch every per-table and
commit-graph Lance branch absent from the manifest branch set (the
authority), children-before-parents. Folded into cleanup_all_tables,
runs before version GC. Idempotent and authority-derived; no-ops once
nothing is orphaned, and would harmlessly find nothing if a future Lance
atomic multi-dataset branch op prevented orphans. Adds TableStore::list_branches
and exposes graph_commits_uri(pub crate). Turns the maintenance red test green.

* test(failpoints): red — branch_delete partial failure converges

Add the branch_delete.before_table_cleanup failpoint hook (inert without
the feature) and a regression test: a cleanup-step failure after the
manifest authority flip must leave branch_delete returning Ok, the branch
gone, the orphan stranded, then reclaimed by cleanup, and the name
reusable. Fails today: cleanup_deleted_branch_tables propagates the error
as a hard failure. Goes green with the next commit.

* fix(branch): best-effort fork reclaim after the manifest flip

Make branch_delete treat per-table forks and the commit-graph branch as
derived state reclaimed best-effort with force_delete_branch after the
manifest authority flip. A reclaim failure (transient error, or the
branch_delete.before_table_cleanup failpoint) is logged via tracing::warn
and swallowed: the branch is already gone and the cleanup reconciler
converges the orphan. cleanup_deleted_branch_tables no longer returns an
error or blocks the call. Turns the partial-failure recovery test green.

* test(failpoints): red — recreate over orphaned fork is actionable

After a partial-failure delete leaves a fork orphaned, recreating the
branch name and writing to the previously-forked table before cleanup
runs currently surfaces the opaque ExpectedVersionMismatch ("stale view
... expected manifest table version N"). Assert instead a clear error
pointing the user at cleanup. Goes green with the next commit.

* fix(branch): actionable orphan-collision error in fork_branch_from_state

When a fork's create_branch collides with an existing target ref, reuse
it only if its head matches source_version (a legitimate concurrent
first-write). A version mismatch means a zombie fork from an incomplete
prior delete: return a manifest_conflict pointing the user at
`omnigraph cleanup`, instead of the opaque ExpectedVersionMismatch.
Turns the recreate-over-orphan red test green.

* docs(invariants): single-authority branch-lifecycle + Lance forward-compat

Record branch delete in the Current Truth Matrix: manifest is the single
authority flipped atomically first, per-table forks + commit-graph branch
are derived state reclaimed best-effort with the cleanup reconciler as
backstop, and reusing a name whose reclaim failed surfaces an actionable
error. Note the reconciler is authority-derived and degrades to a no-op
under a future Lance atomic multi-dataset branch op, the same shape as
invariant 7.

* test(failpoints): red — cleanup isolates a single-table failure

Add the cleanup.table_gc failpoint hook (inert without the feature) and
an error: Option<String> field on TableCleanupStats (mechanical, always
None for now). Regression test: a one-shot version-GC failure for one
table must not abort the whole cleanup — assert cleanup still succeeds,
surfaces the failure per-table in stats, and the independent reconcile
pass still reclaimed an orphan. Fails today: the version-GC collect
aborts on the first table error. Goes green with the next commit.

* fix(maintenance): fault-isolate cleanup per table

Make the cleanup sweep do as much as it can and converge on re-run
instead of aborting wholesale on one table's transient error
(invariant 13). The version-GC loop now records a per-table failure on
its stats row (error: Some) and logs it rather than collecting into a
Result that aborts; reconcile_orphaned_branches isolates per-table and
commit-graph failures into BranchReconcileStats.failures. The CLI reports
any failed tables and tells the user to rerun cleanup. Addresses the
Devin review finding. Turns the single-table-failure test green.

* test(failpoints): red — branch_create heals commit-graph zombie + is atomic

Add the branch_delete.before_commit_graph_reclaim failpoint hook and two
regression tests: (a) recreating a name whose delete left a commit-graph
zombie must succeed (today it dies on Lance's internal Clone error), and
(b) branch_create must roll back the manifest branch when the derived
commit-graph branch fails (today it leaves the manifest branch created
while returning Err). Both fail now; green with the next commit. The
existing branch_create_failpoint_triggers test still passes.

* fix(branch): make branch_create atomic + heal commit-graph zombie

branch_create now flips the manifest authority first, then creates the
derived commit-graph branch in create_commit_graph_branch, force-dropping
any orphaned commit-graph ref left by an incomplete prior delete (the
manifest branch is fresh, so a same-named commit-graph branch is provably
a zombie). If commit-graph creation fails, the manifest branch is rolled
back so the name never half-exists. Addresses the Codex review finding.
Turns the two branch_create red tests green; existing tests unaffected.

* test(failpoints): red — fork collision misclassifies live concurrent fork

Add the fork.before_classify failpoint hook and a concurrency test: when
a concurrent first-write legitimately wins the fork race, the loser must
get a retryable refresh-and-retry, not the misleading run-cleanup orphan
error. Today the version-comparison misclassifies the live fork as an
orphan (the Cursor finding). Goes green with the next commit.

* fix(branch): manifest-arbitrated fork-collision classification

Classify a fork collision by the manifest authority instead of comparing
Lance branch versions. Before forking, open_owned_dataset_for_branch_write
re-reads the live manifest: if the table is already forked on the active
branch, a concurrent first-write won and the loser gets a retryable
refresh-and-retry (not a misleading orphan error). fork_branch_from_state
no longer guesses from versions — a create collision past that check is
an orphan, so it returns the actionable cleanup error. Addresses the
Cursor finding; turns the live-concurrent-fork test green, zombie path
unchanged.

* test(failpoints): close branch-lifecycle test gaps

Three coverage additions for the branch-delete work (behavior already
correct; these lock it in and catch regressions):

- cleanup_isolates_reconcile_failure: inject a force-delete failure into
  the reconcile loop (new cleanup.reconcile_fork hook) and assert the
  sweep continues + converges on re-run. Directly covers the reconcile
  loop the Devin finding was about (previously only version-GC was).
- cleanup_reclaims_orphaned_commit_graph_branch: forge a commit-graph
  orphan via the delete reclaim failpoint and assert cleanup's
  reconcile_commit_graph_orphans drops it (previously untested).
- fork_collision_with_live_concurrent_fork_is_retryable: replace the
  fixed 300ms sleep with a deterministic readiness signal (cfg_callback +
  compare_exchange atomics) so the two-writer ordering can't flake.

Full failpoints suite 31/0.
2026-06-01 13:28:38 +02:00
Ragnor Comerford
2d5c4b1202
docs: rename runs.md/runs.rs → writes and repoint all references (#131)
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The Run state machine was removed in MR-771 (v0.4.0); `docs/dev/runs.md`
and `crates/omnigraph/tests/runs.rs` have since documented and tested the
direct-publish write path, so the "runs" name was misleading.

- git mv docs/dev/runs.md → docs/dev/writes.md (reframe H1 + intro;
  keep MR-771 history note)
- git mv crates/omnigraph/tests/runs.rs → tests/writes.rs (reframe header)
- repoint every runs.md / runs.rs reference across docs, AGENTS.md, and
  source comments
- fix four pre-existing broken `docs/runs.md` links (the file never lived
  at that path) to `docs/dev/writes.md`
- fix the stale v0.4.0 anchor to the live section

No behavior change: every source edit is a comment. Engine builds and the
renamed test passes 25/25; scripts/check-agents-md.sh passes.

The run-removal cleanup itself (run_registry.rs guard, __run__ prefix) is
deferred to MR-770.
2026-05-30 23:20:56 +02:00
Andrew Altshuler
854ad0afcb
feat(server): compose OMNIGRAPH_TARGET_URI with OMNIGRAPH_CONFIG in entrypoint (#129)
The container entrypoint's URI and config branches were mutually
exclusive, so a deployment driven by OMNIGRAPH_TARGET_URI could never
load a policy file. Forward --config alongside the positional URI when
OMNIGRAPH_CONFIG is also set (the URI still wins via resolve_target_uri),
enabling Cedar policy without changing how the URI is provided.

Add docker/entrypoint_test.sh (arg-composition cases) + a CI job, and
document the env-var contract in docs/user/deployment.md.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
2026-05-30 20:17:55 +01:00
Ragnor Comerford
24413844ae
Add Windows release binaries (#127)
* Add Windows release binaries

* Fix Windows installer downloads
2026-05-30 14:23:40 +02:00
Ragnor Comerford
50910b3753
docs: align release artifact docs 2026-05-29 14:04:16 +02:00
devin-ai-integration[bot]
1a4d2cee97
feat: inline query strings in CLI and HTTP server (#110)
* feat(MR-656): inline query strings in CLI and HTTP server

CLI:
- Add -e / --query-string <STRING> to omnigraph read and omnigraph change
- Exactly one of --query, --query-string, --alias is required (3-way XOR)
- Empty --query-string is rejected with a clear error

HTTP:
- New POST /query (read-only, clean field names: query/name/params/branch/snapshot)
- Mutations on /query are rejected with 400 -- use POST /change instead
- ChangeRequest fields polished: query (alias query_source), name (alias query_name)
- POST /read and POST /change remain byte-compatible for existing clients

Tests:
- cli.rs: -e happy-path on read/change, mutex error vs --query, empty -e rejected
- system_local.rs: inline -e read and -e change exercise the local flow
- system_remote.rs: inline -e read/change over HTTP plus direct /query 200/400
- server.rs: /query 200, /query 400 on mutation, /change legacy field alias
- openapi.rs: new /query path, QueryRequest schema, ChangeRequest field-name polish

Docs: cli.md (-e examples), cli-reference.md (read/change rows), server.md (/query)
Co-Authored-By: Ragnor Comerford <ragnor.comerford@gmail.com>

* feat(MR-656): rename read/change to query/mutate with deprecation signals

HTTP server:
- Add POST /mutate as canonical write endpoint (pairs with POST /query).
- Mark POST /read and POST /change as deprecated. Three-channel signal:
  * OpenAPI: `deprecated: true` on the operation (every codegen flags
    the generated SDK method).
  * RFC 9745: response `Deprecation: true` header on every response.
  * RFC 8288: response `Link: </successor>; rel="successor-version"`
    pointing at /query and /mutate respectively.
- Share business logic across /mutate and /change via run_mutate(); the
  /change wrapper is the only place that adds the deprecation headers.
- ChangeRequest field aliases (query_source/query_name) preserved.
- AliasCommand serde now accepts `query`/`mutate` alongside `read`/`change`.

CLI:
- Promote `omnigraph query` / `omnigraph mutate` to top-level canonical
  subcommands (clap visible_alias keeps `omnigraph read` / `omnigraph
  change` working forever).
- Promote `omnigraph lint` / `omnigraph check` to top-level (was nested
  under `omnigraph query lint`, which is now a deprecated argv shim that
  rewrites to the canonical form).
- Argv-level preprocessing prints a one-line deprecation warning to
  stderr when any legacy spelling is used. Canonical names are silent.

Tests:
- Server: /mutate works, /change emits Deprecation+Link headers, /read
  emits Deprecation+Link headers, /query carries no deprecation signal.
- OpenAPI: /read and /change flagged deprecated; /query and /mutate not.
- CLI: canonical `lint` matches deprecated `query lint` / `query check`
  output; `read` / `change` print deprecation warnings.

Docs:
- cli.md: new canonical examples; "Deprecated names" migration table.
- cli-reference.md: top-level table updated; aliases.<name>.command
  accepts both legacy and canonical spellings.
- server.md: endpoint inventory shows /query and /mutate as canonical
  and /read and /change as deprecated; dedicated section explains the
  three-channel deprecation signal.
- og-cheet-sheet.md: use new `omnigraph lint` / `omnigraph check`.
- openapi.json regenerated.

Migration is purely cosmetic — every deprecated form continues to work
indefinitely; only the spelling changes.

Co-Authored-By: Ragnor Comerford <ragnor.comerford@gmail.com>

* fix(MR-656): address Devin Review findings on /query and /change

Two issues raised by Devin Review on PR #110:

1. `POST /query` mutation-rejection error pointed at the deprecated
   `/change` endpoint instead of the canonical `/mutate`. Fixed in
   three places: the runtime error message in `server_query`, the
   utoipa 400-response description, and the handler doc comment. The
   `QueryRequest` schema docstrings in `api.rs` got the same update so
   the openapi.json bodies match. Server and openapi tests updated.

2. `execute_change_remote` serialized `ChangeRequest` directly, which
   emits the new canonical field names `query` / `name` on the wire.
   `#[serde(alias = "query_source")]` only affects deserialization, so
   a newer CLI talking to an older server would have its `/change`
   POST body fail with "missing field: query_source". Fixed by
   extracting a `legacy_change_request_body` helper that hand-rolls
   the JSON with the legacy keys (`query_source` / `query_name`), the
   same byte-stable contract `execute_read_remote` already uses
   against `/read`. Added two unit tests on the helper to lock the
   wire shape in.

Co-Authored-By: Ragnor Comerford <ragnor.comerford@gmail.com>

* docs(dev): RFC 001 — inline + stored queries, envelope, MCP

Tracked artifact consolidating the design across MR-656 (this branch),
MR-976 (Phase 1 envelope hardening parent, with MR-977/978/979/980
sub-issues), and MR-969 (stored queries + MCP).

Sections:

* Two paths, one engine — inline `/query` + `/mutate` (this PR) coexist
  with stored `/queries/{name}` (MR-969). Same `run_query` / `run_mutate`
  backend (the fold-in landed in the previous commit).
* Request envelope ("before") — Idempotency-Key, If-Match, X-Deadline,
  X-Trace-Id, expect, dry_run, fields. Phase 1 ships the load-bearing
  subset on `/mutate`.
* Response envelope ("after") — audit_id, snapshot_id, commit_id, stats,
  warnings. Closes the provenance loop today's `ChangeOutput` leaves
  open.
* `.gq` pragmas — `@description`, `@returns`, `@mcp`. Source-of-truth
  for the stored-query agent contract; no separate YAML registry.
* Multi-graph MCP — per-graph `/graphs/{id}/mcp/tools` + `/mcp/invoke`.
  Token binds to one graph by default; cross-graph agents loop.
* Cedar split — `read`/`change` for inline, `invoke_query` for stored.
  Operators deny ad-hoc for agent groups while keeping curated tool
  list open.
* Rejected alternatives — per-env override files, compiled bundles,
  tool-name prefixing across graphs, body-field graph dispatch.

Index entry added under "Active Implementation Plans" so future agents
land on the RFC before touching queries / mutations / envelope code.
`scripts/check-agents-md.sh` clean (35 links, 34 docs).

* docs(server): clarify why run_query lacks AppState parameter

run_mutate takes state for workload admission; run_query doesn't because
reads aren't admission-gated today. Mark the asymmetry as intentional and
flag the two future events that would grow the signature: Phase 1's
`expect: { max_rows_scanned: N }` budget (MR-976) or per-actor admission
extending to stored-read invocations (MR-969). Prevents the natural
"make these symmetrical" follow-up.

* refactor(server): run_query / run_mutate take &ResolvedActor

Replace `Option<Extension<ResolvedActor>>` in the helpers with
`Option<&ResolvedActor>`. Saves MR-969's stored-query handler from
wrapping a bare actor in axum's `Extension(...)` before calling.
Handler signatures (`server_query`, `server_read`, `server_mutate`,
`server_change`) keep `Option<Extension<ResolvedActor>>` because that
is what axum injects, and unwrap at the call site with
`actor.as_ref().map(|Extension(actor)| actor)`.

Net: -13/+10 LOC, 89/0 server tests pass.

* docs(releases): v0.6.0 — describe inline + canonical-named queries (MR-656)

Extend the v0.6.0 release notes to cover the third piece of work landing
alongside the graph terminology rename and multi-graph server mode:
canonical-named `POST /query` and `POST /mutate` endpoints, the CLI's
new `-e/--query-string` flag, the top-level promotion of `lint` /
`check`, and the three-channel deprecation signal on `/read` and
`/change` (OpenAPI `deprecated: true` + RFC 9745 + RFC 8288).

Additions:

* Top blurb: "Two pieces" -> "Three pieces" with a bullet describing
  the rename + inline flow.
* Breaking Changes: new "Query / mutation rename" subsection covering
  the `ChangeRequest` field rename (with the back-compat serde aliases
  and the CLI's `legacy_change_request_body` byte-stable wire helper)
  and the `omnigraph query lint` -> `omnigraph lint` move.
* New: 5 bullets — the two endpoints, the CLI subcommands, the `-e`
  flag, the deprecation signal channels, the widened `aliases.<name>.command`
  vocabulary.
* User Impact: one bullet making explicit that the rename is cosmetic
  on the client side and migration is voluntary.
* Documentation: pointers to the updated `server.md` / `cli.md` /
  `cli-reference.md` and the new `docs/dev/rfc-001-queries-envelope-mcp.md`.

+15/-1 lines. `./scripts/check-agents-md.sh` clean.

* refactor(cli): demote `check` from visible_alias to deprecation shim

`omnigraph check` was a clap `visible_alias` on `lint`, advertised in
`--help` as an equivalent canonical name. Per MR-981 §6 (long-form
flags as canonical, short forms as visible aliases), visible aliases
on subcommand names hurt agent CX: agents emit either spelling
depending on training-data drift, and there's no length signal
pointing at the canonical name.

Changes:

* Remove `#[command(visible_alias = "check")]` from the `Lint` variant.
  `omnigraph --help` now shows only `lint`.
* Add bare `check` to `rewrite_deprecated_argv` so `omnigraph check
  <args>` still works — it rewrites to `omnigraph lint <args>` and
  emits a one-line stderr deprecation warning, matching the existing
  pattern for `read` / `change` / `query lint` / `query check`.
* Fix the nested `query check` shim to substitute `check` -> `lint` in
  the rewritten argv (previously it relied on `check` being a
  visible_alias to reach the `Lint` variant).
* New test `deprecated_check_top_level_rewrites_to_lint` covers: bare
  `check` produces identical stdout to `lint`, emits the deprecation
  warning, and `check` does NOT appear as an alias in `omnigraph
  --help`.
* Release notes updated to reflect the deprecation-shim treatment and
  cross-reference MR-981 §6 reasoning.

Cargo / Go users typing `check` still work indefinitely; one stderr
nudge per invocation teaches the canonical name. Agents see only
`lint` in `--help --json` so they emit one canonical form.

67/0 omnigraph-cli tests pass; 39 workspace test suites green.

---------

Co-authored-by: Devin AI <158243242+devin-ai-integration[bot]@users.noreply.github.com>
Co-authored-by: Ragnor Comerford <ragnor.comerford@gmail.com>
Co-authored-by: Ragnor Comerford <hello@ragnor.co>
2026-05-29 13:41:54 +02:00
Ragnor Comerford
e0f13b32c5
(feat): multi-graph server mode (#119)
* mr-668: add GraphId newtype + Cloud-mode forward identity stubs (PR 1/10)

PR 1 of the MR-668 multi-graph server work. Pure types, no runtime
behavior changes yet.

Ships the validated identity vocabulary that the rest of the implementation
will consume:

- `GraphId(String)` — `^[a-zA-Z0-9-]{1,64}$`, leading underscore rejected
  (engine reserves every `_*` filename), reserved route names rejected
  (`policies`, `healthz`, `openapi`, `openapi.json`, `graphs`). Validation
  lives in `try_from` only; serde `Deserialize` re-runs it so JSON payloads
  cannot bypass.
- `TenantId(String)` — same regex shape as GraphId. `None` in Cluster
  mode; reserved for Cloud mode (RFC 0003) where it carries the OAuth
  `org_id` claim.
- `GraphKey { tenant_id: Option<TenantId>, graph_id }` — the registry
  HashMap key. `cluster()` constructor for the Cluster-mode default.
- `Scope` enum with `Full` variant — Cluster mode default; RFC 0004 will
  extend with OAuth scopes (`graph:read`/`write`/`admin`/`*`).
- `AuthSource` enum with `Static` variant — Cluster mode default; RFC
  0001 step 1 will add `Oidc`.
- `ResolvedActor { actor_id, tenant_id, scopes, source }` — replaces the
  upcoming refactor of `AuthenticatedActor(Arc<str>)` in PR 4a.

Per MR-668 design decision 13: ship the Cloud-mode forward type shapes
now (no `TokenVerifier` trait yet — that's RFC 0001 step 1) so handler
signatures stay stable across the Cluster → Cloud trajectory. `Scope`
and `AuthSource` use `#[non_exhaustive]` so future variants don't break
caller matches.

Tests: 26 new (15 graph_id + 11 identity), all passing. No regression
in the existing 36 server library tests.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: Omnigraph::init error-path cleanup + three failpoints (PR 2a/10)

PR 2a of the MR-668 multi-graph server work. Bug fix: a partially-failed
`Omnigraph::init` previously left orphan schema files at the graph URI,
making the URI unusable for a retry (the next `init` would refuse because
`_schema.pg` already exists).

Changes:

1. `init_with_storage` now wraps the I/O phase. On any error from
   `init_storage_phase`, calls `best_effort_cleanup_init_artifacts` to
   remove the three schema files before returning the original error:
   - `_schema.pg`
   - `_schema.ir.json`
   - `__schema_state.json`
   Cleanup is best-effort: a failure to delete is logged via
   `tracing::warn` but does NOT mask the init error.

2. Three failpoints added at the init phase boundaries:
   - `init.after_schema_pg_written`
   - `init.after_schema_contract_written`
   - `init.after_coordinator_init`

3. Four new failpoint tests in `tests/failpoints.rs` pin the cleanup
   behavior at each boundary plus the "original error wins over cleanup
   error" contract. All 23 failpoint tests pass.

Coverage gap (documented in code comments):
Lance per-type datasets and `__manifest/` directory created by
`GraphCoordinator::init` are NOT cleaned up after a coordinator-init-phase
failure. Recursive directory deletion requires `StorageAdapter::delete_prefix`,
which was deferred along with `DELETE /graphs/{id}` (originally PR 2b). When
that primitive lands, the third failpoint test can be tightened to assert
the graph root is fully empty.

Tests: 4 new (init_failpoint_*), all 23 failpoint tests green. No
regression in the 105 engine library tests or 64 end_to_end tests.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: add GraphHandle + GraphRegistry data structure (PR 3/10)

PR 3 of the MR-668 multi-graph server work. Pure data structure — no
routing changes yet (that's PR 4a).

New file: `crates/omnigraph-server/src/registry.rs`

- `GraphHandle { key: GraphKey, uri: String, engine: Arc<Omnigraph>,
  policy: Option<Arc<PolicyEngine>> }` — the per-graph state that the
  routing middleware (PR 4a) will inject as a request extension.
- `RegistrySnapshot { graphs: HashMap<GraphKey, Arc<GraphHandle>> }` —
  immutable snapshot; replaced atomically via `ArcSwap`.
- `GraphRegistry { snapshot: ArcSwap<_>, mutate: Mutex<()> }` — lock-free
  reads, mutex-serialized mutations.
- `RegistryLookup { Ready(Arc<GraphHandle>) | Gone }` — two-valued, no
  `Tombstoned` variant since DELETE is deferred in v0.7.0 scope.
- `InsertError { DuplicateKey | DuplicateUri }` — both rejection cases
  for create-graph (maps to HTTP 409 in PR 7).
- Methods: `new`, `from_handles` (bulk startup-time init), `get`, `list`,
  `len`, `insert`.

Race semantics pinned by three multi-thread tests:
- `concurrent_insert_same_key_exactly_one_succeeds` — N=8 spawned
  inserts with the same key; exactly 1 returns Ok, 7 return DuplicateKey.
- `concurrent_insert_distinct_keys_all_succeed` — N=8 spawned inserts
  with distinct keys; all succeed.
- `concurrent_reads_during_inserts_see_consistent_snapshots` — reader
  loop concurrent with sequential writes; every listed handle's key
  resolves via `get()` (no torn state).

Why no tombstones field: `DELETE /graphs/{id}` is deferred to bound
the scope of v0.7.0. Without a delete endpoint, there's no use for
tombstones — every key in the registry is `Ready`, and every key
not in the registry is `Gone`. When DELETE lands later, the
`Tombstoned` variant + `tombstones: HashSet<GraphKey>` slot in
additively without breaking caller signatures (the `Gone` variant
remains the "not currently active" case).

Why `tokio::sync::Mutex`: insert is async because PR 7's flow holds
this mutex across the atomic YAML rewrite step (file I/O). std::Mutex
would footgun across .await.

Dependency additions: `arc-swap = { workspace = true }`,
`thiserror = { workspace = true }` (used by InsertError).

Tests: 12 new (12 passing). 74 server lib tests total green
(62 from PR 1 + 12 new). Clippy clean on server crate.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: router restructure + handler refactor for multi-graph (PR 4a/10)

PR 4a of the MR-668 multi-graph server work. The heaviest single PR —
rewires every handler to extract `Arc<GraphHandle>` from a routing
middleware, replaces `AuthenticatedActor(Arc<str>)` with `ResolvedActor`
everywhere, and adds the `ServerMode` discriminator.

Behavior changes:
- **Single mode** (legacy `omnigraph-server <URI>`): flat routes
  (`/snapshot`, `/read`, `/branches`, …) continue to work exactly as
  v0.6.0. Internally, the registry holds a single handle keyed by the
  sentinel `SINGLE_GRAPH_KEY_ID = "default"`; routing middleware injects
  that handle on every request. No HTTP-visible change.
- **Multi mode** (new): routes nest under `/graphs/{graph_id}/...`.
  Routing middleware extracts the graph id from the path, looks it up
  in the registry, and injects the handle. 404 if not found.
  (Multi-mode startup itself lands in PR 5; this PR provides the
  router-side wiring.)

AppState refactor:
- `engine: Arc<Omnigraph>` and `policy_engine: Option<Arc<PolicyEngine>>`
  fields removed — both now live inside `GraphHandle` in the registry.
- `mode: ServerMode { Single { uri } | Multi { config_path } }` added.
- `registry: Arc<GraphRegistry>` added.
- `server_policy: Option<Arc<PolicyEngine>>` added (placeholder for
  management endpoints in PR 6b; unused today).
- Existing constructors (`new`, `new_with_bearer_token{s,_and_policy}`,
  `new_with_workload`, `open*`) build a single-mode AppState
  internally and remain source-compatible. Tests that constructed
  AppState via these constructors continue to work.
- `with_policy_engine` post-construction setter — rebuilds the
  single-mode handle with the policy attached. Engine-layer
  enforcement is NOT reinstalled (matches the old single-field
  semantics; `open_with_bearer_tokens_and_policy` is the path that
  installs both layers).
- `new_multi` constructor added for PR 5's startup loop.
- `uri()` now returns `Option<&str>` (Some in single, None in multi).

Routing middleware:
- `resolve_graph_handle` injects `Arc<GraphHandle>` as a request
  extension. Mode-aware: single returns the only handle; multi parses
  `/graphs/{graph_id}/...` from the URI. Returns 404 in multi mode
  when the graph id is unregistered. Records `graph_id` on the
  current tracing span.
- `require_bearer_auth` updated to insert `ResolvedActor` (was
  `AuthenticatedActor`).

Handler refactor — every protected handler:
- Gains `Extension(handle): Extension<Arc<GraphHandle>>` param.
- Replaces `state.engine` → `handle.engine`.
- Replaces `state.policy_engine()` → `handle.policy.as_deref()`.
- Replaces `state.uri()` → `handle.uri.as_str()` (or `.clone()`
  where String is needed).
- Replaces `Arc::clone(&state.engine)` → `Arc::clone(&handle.engine)`
  (the spawn-and-clone pattern in `server_export` — proof that a
  long-running export survives the registry being mutated later).

authorize_request signature:
- Was: `(state: &AppState, actor: Option<&AuthenticatedActor>, request: PolicyRequest)`.
- Now: `(actor: Option<&ResolvedActor>, policy: Option<&PolicyEngine>, request: PolicyRequest)`.
- Per-graph callers pass `handle.policy.as_deref()`. The (future PR 6b)
  management endpoints will pass `state.server_policy.as_deref()`.

MR-731 invariant preserved:
- The single chokepoint `request.actor_id = actor.actor_id.as_ref().to_string()`
  inside `authorize_request` still overwrites any client-supplied
  actor identity. Regression test
  `actor_id_resolves_from_bearer_token_ignoring_client_supplied_headers`
  at `tests/server.rs:1114-1216` passes unchanged.

Tests: 0 new (the registry race tests in PR 3 already cover the
data structure; this PR exercises them indirectly via the existing
test suite). 74 lib + 57 server integration + 60 openapi = 191 tests
green. Clippy clean.

LOC: +397 insertions, -153 deletions in `crates/omnigraph-server/src/lib.rs`.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: OpenAPI multi-mode cluster filter (PR 4b/10)

PR 4b of the MR-668 multi-graph server work. In multi mode, the served
`/openapi.json` reports cluster routes (`/graphs/{graph_id}/...`) instead
of the legacy flat protected paths — matching what `build_app` actually
mounts (PR 4a's `Router::nest`). Single mode is unchanged.

Implementation:
- New `server_openapi` branch: when `state.mode()` is `Multi`, call
  `nest_paths_under_cluster_prefix(&mut doc)` after `ApiDoc::openapi()`.
- The rewrite consumes `doc.paths.paths`, then for every path-item:
  - If the path is in `ALWAYS_FLAT_PATHS` (`/healthz` for now), keep
    it flat.
  - Otherwise, prefix every operation_id with `cluster_` and reinsert
    the item at `/graphs/{graph_id}<original_path>`.
- Single mode hits no extra work — the path map is untouched.
- The static `ApiDoc::openapi()` still emits the flat surface, so
  in-process callers (the existing `openapi_json()` helper in tests)
  see the unmodified spec.

Why cluster_ prefix on operation IDs: OpenAPI specs require unique
operation_ids across the document. With both flat (single-mode) and
cluster (multi-mode) surfaces ever co-existing in a generated SDK,
the prefix prevents collision. The current served doc only carries
one surface, so the prefix is forward-compat with potential future
dual-surface generation.

Tests: 6 new in `tests/openapi.rs`, all via the `/openapi.json` route
(not the static `ApiDoc::openapi()` helper):
- `multi_mode_openapi_lists_cluster_paths` — every protected path
  appears as a cluster variant.
- `multi_mode_openapi_drops_flat_protected_paths` — flat protected
  paths are absent.
- `multi_mode_openapi_keeps_healthz_flat` — `/healthz` survives.
- `multi_mode_openapi_prefixes_operation_ids_with_cluster` — every
  cluster operation_id starts with `cluster_`.
- `multi_mode_operation_ids_are_unique` — no operation_id collisions.
- `single_mode_openapi_unchanged_by_cluster_filter` — single mode
  still emits the legacy flat surface (regression).

New test helper `app_for_multi_mode(graph_ids)` exercises the new
`AppState::new_multi` constructor from PR 4a — first user of multi-mode
construction outside of unit tests.

Result: 66 openapi tests + 57 server integration tests + 74 lib tests
= 197 green. No regression in the existing OpenAPI drift check
(`openapi_spec_is_up_to_date` still validates the static flat surface
matches the committed openapi.json).

LOC: +67 in lib.rs (rewrite logic), +219 in tests/openapi.rs (test
suite + helper).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: multi-graph startup + mode inference (PR 5/10)

PR 5 of the MR-668 multi-graph server work. This is the first PR that
makes multi mode actually usable end-to-end: operators invoking
`omnigraph-server --config omnigraph.yaml` with a non-empty `graphs:`
map and no single-mode selector now get a running multi-graph server.

Mode inference (MR-668 decision 2, four-rule matrix in
`load_server_settings`):
  1. CLI `<URI>` positional        → Single
  2. CLI `--target <name>`         → Single (URI from graphs.<name>)
  3. `server.graph` in config      → Single (URI from graphs.<name>)
  4. `--config` + non-empty `graphs:` + no single-mode selector
                                   → Multi (all entries in `graphs:`)
  5. otherwise                     → error with migration hint

Rule 5's error message names every escape hatch so operators can fix
their invocation without grepping docs.

Config schema extensions:
  - `TargetConfig.policy: PolicySettings` (per-graph Cedar policy file).
    `#[serde(default)]` so existing single-graph YAMLs keep parsing.
  - `ServerDefaults.policy: PolicySettings` (server-level Cedar policy
    for management endpoints — loaded in PR 5, wired into `GET /graphs`
    in PR 6b).
  - `OmnigraphConfig::resolve_target_policy_file(name)` and
    `resolve_server_policy_file()` helpers — both resolve relative to
    the config file's `base_dir`.

Public types added to `omnigraph-server`:
  - `ServerConfigMode { Single { uri, policy_file } | Multi { graphs,
    config_path, server_policy_file } }`.
  - `GraphStartupConfig { graph_id, uri, policy_file }` — one entry
    per graph in multi mode.

`ServerConfig` shape change:
  - WAS: `{ uri: String, bind, policy_file, allow_unauthenticated }`.
  - NOW: `{ mode: ServerConfigMode, bind, allow_unauthenticated }`.
  - Breaking for any code that constructs `ServerConfig` directly.
    `main.rs` is unaffected (uses `load_server_settings`).

`serve()` now forks on `ServerConfig.mode`:
  - Single: existing flow via `AppState::open_with_bearer_tokens_and_policy`.
  - Multi: parallel open via `futures::stream::iter(graphs)
    .map(open_single_graph).buffer_unordered(4).collect()`. Bound 4 is
    a rule-of-thumb for I/O-bound work — at N≤10 this trades startup
    latency for a small amount of concurrent S3/Lance open pressure.
    Fail-fast: first open error aborts startup; in-flight opens drop
    their engine via Arc (Lance datasets close cleanly).

New helper `open_single_graph(GraphStartupConfig)`:
  - Validates `GraphId` per the regex in PR 1.
  - `Omnigraph::open(uri).await` with descriptive error context.
  - Loads per-graph policy file and re-applies it via
    `Omnigraph::with_policy` (engine-layer enforcement, MR-722).
  - Returns `Arc<GraphHandle>` ready for the registry.

Routing middleware bug fix:
  - `Router::nest("/graphs/{graph_id}", inner)` rewrites
    `request.uri().path()` to the inner suffix (e.g. `/snapshot`).
    The previous middleware tried to parse `{graph_id}` from
    `request.uri().path()` and got 400 instead of 200. Fixed by reading
    from `axum::extract::OriginalUri` request extension, which preserves
    the pre-rewrite URI.
  - Caught by the two new tests
    `cluster_routes_dispatch_per_graph_handle` and
    `cluster_route_for_unknown_graph_returns_404`.

Tests (14 new, all passing):
  - Four-rule matrix: one test per branch + the joint case
    `mode_inference_cli_uri_overrides_graphs_map` + the empty-graphs-map
    error case.
  - Per-graph + server-level policy file path resolution.
  - Reserved `GraphId` rejection at startup.
  - End-to-end multi-graph routing: two graphs side by side, each
    cluster route hits the right engine.
  - Unknown graph id under cluster prefix → 404.
  - Flat routes 404 in multi mode.

Inline `ServerConfig` test (`serve_refuses_to_start_in_state_1_without_unauthenticated`)
and three `server_settings_*` tests updated to the new `mode` shape.

Result: 211 server tests green (74 lib + 71 integration + 66 openapi),
MR-731 regression test still pinned and passing.

LOC: +45 config.rs, +281 lib.rs (net), +395 tests/server.rs.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: Cedar resource-model refactor (PR 6a/10)

PR 6a of the MR-668 multi-graph server work. Policy-crate-only refactor —
no HTTP handler changes, no operator-supplied policy.yaml changes. Sets
up the chassis that PR 6b's `GET /graphs` consumes.

Two new `PolicyAction` variants:
  - `GraphCreate` — gates `POST /graphs` (deferred behavioral PR).
  - `GraphList`   — gates `GET /graphs` (lands in PR 6b).

Note: `GraphDelete` is intentionally NOT added in this PR. `DELETE
/graphs/{id}` is deferred from MR-668's v0.7.0 scope to bound complexity
(no `delete_prefix`, no tombstone, no `RegistryLookup::Tombstoned`).
Adding the Cedar action without a consumer would be the same kind of
"dead vocabulary" trap the `Admin` variant already documents.

New `PolicyResourceKind { Graph, Server }` enum, plus a
`PolicyAction::resource_kind()` method that classifies every action.
Per-graph actions (Read, Change, BranchCreate, …) bind to
`Omnigraph::Graph::"<graph_label>"`; server-scoped actions
(GraphCreate, GraphList) bind to the singleton
`Omnigraph::Server::"root"`. `Admin` stays classified as per-graph for
now — MR-724 will pick the final shape when the first consumer surface
ships.

Cedar schema string additions:
  - `entity Server;`
  - `action "graph_create" appliesTo { principal: Actor, resource: Server, ... }`
  - `action "graph_list"   appliesTo { principal: Actor, resource: Server, ... }`

Compiler updates:
  - `compile_policy_source` picks the resource literal based on the
    action's `resource_kind`. Existing graph-only policies generate
    the same Cedar source as before — pinned by
    `per_graph_rules_continue_to_work_alongside_server_rules`.
  - `compile_entities` includes the `Server::"root"` entity only when
    a rule references a server-scoped action. Keeps test assertions
    for graph-only policies tight.
  - `PolicyEngine::authorize` builds the right resource UID at
    request time based on `request.action.resource_kind()`.

Validation rules added to `PolicyConfig::validate`:
  - A rule may not mix server-scoped and per-graph actions (different
    resource kinds need different `permit` clauses).
  - Server-scoped actions cannot have `branch_scope` or
    `target_branch_scope` — there's no branch context at the server
    level.

Operator impact: zero. The Cedar schema `Omnigraph::Server` entity is
internally referenced by `compile_policy_source`; operator policy.yaml
files only declare actions in `rules[].allow.actions` and never
reference the resource entity directly. Decision 6's "internal rename
only; operator policies unaffected" contract is preserved and pinned
by `per_graph_rules_continue_to_work_alongside_server_rules`.

Tests: 5 new (11 policy tests total, up from 6):
  - `graph_list_action_authorizes_against_server_resource`
  - `graph_create_action_authorizes_against_server_resource`
  - `server_scoped_rule_cannot_use_branch_scope`
  - `rule_mixing_server_and_per_graph_actions_is_rejected`
  - `per_graph_rules_continue_to_work_alongside_server_rules`

No regression: 145 server tests (74 lib + 71 integration) still green.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: GET /graphs endpoint + per-graph policy wire-up (PR 6b/10)

PR 6b of the MR-668 multi-graph server work. First management endpoint —
`GET /graphs` lists every graph registered with the server, gated by the
server-level Cedar policy from PR 6a.

New API shapes (in `omnigraph-server::api`):
  - `GraphInfo { graph_id, uri }` — one entry per registered graph.
  - `GraphListResponse { graphs: Vec<GraphInfo> }` — sorted alphabetically
    by `graph_id` for deterministic output.

Handler `server_graphs_list`:
  - Mounted at `GET /graphs` in both modes.
  - Single mode: returns 405 (resource exists in the API surface, just
    not operational without a `graphs:` map). 405 chosen over 404 so
    clients see "resource exists, wrong context" rather than "no such
    resource".
  - Multi mode: requires bearer auth (when configured); Cedar-gated by
    `PolicyAction::GraphList` against `Omnigraph::Server::"root"`
    (PR 6a's chassis). Returns the sorted registry list.

Cedar gate composition:
  - When no `server.policy.file` is configured, the MR-723 default-deny
    falls through: `GraphList` is not `Read`, so an authenticated actor
    without a server policy gets 403. This is the right default — don't
    expose the registry until the operator explicitly authorizes it.
  - When a server policy is configured, Cedar evaluates the rule. The
    test `get_graphs_with_server_policy_authorizes_per_cedar` pins the
    admin-allow / viewer-deny split.

Routing:
  - New `management` sub-router holding `/graphs` (auth-required, no
    `resolve_graph_handle` middleware — operates on the registry, not
    a single graph).
  - Single mode merges flat protected routes + management.
  - Multi mode merges nested `/graphs/{graph_id}/...` + management.

OpenAPI:
  - `server_graphs_list` registered in `ApiDoc::paths(...)`.
  - `EXPECTED_PATHS` in `tests/openapi.rs` gains `/graphs`.
  - `openapi.json` regenerated (auto-tracked by
    `openapi_spec_is_up_to_date` in CI).

Tests: 4 new in `tests/server.rs::multi_graph_startup`:
  - `get_graphs_lists_registered_graphs_in_multi_mode`
  - `get_graphs_returns_405_in_single_mode`
  - `get_graphs_requires_bearer_auth_when_configured`
  - `get_graphs_with_server_policy_authorizes_per_cedar`

What's NOT in this PR (deferred):
  - Per-graph policy enforcement is wired through `handle.policy`
    (PR 4a already did this); PR 6b doesn't add new per-graph
    behavior beyond making sure the server policy lookup composes
    cleanly alongside it.
  - `POST /graphs` (PR 7) and `DELETE /graphs/{id}` (out of scope
    for v0.7.0).
  - CLI `omnigraph graphs list` (PR 8 will add).

Result: 215 server tests green (74 lib + 66 openapi + 75 integration),
11 policy tests green. MR-731 spoof regression preserved across all
this work.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: POST /graphs runtime create endpoint (PR 7/10)

PR 7 of the MR-668 multi-graph server work. Operators can now add a
graph to a running multi-graph server without restarting:

  curl -X POST http://server/graphs \
    -H "Content-Type: application/json" \
    -d '{
          "graph_id": "beta",
          "uri": "/data/beta.omni",
          "schema": { "source": "node Person { name: String @key }\n" },
          "policy": { "file": "./policies/beta.yaml" }
        }'

DELETE remains deferred (out of v0.7.0 scope per the trimmed plan —
no `delete_prefix`, no tombstones).

Body shape (decision 7):
  - Nested `schema: { source: "..." }` (mirrors the `policy: { file }`
    pattern; leaves room for future fields without breakage).
  - Optional nested `policy: { file: "..." }` for per-graph Cedar.
  - 32 MiB body limit (reuses `INGEST_REQUEST_BODY_LIMIT_BYTES`).
  - Asymmetric with `SchemaApplyRequest` which keeps flat
    `schema_source: String` — documented in api.rs.

Atomic YAML rewrite + drift detection:
  - New `config::rewrite_atomic(path, new_config, expected_hash)`:
    flock → re-read + hash check → serialize → write `.tmp` → fsync
    → rename → fsync parent dir. Returns the new hash for the caller
    to update its in-memory baseline.
  - New `config::hash_config_file(path)` — SHA-256 of the on-disk
    bytes, used at startup and after each rewrite.
  - New `RewriteAtomicError { Drift | Io | Serialize }` enum.
  - `AppState.config_hash: Option<Arc<Mutex<[u8;32]>>>` carries the
    in-memory baseline. Updated after every successful rewrite so
    subsequent POSTs don't false-trigger drift.
  - The mutex is `std::sync::Mutex` (brief critical section, no .await
    inside). The flock itself serializes file access process-wide
    AND across multiple server instances (defense in depth).
  - All sync I/O runs inside `tokio::task::spawn_blocking` — flock
    is sync.

Handler ordering (the load-bearing sequence):
  1. Mode check: 405 in single mode.
  2. Cedar authorize: `GraphCreate` against `Omnigraph::Server::"root"`.
  3. Validate body: `GraphId::try_from` (regex + reserved-name), empty
     schema/uri checks, per-graph policy file parse.
  4. Pre-check registry for duplicate graph_id / duplicate uri (409).
  5. `Omnigraph::init` the new engine.
  6. Atomic YAML rewrite (drift detection inside).
  7. Publish in registry (atomic re-check via `GraphRegistry::insert`).

Failure modes (documented in handler rustdoc):
  - Init fails → orphan storage at `req.uri` (PR 2a cleans up schema
    files; Lance datasets remain orphans until `delete_prefix` lands).
  - YAML rewrite fails (drift, IO) → orphan storage; YAML unchanged.
  - Registry insert fails (race) → YAML has entry but registry doesn't;
    next restart opens it cleanly.

New dependency: `fs2 = "0.4"` (workspace + omnigraph-server). POSIX-only
file locking. Linux/macOS deployment supported; Windows out of scope.

Tests (10 new in `tests/server.rs::multi_graph_startup`):
  - `post_graphs_creates_a_new_graph_end_to_end` — happy path, includes
    YAML inspection to confirm the rewrite landed.
  - `post_graphs_baseline_hash_updates_between_rewrites` — two POSTs in
    a row both succeed (drift baseline updates correctly).
  - `post_graphs_duplicate_graph_id_returns_409`
  - `post_graphs_duplicate_uri_returns_409`
  - `post_graphs_invalid_graph_id_returns_400` (reserved name)
  - `post_graphs_empty_schema_source_returns_400`
  - `post_graphs_returns_405_in_single_mode`
  - `post_graphs_yaml_drift_detection_returns_503` — operator hand-edits
    omnigraph.yaml; server refuses to clobber.
  - `hash_config_file_is_deterministic_and_detects_changes`
  - `rewrite_atomic_refuses_when_hash_drifts`

OpenAPI: `server_graphs_create` registered in `ApiDoc::paths(...)`;
openapi.json regenerated.

Result: 225 server tests green (74 lib + 66 openapi + 85 integration),
all MR-731 regressions still pinned.

LOC: ~580 lib.rs net (handler + helpers), ~120 config.rs (rewrite
machinery), +71 api.rs (request/response shapes), +332 tests/server.rs.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: CLI omnigraph graphs list/create (PR 8/10)

PR 8 of the MR-668 multi-graph server work. CLI parity for the
v0.7.0 management surface: operators can now manage graphs from
the command line against a running multi-graph server.

  omnigraph graphs list --target dev --json
  omnigraph graphs create \
    --target dev \
    --graph-id beta \
    --graph-uri /data/beta.omni \
    --schema schema.pg

DELETE is intentionally absent — server-side DELETE was deferred from
v0.7.0 scope, and shipping a client subcommand for a server endpoint
that doesn't exist would be dead vocabulary. The help output, the
subcommand enum, and the test that pins it (`graphs_subcommand_help_
lists_list_and_create`) all agree.

CLI architecture (modeled on `BranchCommand`):
  - New `Command::Graphs { command: GraphsCommand }` top-level variant.
  - `GraphsCommand { List, Create }` enum.
  - List: GET `<base>/graphs`. Stdout is `<graph_id>\t<uri>` per line,
    or JSON via `--json`.
  - Create: reads `--schema <path>` from local disk, inlines as
    `schema: { source: <file> }` in the POST body (nested per
    MR-668 decision 7). Optional `--policy-file <path>` becomes
    `policy: { file: <path> }`. Returns 201 → "created graph X at Y"
    or JSON via `--json`.
  - Both subcommands reject local URI targets with a clear
    "remote multi-graph server URL" error.

New API type imports in the CLI: `GraphCreateRequest`,
`GraphCreateResponse`, `GraphListResponse`, `GraphSchemaSpec`,
`GraphPolicySpec` — all from `omnigraph-server::api`.

Tests:
  - cli.rs (4 new, non-network):
      * `graphs_subcommand_help_lists_list_and_create` — pins the
        deferral of `delete` (catches scope creep).
      * `graphs_list_against_local_uri_errors_with_remote_only_message`
      * `graphs_create_against_local_uri_errors_with_remote_only_message`
      * `graphs_create_with_missing_schema_file_errors` — pins the
        IO context in the schema-read error path.
  - system_remote.rs (1 new, `#[ignore]` like its peers):
      * `graphs_list_and_create_against_multi_graph_server` — spawns a
        multi-mode server, calls `graphs list` (sees `alpha`),
        `graphs create` (adds `beta`), `graphs list` again (sees both),
        and confirms the new graph is reachable via its cluster route.

CLI suite: 62 tests green (58 existing + 4 new). The new ignored
end-to-end test runs locally with `cargo test --ignored`.

LOC: +159 main.rs (enum + handlers), +88 cli.rs (unit tests),
+131 system_remote.rs (integration test).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: composite e2e tests, race fix, v0.7.0 release (PR 9/10)

PR 9 — the final integration PR for MR-668 multi-graph server work.
Closes the v0.7.0 release.

Composite lifecycle tests (closes gaps flagged in PR 7's coverage
review):
  - `multi_graph_lifecycle_post_query_restart_persistence` — POST a
    graph, query it via cluster route, reload the config from disk
    and confirm `load_server_settings` sees the rewritten YAML.
    Validates the "restart resolves orphans" failure-mode story.
  - `per_graph_policy_enforced_on_post_created_graph` — POST a graph
    with a per-graph policy attached, then send authenticated read
    and change requests. Per-graph Cedar enforcement fires correctly
    on a POST-created graph (engine-layer policy reinstalled via
    `Omnigraph::with_policy` inside the create flow).
  - `concurrent_post_graphs_distinct_ids_all_succeed` — 4 concurrent
    POSTs with distinct graph_ids all return 201. Caught a real
    race in `rewrite_atomic` (see below).

Race fix — `rewrite_atomic_with_modify`:

The first composite test surfaced a real bug. The old
`rewrite_atomic(path, new_config, expected_hash)` captured the
baseline hash OUTSIDE the flock, then called rewrite_atomic which
re-acquired it inside. Under concurrent writers:

  - POST A: captures baseline H0, calls rewrite_atomic.
  - POST B: captures baseline H0 too (before A's update lands).
  - A: acquires flock, on-disk == H0, writes H1, releases.
  - A: updates baseline H0 → H1.
  - B: tries to acquire flock — waits.
  - B: acquires flock. On-disk is now H1. Expected (captured
       before A finished) is H0. MISMATCH → spurious Drift error.

Worse: even if the timing happens to align, B's `updated` config
was constructed from BYTES read before the flock. B writes a config
that doesn't include A's new graph — silent data loss.

The fix: new `config::rewrite_atomic_with_modify(path, baseline,
modify)` takes a closure. Inside the flock + baseline mutex:
  1. Read on-disk bytes, hash, compare to baseline.
  2. Parse on-disk YAML.
  3. Call `modify(parsed)` to produce the new config — receives
     fresh on-disk state, returns the modification.
  4. Serialize + write + fsync + rename + update baseline.

Everything is read-modify-write under the same critical section.
Concurrent writers serialize cleanly. Test confirmed this is no
longer a race.

The old `rewrite_atomic(path, new_config, expected_hash)` API stays
for tests that don't need the read-modify-write shape; the POST
handler switches to the new shape.

Version bump v0.6.0 → v0.7.0:
  - All 5 `crates/*/Cargo.toml` (compiler, engine, policy, cli, server)
    plus their inter-crate `path` dep version constraints.
  - `Cargo.lock` regenerated by `cargo build --workspace`.
  - `AGENTS.md` "Version surveyed" line, capability matrix HTTP-server
    row updated to mention multi-graph + cluster routes + atomic YAML
    rewrite.
  - `openapi.json` regenerated.

Docs:
  - `docs/releases/v0.7.0.md` (new) — release notes with breaking
    changes, new features, deferred items (DELETE, `delete_prefix`,
    actor forwarding), and the single→multi migration recipe.
  - `docs/user/server.md` — substantial section additions for the
    two modes, mode inference, cluster endpoint table, management
    endpoints, `omnigraph.yaml` ownership contract, `POST /graphs`
    body shape + status codes.
  - `docs/user/cli.md` — `omnigraph graphs list/create` section,
    deferred-DELETE note.
  - `docs/user/policy.md` — server-scoped Cedar actions
    (`graph_create`, `graph_list`), per-graph vs server-level policy
    composition, example server-level policy.

Workspace test pass: 573 tests green across all crates. Zero
failures. MR-731 spoof regression still pinned and passing across
the entire 10-PR series.

This commit closes MR-668. v0.7.0 is ready for tagging.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: remove POST /graphs and CLI graphs create (defer runtime graph mgmt)

The POST /graphs runtime-create endpoint shipped in PR 7/10 has three
unresolved high-severity bugs:

  - flock-on-renamed-inode race: the YAML flock is taken on
    omnigraph.yaml itself, then a temp file is renamed over it.
    Cross-process writers end up locking different inodes — both
    believing they hold exclusive access.
  - duplicate-check outside the file lock: precheck runs against
    the in-memory registry only; the locked closure does
    config.graphs.insert(...) unconditionally. Concurrent same-id
    POSTs can persist the loser in YAML while the in-memory registry
    keeps the winner — they disagree after restart.
  - best_effort_cleanup_init_artifacts deletes _schema.pg /
    _schema.ir.json / __schema_state.json on any init failure. An
    accidental re-init against an existing graph's URI destroys its
    schema; subsequent open() fails at read_text(_schema.pg).

The correct fix is a Lance-style cluster catalog (reserve → init →
publish with recovery sidecars), parallel to the engine's existing
__manifest discipline. That work is out of scope for v0.7.0.

For now, disable runtime add/remove from the network and CLI surface.
Operators add graphs by editing omnigraph.yaml and restarting. The
GET /graphs read-only enumeration stays.

Removed:
- POST /graphs handler + router fragment + utoipa registration
- 13 post_graphs_* server tests + 3 composite POST tests +
  multi_mode_app_with_real_config / post_graph helpers
- CLI omnigraph graphs create subcommand + its handler + cli.rs tests
- system_remote.rs combined list+create test trimmed to list-only
- YAML rewrite infra: rewrite_atomic[_with_modify], RewriteAtomicError,
  staging_path, hash_config_file, AppState::config_hash field +
  threading through new_multi and open_multi_graph_state
- fs2 dependency (verified absent from cargo tree)
- sha2/fs2 imports in config.rs (only the rewrite path used them)
- Cedar PolicyAction::GraphCreate variant + "graph_create" match arms
  + action def in Cedar schema + graph_create_action_authorizes_against_server_resource test
- GraphCreateRequest / GraphCreateResponse / GraphSchemaSpec /
  GraphPolicySpec API types (only the POST handler / CLI imported them)

Kept:
- GET /graphs (read-only enumeration) and graph_list Cedar action
- omnigraph graphs list CLI subcommand
- All multi-graph startup, mode inference, cluster routes,
  per-graph + server-level Cedar policies
- server_settings_drive_multi_graph_startup_end_to_end (the test
  that covers operator-authored YAML + restart — the path that
  survives)
- best_effort_cleanup_init_artifacts and the three init failpoints
  (still reachable from CLI `omnigraph init`; preflight fix deferred
  as a follow-up)
- GraphRegistry::insert and its concurrency tests — production
  callers gone, but the method is the natural seam for the future
  cluster-catalog work

Also fixed (transcript issue 4):
- ALWAYS_FLAT_PATHS now includes /graphs so multi-mode OpenAPI
  advertises the management route correctly (was previously rewritten
  to /graphs/{graph_id}/graphs)
- multi_mode_openapi_keeps_healthz_flat → renamed to
  multi_mode_openapi_keeps_management_paths_flat, asserts both
  /healthz and /graphs stay flat
- multi_mode_openapi_prefixes_operation_ids_with_cluster skips
  /graphs in addition to /healthz

Doc fixes:
- docs/user/cli.md: graphs list example was --target http://...,
  but --target is a config-graph-name lookup; corrected to --uri.
  Removed the graphs create example.
- docs/user/server.md: dropped POST /graphs row, "omnigraph.yaml
  ownership", and "POST /graphs body shape" sections. Added a
  paragraph stating runtime add/remove is not exposed in v0.7.0.
- docs/user/policy.md: dropped graph_create action; reworded the
  "Configuration" line to clarify that server-scoped rules (graph_list)
  take neither branch_scope nor target_branch_scope.
- docs/releases/v0.7.0.md: rewrote release narrative — multi-graph
  mode ships; runtime add/remove deferred.
- AGENTS.md: HTTP server bullet and capability matrix row updated to
  reflect read-only GET /graphs and the operator-edit workflow.
- openapi.json regenerated; /graphs has only .get, no .post.

Diff: 17 files, +123 −1525 LOC.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: comment cleanup and policy format style

Strip "PR Na/Nb" sub-PR references throughout MR-668 surfaces — they
were useful during the 10-PR delivery sequence but rot now that the
work is in the tree. Keep the MR-668 umbrella references.

Also:
- Add explicit `when = when` and `resource_literal = resource_literal`
  named args in `compile_policy_source`'s outer `format!` to match the
  surrounding crate style (already explicit for `group` and `action`).
- Rename the best-effort cleanup tracing target from
  "omnigraph::init" to "omnigraph::init::cleanup" so operators can
  filter init-failure cleanup events separately from init's other
  log lines.

No behavior change.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: drop actor_id from PolicyRequest; pass actor as separate arg

The MR-731 "server-authoritative actor identity" invariant was enforced
by an in-function chokepoint (`request.actor_id = actor.actor_id...`
overwrite inside `authorize_request`). That worked but relied on every
caller passing in a `PolicyRequest` and trusting the overwrite — a
comment-enforced invariant.

Move the invariant into the type system:

* `PolicyRequest` no longer carries `actor_id`. The struct now models
  what a caller wants to do, not who they are.
* `PolicyEngine::authorize(actor_id: &str, request: &PolicyRequest)`
  and `validate_request(actor_id, request)` take identity as a
  separate argument. The same shape `PolicyChecker::check` already had
  for the engine layer.
* `authorize_request` in the HTTP layer extracts `actor_id` from the
  bearer-resolved `ResolvedActor` and passes it positionally — no
  overwrite step that could be skipped.
* CLI `omnigraph policy explain` updated (the only other consumer
  that built a `PolicyRequest`).

Public API break for the `omnigraph-policy` crate. Worth it: handlers
can no longer accidentally populate `actor_id` from a request body
field, and external consumers are forced by the compiler to source
actor identity from a trusted path.

The MR-731 chokepoint test
`actor_id_resolves_from_bearer_token_ignoring_client_supplied_headers`
still passes — the bearer-resolved actor is what reaches the engine.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: consolidate AppState single-mode constructors; delete with_policy_engine

The prior `with_policy_engine` constructor reused the engine `Arc`
from the existing handle (`engine: Arc::clone(&existing.engine)`)
without re-applying `Omnigraph::with_policy`. Combined with
`new_with_workload`, the documented composition pattern was
`AppState::new_with_workload(...).with_policy_engine(p)` — which
produced an `AppState` whose HTTP layer enforced Cedar but whose
underlying engine had no `PolicyChecker` installed. Any caller
reaching the engine via `state.registry().list()[i].engine` could
bypass policy entirely. The doc comment named this gap; the type
system didn't.

Make composition impossible to get wrong:

* Add `AppState::new_single(uri, db, tokens, Option<PolicyEngine>,
  WorkloadController)` — canonical single-mode constructor that
  takes every option together and routes through `build_single_mode`
  (which applies `db.with_policy(checker)` to the engine itself).
* `new`, `new_with_bearer_token`, `new_with_bearer_tokens`,
  `new_with_bearer_tokens_and_policy`, `new_with_workload` all become
  thin wrappers around `new_single`.
* Delete `with_policy_engine`. There is no post-construction policy
  install path any more; the single linear construction forces
  HTTP-layer and engine-layer policy to install together or not at all.

Regression test `engine_layer_policy_fires_via_direct_arc_omnigraph_from_new_single`
constructs an `AppState::new_single` with a deny-all policy, pulls
the `Arc<Omnigraph>` from the registry handle (the same path an
embedded SDK consumer would take), and asserts a direct `mutate_as`
call returns `OmniError::Policy`. Pre-fix this test would have
succeeded the mutation.

Test caller in `ingest_per_actor_admission_cap_returns_429`
migrates from `.with_policy_engine(...)` to `new_single(...,
Some(policy_engine), workload)`.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: derive any_per_graph_policy on RegistrySnapshot; simplify dup check

`AppState::requires_bearer_auth` walked the entire registry per
request (cloning Arcs into a `Vec`, then `.iter().any(|h| h.policy
.is_some())`) to decide whether the auth middleware should challenge.
The walk is unnecessary — the answer only changes when the registry
mutates, which is exactly the moment a new snapshot is constructed.

Move the flag onto the snapshot itself:

* `RegistrySnapshot { graphs, any_per_graph_policy: bool }`.
* `RegistrySnapshot::new(graphs)` is the only construction path —
  it derives the flag from `graphs.values().any(|h| h.policy
  .is_some())` so the cached value can't drift from the source data.
* `Default` delegates to `new(HashMap::new())`.
* `GraphRegistry::from_handles` and `insert` build snapshots via
  `RegistrySnapshot::new(...)`.
* `GraphRegistry::snapshot_ref()` exposes the current snapshot
  through an `arc_swap::Guard`; callers that need cached derived
  state go through this accessor (callers that only want `graphs`
  still use `list` / `get`).

`requires_bearer_auth` becomes one `ArcSwap::load` + bool read.

Also (drive-by, same file, same hunk): replace the dead
`if let Some(other) = seen_uris.get(...)` + `let _ = other;` pattern
in `from_handles` with a plain `seen_uris.contains_key(...)`.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: fail-fast multi-graph startup with try_collect

The `open_multi_graph_state` doc comment claims "Fail-fast — the
first open error aborts startup; other in-flight opens are dropped"
but the code did

    .buffer_unordered(4)
    .collect::<Vec<_>>()
    .await
    .into_iter()
    .collect::<Result<Vec<_>>>()?;

which drains every future in the stream before propagating the first
`Err`. With N S3-backed graphs and graph #2 failing fast, the caller
still waits for #1, #3, #4, … to either succeed or fail before
seeing the error.

Replace the four-line dance with `futures::TryStreamExt::try_collect`,
which short-circuits on the first `Err` and drops the rest. The
doc comment now matches behavior.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: drop unused State extractor from 7 read-only handlers

After the routing-middleware refactor moved the engine into the per-graph
`GraphHandle` (extracted via `Extension<Arc<GraphHandle>>`), seven
read-only handlers — `server_snapshot`, `server_read`, `server_export`,
`server_schema_get`, `server_branch_list`, `server_commit_list`,
`server_commit_show` — kept an unused `State(_state): State<AppState>`
extractor. Drop it. Each request avoids one `FromRequestParts` clone
of `AppState`'s Arcs.

Handlers that actually use state (workload admission for write paths,
`server_policy` for management endpoints) keep theirs.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: emit info! for graph routing decision

`tracing::Span::current().record("graph_id", ...)` in the routing
middleware silently no-ops here: no upstream `#[tracing::instrument]`
on the handlers declares a `graph_id` field, and `TraceLayer::new_for_http`
doesn't either. The recorded value never lands anywhere visible.

Replace with an explicit `info!(graph_id = %handle.key.graph_id,
"graph routed")` event so operators can grep logs and correlate
requests with the active graph. In single mode the value is the
sentinel `"default"`.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: align GET /graphs 405 body code with HTTP status

The single-mode `GET /graphs` handler returned an `ApiError` built
via struct literal with `status: METHOD_NOT_ALLOWED, code: BadRequest`.
The body code disagreed with the HTTP status — clients deserializing
on `code` saw `bad_request`, clients deserializing on `status` saw
405. Same bug class as the earlier 503+Conflict mismatch on the
removed YAML drift path.

Close the class for this one remaining instance:

* Add `ErrorCode::MethodNotAllowed` to the API enum.
* Add `ApiError::method_not_allowed(msg)` — pairs the 405 status
  with the matching code.
* Replace the struct literal in `server_graphs_list` with the
  constructor.
* Regenerate `openapi.json` (adds `method_not_allowed` to the
  ErrorCode schema enum).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: drop unused axum::handler::Handler import

The import landed in earlier work but no current call site uses it.
Emitted an `unused_imports` warning on every server build.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: drop unused fs2 workspace dependency

`fs2 = "0.4"` lingered in [workspace.dependencies] after the
POST /graphs flock-on-rename design was pulled. `cargo tree -i fs2`
reports no consumers in the workspace and the dep is not in
Cargo.lock. Removing the declaration closes the "phantom dep" class.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: AGENTS.md Cedar row no longer hardcodes action count

The "8 actions" claim drifted as soon as MR-668 added `graph_list`.
Bumping the count would just push the drift one PR forward; the
correct-by-design fix is to defer to the canonical list in
docs/user/policy.md and stop maintaining a duplicate count.

Closes the "doc hardcodes a count that drifts from the enum" class.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: cfg(test)-gate GraphRegistry::insert and its mutex

`insert` and the `mutate: Mutex<()>` that serializes it had no
runtime consumer in v0.7.0 — the only insertion path at startup
is `from_handles`, and runtime add/remove is deferred until a
managed cluster catalog ships. Leaving both `pub` and live made
them a "looks like API, isn't" footgun: a future change could
build on `insert` without re-establishing the concurrency contract
with an actual consumer in scope.

Gate both together (`#[cfg(test)]` on the method, the field, and
the `tokio::sync::Mutex` import) so the race-pinning tests still
compile but production cannot reach them. When a real consumer
ships, ungate both — they're a unit. Closes the "public API with
no runtime consumer drifts toward incorrect" class.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: drop vestigial PolicyEngine surface

* `validate_request` had zero callsites — pure surface for nothing.
* `deny`'s `_actor_id` and `_request` parameters were both unused
  (the underscore prefix gave it away); the message is built by the
  caller before `deny` ever sees the request. Trim both.

Closes the "public API that the type system can't justify" class
for the policy engine. No behavior change; every existing test
stays green because the deletions never had a runtime effect.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: regression test for init re-init footgun (red)

A second `Omnigraph::init` against an existing graph URI today
destroys the existing graph's schema artifacts. `init_storage_phase`
overwrites `_schema.pg` before any preflight, and on the inner
`GraphCoordinator::init` failure that follows,
`best_effort_cleanup_init_artifacts` deletes all three schema files.
The existing Lance datasets and `__manifest/` survive but the
schema metadata is gone — unrecoverable without operator surgery.

This test exercises that path and currently fails with
"_schema.pg must not be deleted by a failed re-init", confirming
the destructive cleanup branch fires. The fix in the next commit
makes the test pass by preflighting with `storage.exists()` and
returning a typed error before any write touches disk.

Per AGENTS.md rule 12, the test commit lands just before the fix
commit so the red → green pair is visible in `git log` and a
reviewer can check out this commit alone to reproduce.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: close init re-init footgun via InitOptions preflight (green)

`Omnigraph::init` is "create a new graph"; existing graphs need
an explicit overwrite. Today's behavior — silently overwrite
schema files, then on inner failure delete them via best-effort
cleanup — is destructive against an existing graph regardless of
which branch fires.

Correct-by-design fix:

* New `InitOptions { force: bool }` struct (default `force: false`).
* New `Omnigraph::init_with_options(uri, schema, options)`. The
  old `Omnigraph::init(uri, schema)` is a thin shortcut that
  passes `InitOptions::default()`.
* `init_with_storage` runs a `storage.exists()` preflight on the
  three schema URIs BEFORE any parse, write, or coordinator call.
  Any hit → typed `OmniError::AlreadyInitialized { uri }`. The
  destructive code paths (the `write_text` overwrite and the
  best-effort cleanup) are now unreachable in strict mode against
  an existing graph.
* `force: true` skips the preflight; existing operators who
  actually mean to overwrite opt in explicitly.
* CLI: `omnigraph init --force` maps to `InitOptions { force: true }`.
* HTTP: `OmniError::AlreadyInitialized` maps to 409 via
  `ApiError::from_omni`. Not currently HTTP-reachable (POST /graphs
  was pulled), but the wiring lands here so a future runtime
  create endpoint has one canonical translation.

Closes the "init is destructive against existing state" class.
The regression test added in the previous commit
(`init_on_existing_graph_uri_does_not_destroy_existing_schema`)
turns green: the original schema files now survive a second
init attempt byte-for-byte, and the call errors cleanly with
`AlreadyInitialized`. The four existing
`init_failpoint_after_*_cleans_up_*` tests stay green — strict
mode's preflight passes on a fresh tempdir, and cleanup still
runs as before when a failpoint fires mid-write.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: split PolicyEngine::load into kind-typed loaders

Pre-fix, every caller of `PolicyEngine::load(path, graph_id)`
passed *some* `graph_id` argument — even when the policy was
server-scoped and Cedar's resolution would never touch a Graph
entity. The server-level loader at lib.rs passed the meaningless
sentinel `"server"`. A graph policy file containing a `graph_list`
rule compiled fine; a server policy file containing a `read` rule
compiled fine. Both silently no-op'd at request time because the
engine kind and the rule's resource kind disagreed.

Correct-by-design fix: replace `load` with two kind-typed loaders.

* `PolicyEngine::load_graph(path, graph_id)` — for per-graph
  policy files. Rejects any rule whose action `resource_kind()`
  is `Server`.
* `PolicyEngine::load_server(path)` — for server-level policy
  files. Takes no `graph_id`: server-scoped actions resolve against
  the singleton `Omnigraph::Server::"root"` entity, never a Graph.
  Rejects any rule whose action `resource_kind()` is `Graph`.

The old `load` is hard-deleted in the same commit because every
in-tree consumer migrates here (no semver promise on the workspace
crate, no external pinners). New `PolicyEngineKind` enum types
the loader's intent; `validate_kind_alignment` is the load-time
check that closes the "wrong action, wrong file, silent no-op"
class — operators get a load-time error instead of confused-and-
silent behavior at request time.

Callsites migrated:
* server lib.rs:374 (single-mode per-graph)   → load_graph
* server lib.rs:1065 (multi-mode server)      → load_server
* server lib.rs:1103 (multi-mode per-graph)   → load_graph
* CLI main.rs:732 (resolve_policy_engine)     → load_graph
* tests/server.rs ×5 (4 graph, 1 server)      → load_graph/load_server
* policy_engine_chassis.rs                    → load_graph

Four new in-source tests pin the contract: both rejection paths
and both positive paths.

Closes the "operator puts an action in the wrong file and the
rule silently never matches" class.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: introduce GraphRouting, retire single_mode_handle

Pre-fix, `AppState` always carried `Arc<GraphRegistry>` even when
serving one graph. Single mode populated the registry with one
handle keyed by the `SINGLE_GRAPH_KEY_ID = "default"` sentinel;
`single_mode_handle` walked the registry, asserted `len == 1`,
and returned the single element with a 500-class "programmer
error" branch on mismatch. Three smells in a row — magic key,
walk-and-assert, programmer-error guard — all because the
single-mode runtime was forced through a multi-mode abstraction.

Correct-by-design fix: type the routing.

* New `pub enum GraphRouting { Single { handle }, Multi { registry,
  config_path } }` on `AppState`. The `Single` arm carries the handle
  directly — no registry, no key, no walk.
* `resolve_graph_handle` middleware matches on `routing`. Single mode
  returns the handle in O(1); multi mode does the same path-extract +
  registry lookup as before. The 500-class programmer-error branch
  is gone — the type system now makes the violated invariant
  ("single mode has exactly one handle") unrepresentable.
* `requires_bearer_auth` reads `handle.policy.is_some()` directly
  in the Single arm; Multi arm still uses the cached
  `any_per_graph_policy` flag.

`ServerMode` and the legacy `registry` field on `AppState` are still
populated for now — C-3 removes both once every reader is migrated.
The `SINGLE_GRAPH_KEY_ID` sentinel and `ServerMode` will also go
away in C-3.

Closes the "single mode forced through a multi-mode abstraction"
class. All 76 server integration tests stay green: handlers still
extract `Extension<Arc<GraphHandle>>` from the request, so the
middleware's internal change is invisible to them.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: remove ServerMode, registry field, and the SINGLE_GRAPH sentinel

C-1/C-2 introduced `GraphRouting` and pointed the middleware at it.
This commit removes the legacy shape that's now dead:

* `ServerMode` enum — deleted. Single mode's `uri` lives on
  `handle.uri`; multi mode's `config_path` lives on the
  `GraphRouting::Multi` arm.
* `AppState.mode: ServerMode` field — deleted.
* `AppState.registry: Arc<GraphRegistry>` field — deleted. Multi
  mode's registry is on `GraphRouting::Multi { registry, .. }`;
  single mode has no registry at all.
* `AppState::mode()`, `AppState::uri()`, `AppState::registry()`
  accessors — deleted. New `AppState::routing() -> &GraphRouting`
  is the single public entry point.
* `SINGLE_GRAPH_KEY_ID` constant — deleted. `GraphHandle.key` is
  still required by the struct, but in single mode the key is now
  only a tracing label (`"default"`, inlined with a comment naming
  its sole remaining purpose). Single-mode flat routes never carry
  a `{graph_id}` parameter, so the key is never compared against
  user input, and there is no registry where it could be a map
  key. C-1/C-2 already removed the registry walk that the sentinel
  was named for.

Callers migrated:
* `build_app` (lib.rs:944) — matches on `state.routing()` instead
  of `state.mode()`.
* `server_graphs_list` (lib.rs:1162) — destructures the Multi arm
  to get the registry; Single arm short-circuits to 405.
* `server_openapi` (lib.rs:1217) — matches the Multi arm for the
  cluster-prefix rewrite.
* `tests/server.rs:3735` — the B2 footgun regression test now
  matches on `state.routing()` to extract the single-mode handle
  (the test's earlier `state.registry().list().next()` shape was
  the closest pre-fix analog to "embedded consumer reaches the
  engine"; the new shape is more direct).

Closes the entire "single mode forced through a multi-mode
abstraction" class. After this commit:
* No magic sentinel as a routing key.
* No `single_mode_handle` walk-and-assert helper.
* No 500-class "programmer error" branch in the middleware.
* No two-field discriminant on `AppState` where one would do.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: regression test for nested-route path extraction (red)

`server_branch_delete` and `server_commit_show` use bare
`Path<String>` extractors. In single-mode flat routes
(`/branches/{branch}`, `/commits/{commit_id}`) this works — one
capture, one value. In multi-graph cluster routes
(`/graphs/{graph_id}/branches/{branch}`,
`/graphs/{graph_id}/commits/{commit_id}`) axum 0.8 propagates the
outer `{graph_id}` capture into the inner handler, so the
extractor sees two captures and 500s with
"Wrong number of path arguments. Expected 1 but got 2."

`cluster_routes_dispatch_per_graph_handle` only exercises
`/snapshot` (no Path extractor), so the regression slipped through.
This test closes that gap structurally: every cluster route with
an inner path param gets exercised here.

Currently fails with the exact symptom above. Fix in the next
commit makes it pass.

Per AGENTS.md rule 12, the red test commit lands just before the
fix so the pair is visible in `git log` and a reviewer can check
out this commit alone to reproduce.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: named-field path-param structs for nested cluster routes (green)

`Path<String>` deserializes one path-param value positionally.
Single-mode flat routes (`/branches/{branch}`,
`/commits/{commit_id}`) have one capture; multi-mode nested routes
(`/graphs/{graph_id}/branches/{branch}`,
`/graphs/{graph_id}/commits/{commit_id}`) have two — axum 0.8
propagates the outer capture into nested handlers. Same handler,
two different shapes; the multi-mode shape 500s with
"Wrong number of path arguments. Expected 1 but got 2."

Symptomatic fix: change to `Path<(String, String)>` and ignore the
first element. Breaks again the moment we add another nest layer
(e.g. tenant in Cloud mode).

Correct-by-design fix: named-field structs deserialized by name
from axum's path-param map. Each handler picks only the fields it
needs. Stable across single / multi / future-cloud nest depths
because deserialization is by field name, not position.

* New `BranchPath { branch: String }` (file-local to lib.rs)
* New `CommitPath { commit_id: String }`
* `server_branch_delete` extractor → `Path<BranchPath>`
* `server_commit_show` extractor → `Path<CommitPath>`

Closes the "handler path-extractor type is positional and breaks
when route nesting changes" class. Red test from the previous
commit turns green. All 77 server tests pass (single-mode branch
delete + commit show, plus new multi-mode coverage).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: centralize policy-requires-tokens check in the runtime classifier

Single-mode `open_with_bearer_tokens_and_policy` bailed at lib.rs:380
when policy was installed and no tokens. Multi-mode
`open_multi_graph_state` had no equivalent: the server started, every
request 401'd because no token could ever match, and the operator
spent time debugging a misconfiguration the single-mode path would
have caught at startup.

The doc/code contradiction made the gap easy to miss: the
`ServerRuntimeState::PolicyEnabled` docstring said tokens-or-not
was "unusual but valid — every request fails 401 without a bearer,
which is effectively 'locked'." The single-mode bail contradicted
that. In practice, silent-401-on-every-request is bug-shaped, not
feature-shaped (operators wanting deny-all should configure tokens
plus a deny-all Cedar rule to get meaningful 403s with
policy-decision logging).

Symptomatic fix: add a copy of the bail to multi-mode. Two copies
that can drift again the next time a startup path is added.

Correct-by-design fix: hoist the check into
`classify_server_runtime_state` so both modes get the same
enforcement from one source of truth. The classifier becomes the
single source of truth for "should we start?" and adding a startup
invariant there is now the natural extension point for any future
mode.

Classifier matrix is now complete:

| has_tokens | has_policy | allow_unauthenticated | Result |
|---|---|---|---|
| F | F | F | bail (existing) |
| F | F | T | Open (existing) |
| T | F | * | DefaultDeny (existing) |
| F | T | * | bail (NEW — closes the gap) |
| T | T | * | PolicyEnabled (existing) |

Changes:

* `classify_server_runtime_state` (lib.rs:870-890) gains the
  `(false, true, _) => bail!(…)` arm with a clear message naming
  the failure mode and the two valid resolutions.
* `open_with_bearer_tokens_and_policy` (lib.rs:369+) drops its
  redundant local bail — the classifier rejected the invalid case
  before construction was reached.
* `ServerRuntimeState::PolicyEnabled` docstring is rewritten:
  drops the "(unusual but valid)" carve-out and states plainly
  that PolicyEnabled requires tokens. Names the explicit
  alternative (tokens + deny-all Cedar rule) for operators who
  want the all-requests-denied behavior.
* `classify_policy_enabled_always_wins` test is renamed to
  `classify_policy_enabled_requires_tokens` and the now-invalid
  `(false, true, _)` assertion is removed (covered by the new
  rejection test).
* New `classify_policy_without_tokens_is_rejected` test covers the
  new arm.
* New `serve_refuses_to_start_with_policy_but_no_tokens_multi_mode`
  integration test pins the multi-mode propagation path —
  symmetric with the existing single-mode
  `serve_refuses_to_start_in_state_1_without_unauthenticated`.

Closes the "single mode and multi mode startup branches can drift
on safety invariants" class.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: close coverage gaps surfaced by the test-coverage audit

The bot-review pass and the subsequent coverage audit surfaced two
material gaps in PR #119's test surface — both easy to close, both
worth closing before merge.

* **Gap 1 — cluster-route sweep.** The Bug-1 path-extractor
  regression slipped through because
  `cluster_routes_dispatch_per_graph_handle` only exercised
  `/snapshot`. The other six protected cluster routes (`/read`,
  `/change`, `/export`, `/schema`, `/schema/apply`, `/ingest`,
  `/branches/merge`) were implicitly trusted to work without any
  multi-mode integration test.

  Add `all_protected_cluster_routes_resolve_to_their_handler`
  (`tests/server.rs`) that hits each protected cluster route with
  a minimal request and asserts the response is consistent with
  the handler being reached — no 404 (router didn't match), no 500
  with "Wrong number of path arguments" (Bug-1 class), no 500 with
  "missing extension" (routing middleware didn't inject the handle).
  Status code is a negative assertion because each handler's
  happy-path inputs differ; what matters is "the request reached
  the handler," not "the handler returned 200" — that's already
  pinned by the single-mode tests.

* **Gap 2 — `--force` happy path.** The strict re-init regression
  test (`init_on_existing_graph_uri_does_not_destroy_existing_schema`)
  pins the error path; nothing pinned the `force: true` escape
  hatch actually doing what its docstring claims.

  Add `init_with_force_recovers_from_orphan_schema_files`
  (`tests/lifecycle.rs`). Writes a bare `_schema.pg` to simulate
  orphan files from a failed prior init, confirms strict mode
  bails as expected, then confirms `init_with_options(force: true)`
  succeeds and produces a functional graph.

  Note: the test follows the documented semantics — force skips
  the preflight only, it does NOT purge existing Lance state. An
  earlier draft of the test (against full overwrite of an existing
  populated graph) failed because `GraphCoordinator::init` errored
  on the existing `__manifest`, which is exactly the limitation
  the `InitOptions::force` docstring already calls out. Recursive
  purge needs `StorageAdapter::delete_prefix` (tracked separately).

Coverage is now fully aligned with the PR's claims.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: regression test for GraphList open-mode bypass (red)

Cursor bot's review at commit 4120448 surfaced that
`server_graphs_list` returns 200 in Open mode (`--unauthenticated`,
no tokens, no policy), exposing the full graph registry — graph
IDs and URIs that may contain S3 bucket paths or internal
hostnames — to any unauthenticated caller.

Root cause: `authorize_request`'s no-policy fallback only denies
when `actor.is_some()`. In Open mode `actor: None`, so the
denial branch never fires and the call returns `Ok(())`. The
docstring on `server_graphs_list` claims the endpoint is
"Cedar-gated" and that we "don't leak the registry until the
operator explicitly authorizes it" — but Open mode has no Cedar
at all, so the docstring intent and the code disagree.

This commit renames the existing
`get_graphs_lists_registered_graphs_in_multi_mode` test to
`get_graphs_denied_in_open_mode_without_server_policy` and flips
the assertion from 200 → 403. Today this fails (server returns
200) — exactly the symptom the bot named. The fix in the next
commit tightens the no-policy fallback to deny server-scoped
actions unconditionally, regardless of mode.

Per AGENTS.md rule 12, the red test commit lands just before
the fix so the red → green pair is visible in `git log` and a
reviewer can check out this commit alone to reproduce.

Sort-order coverage that previously lived in the renamed test
moves to `get_graphs_with_server_policy_authorizes_per_cedar`
in the next commit, where the admin-200 response is operator-
authorized and a non-empty body is asserted.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: server-scoped actions always require explicit policy (green)

`server_graphs_list` returned 200 in Open mode (`--unauthenticated`,
no tokens, no policy) because `authorize_request`'s no-policy
fallback only denied when `actor.is_some()` AND action != Read.
In Open mode `actor: None`, so the denial branch never fired and
the call returned `Ok(())` — leaking the registry (graph IDs +
URIs that may contain S3 bucket paths or internal hostnames) to
any unauthenticated caller. The docstring on `server_graphs_list`
claimed it was "Cedar-gated" and that the server should "not leak
the registry until the operator explicitly authorizes it" —
docstring intent and code disagreed.

Symptomatic fix: special-case GraphList. Breaks the moment
another server-scoped action (`graph_create`, `graph_delete`) is
added.

Correct-by-design fix: tie authorization to the action's
`resource_kind()`. Server-scoped actions
(`PolicyResourceKind::Server`) always require explicit policy
authorization — there is no runtime state where they're served
by default. Per-graph actions keep the existing default-deny
logic (DefaultDeny denies non-Read for authenticated actors;
Open mode allows everything per the operator's `--unauthenticated`
opt-in for graph DATA, but not for server topology).

The fix uses the existing `PolicyResourceKind` enum that #119
already added — no new abstraction. Future server-scoped actions
(runtime `graph_create`/`graph_delete` when the cluster catalog
ships) automatically pick up the same enforcement without any
per-action handler change.

Changes:

* `crates/omnigraph-server/src/lib.rs:51` — re-export
  `PolicyResourceKind` (the kind discriminator was already public
  on the omnigraph-policy crate; needed in scope here).
* `crates/omnigraph-server/src/lib.rs:1457` — `authorize_request`'s
  no-policy fallback gains a server-scoped-action check that fires
  before the actor-based default-deny logic. Error message names
  the failure mode and points at `server.policy.file`.
* `crates/omnigraph-server/tests/server.rs:5037` —
  `get_graphs_with_server_policy_authorizes_per_cedar` extended
  to register two graphs in non-alphabetical order and assert
  the admin-200 response is sorted alphabetically. Restores the
  sort-order coverage that lived in
  `get_graphs_lists_registered_graphs_in_multi_mode` before the
  red commit renamed it to assert denial.

Also bundles a small adjacent cleanup that the bot-review flagged:

* `crates/omnigraph-server/src/graph_id.rs:124` — drop the
  unreachable `"openapi.json"` entry from `is_reserved`. The
  regex `^[a-zA-Z0-9-]{1,64}$` rejects every dot-containing name
  before `is_reserved` can run, so dotted entries in this list
  were dead code that misled readers into thinking the list
  needed to cover them. Comment now names the structural
  exclusion. The `rejects_reserved_route_names` test loses its
  `openapi.json` row (covered by `rejects_dots` via the regex).

Closes the "server-scoped management actions silently leak in
Open mode" class. Red test from the previous commit
(`get_graphs_denied_in_open_mode_without_server_policy`) turns
green; all 78 server integration tests + 76 lib tests pass.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: fold multi-graph work into v0.6.0 (no separate v0.7.0 release)

The branch had bumped workspace versions to 0.7.0 and added a
dedicated `docs/releases/v0.7.0.md` for the multi-graph work.
Per scope decision: ship the graph-rename and the multi-graph
mode in one v0.6.0 release.

Changes:

* Workspace versions bumped 0.7.0 → 0.6.0 in every crate manifest
  (`omnigraph`, `omnigraph-compiler`, `omnigraph-policy`,
  `omnigraph-server`, `omnigraph-cli`) and their internal
  `path = ..., version = "..."` dependency constraints.
* `docs/releases/v0.7.0.md` content merged into
  `docs/releases/v0.6.0.md`, retargeted to a single coherent
  v0.6.0 release note covering both the graph terminology rename
  and the multi-graph server mode. The original v0.7.0.md is
  deleted.
* All `v0.7.0` / `0.7.0` doc and comment references throughout
  `crates/`, `docs/`, `AGENTS.md`, and `openapi.json` retargeted
  to `v0.6.0` / `0.6.0`. `Cargo.lock` regenerated to match.
* OpenAPI spec regenerated via `OMNIGRAPH_UPDATE_OPENAPI=1
  cargo test -p omnigraph-server --test openapi
  openapi_spec_is_up_to_date` — `"version": "0.6.0"` now.

Verification:

* `cargo build --workspace` — clean (6 pre-existing engine
  warnings only).
* `cargo test --workspace --locked` — zero failures across all
  39 test result groups.
* `bash scripts/check-agents-md.sh` — passes (34 links / 33 docs).
* `grep -rn "0\.7\.0\|v0\.7\.0" --include='*.rs' --include='*.md'
  --include='*.json' --include='*.toml' .` returns no workspace
  hits. The three remaining `0.7.0` strings in `Cargo.lock`
  belong to unrelated 3rd-party crates (`pem-rfc7468`, `radium`,
  `rand_xoshiro`).

The git tag and crates.io publish happen later — this commit
just consolidates the surface so the eventual release is one
coherent v0.6.0 covering all the work since v0.5.0.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* mr-668: sanitize internal refs from v0.6.0 release notes

cubic-dev-ai P2 comments flagged that the release notes carried
internal Linear ticket and RFC references (MR-668, MR-731,
MR-723, RFC 0003, RFC 0004). Per AGENTS.md maintenance rule 5,
"Release docs are public project history. Describe capabilities,
behavior changes, breaking changes, upgrade notes, and user
impact; do not reference private ticket systems, internal
codenames, or planning shorthand that an outside contributor
cannot inspect." The bot's comments are correct against our own
published contract — they were a docs-quality regression
introduced when I drafted these notes.

Replaced each internal reference with the public-facing concept
it stood for. The substantive content (capabilities, behavior,
guarantees) was already present alongside the refs; sanitization
just trimmed the bracketed ticket labels:

* Line 6: dropped `(MR-668)` from the multi-graph mode summary —
  the descriptive name was already self-sufficient.
* Line 24: `MR-731 spoof defense` → `the bearer-derived-actor-
  identity guarantee`; `Forward-compat for Cloud mode (RFC 0003)
  and OAuth provider (RFC 0004)` → "forward-compat seams for
  future multi-tenant and OAuth deployments; they're inert in
  this release" — describes what the operator sees instead of
  pointing at planning docs.
* Line 26: `MR-731's server-authoritative-actor invariant` →
  "the server-authoritative-actor invariant: actor identity is
  always sourced from the bearer-token match resolved at the
  auth boundary" — the public-facing statement of the guarantee.
* Line 36: `(MR-723 default-deny otherwise rejects …)` →
  "without a server policy the default-deny posture rejects …"
  — same content, no ticket label.
* Line 121: `MR-731 spoof regression test` → "The bearer-auth-
  derived-actor-identity regression test (client-supplied
  identity headers are ignored; the server-resolved actor is the
  only identity Cedar sees)" — describes what the test guards
  instead of naming the originating ticket.

Verified: `grep -E 'MR-\d+|RFC[ -]?\d+' docs/releases/v0.6.0.md`
returns no matches; the rest of `docs/releases/` is also clean.
`scripts/check-agents-md.sh` passes.

Note: cubic-dev-ai also flagged `crates/omnigraph-cli/src/main.rs:276`
("doc comment incorrectly references v0.6.0 for a command that
only exists in v0.7.0"). That comment is based on a stale model
of the release surface — after folding v0.7.0 into v0.6.0 in
the previous commit, the multi-graph CLI surface IS in v0.6.0
and the comment is correct as written. No change needed.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix: close validated init and multi-graph gaps

* chore: address review cleanup comments

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2026-05-28 16:19:31 +02:00
Ragnor Comerford
cc2412dc65
Rename repo terminology to graph (#118)
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2026-05-24 16:46:00 +01:00
Andrew Altshuler
aadfa11ecb
schema: HTTP allow_data_loss exposure + e2e drop coverage (MR-694 follow-up) (#107)
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The schema-lint chassis v1.2 (PR #100) shipped `--allow-data-loss` on
the CLI, but `SchemaApplyRequest` had no equivalent field — Hard-mode
drops were CLI-only. This commit closes that feature gap and adds e2e
test coverage for drop modes across HTTP + CLI, plus data preservation
on additive apply, plus a CLI↔SDK plan-parity assertion.

Feature gap closed:

- `crates/omnigraph-server/src/api.rs` — added `allow_data_loss: bool`
  (default false via `#[serde(default)]`) to `SchemaApplyRequest`.
  Added `Default` derive so test usages can use `..Default::default()`.
- `crates/omnigraph-server/src/lib.rs` — `server_schema_apply` now
  constructs `SchemaApplyOptions { allow_data_loss: request.allow_data_loss }`
  and threads through to `apply_schema_as`.
- `crates/omnigraph-cli/src/main.rs` — remote-URI schema-apply path
  used to bail with "--allow-data-loss not yet supported on remote";
  now forwards the flag into the JSON payload so the CLI behaves
  identically against local and remote URIs.
- `openapi.json` — regenerated; only diff is the new field on
  `SchemaApplyRequest`.

Tests added (8 new):

* `crates/omnigraph-server/tests/server.rs` (+5):
  - `schema_apply_route_soft_drops_property_via_http` — POST schema
    removing nullable property, verify catalog reflects the drop AND
    `snapshot_at_version(pre)` still has `age` in the field list
    (time-travel reachability is the Soft contract).
  - `schema_apply_route_soft_drops_node_type_via_http` — POST schema
    removing `Company` node + cascading `WorksAt` edge.
  - `schema_apply_route_hard_drops_property_with_allow_data_loss` —
    POST with `allow_data_loss: true`, verify plan step reports
    `mode: hard`.
  - `schema_apply_route_keeps_drops_soft_without_flag` — same schema
    without flag, verify `mode: soft`. Pins default semantics against
    accidental Hard promotion.
  - `schema_apply_route_additive_property_preserves_existing_rows` —
    load fixture, POST adding nullable property, verify row count
    preserved (SDK suite covers data preservation on drops + renames;
    additive AddProperty wasn't pinned).
  Plus helpers `schema_without_age` and `schema_without_company`.

* `crates/omnigraph-cli/tests/cli.rs` (+3):
  - `schema_apply_allow_data_loss_flag_promotes_drops_to_hard` — CLI
    `omnigraph schema apply --allow-data-loss --schema X.pg --json`,
    verify plan step has `mode: hard`.
  - `schema_apply_without_allow_data_loss_keeps_soft_drops` — without
    flag, verify Soft.
  - `schema_plan_parity_cli_and_sdk` — same `.pg` source through
    `Omnigraph::plan_schema` (SDK) and `omnigraph schema plan --json`
    (CLI), assert the steps array is byte-identical post-JSON. HTTP
    has no `/schema/plan` endpoint; apply-side parity is implicitly
    covered by the HTTP drop tests + CLI drop tests using identical
    fixtures.

Docs:

- `docs/user/schema-language.md` — new "Destructive drops" section
  documenting Soft vs Hard semantics and that `allow_data_loss` is
  now honored uniformly across CLI / HTTP / SDK.

Verification: every new test passes; full `cargo test --workspace --locked`
green; `scripts/check-agents-md.sh` passes.

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
2026-05-19 01:56:46 +03:00
Andrew Altshuler
f3f2a051ba
policy: server 3-state default-deny matrix (MR-723) (#105)
Closes the "tokens but no policy" trap. Pre-MR-723, an operator who
configured bearer tokens and forgot to set policy.file got a server
that required auth and then permitted every action — the illusion of
protection. After MR-723, that configuration is default-deny: only
`read` actions succeed; every other action returns HTTP 403.

Three startup states, classified deterministically:

- **Open** — no tokens, no policy. Requires explicit
  `--unauthenticated` flag or `OMNIGRAPH_UNAUTHENTICATED=1`; otherwise
  `serve()` refuses to start. Forces the operator to opt in to
  "fully open dev mode" so it can't happen accidentally.
- **DefaultDeny** — tokens configured, no policy. `authorize_request`
  rejects every action except `Read` with 403. The warn-log on
  startup names the misconfiguration explicitly.
- **PolicyEnabled** — policy file configured. Cedar evaluates every
  request, unchanged from pre-MR-723.

What landed:

- `ServerConfig.allow_unauthenticated: bool` + `--unauthenticated` flag
  on the `omnigraph-server` bin + `OMNIGRAPH_UNAUTHENTICATED` env var
  (`load_server_settings` honors both).
- New `classify_server_runtime_state(has_tokens, has_policy,
  allow_unauthenticated) -> Result<ServerRuntimeState>` pure function.
  `serve()` calls it before opening the engine and bails with a clear
  error when the operator hits the no-tokens-no-policy-no-flag cell.
- `authorize_request` state-2 branch: when `policy_engine()` is None
  but the bearer-auth middleware delivered an authenticated actor, any
  action other than `Read` returns 403 with a message that names the
  misconfiguration.
- `AppState::with_policy_engine(self, engine)` builder method so
  integration tests that need a custom workload (`new_with_workload`)
  can still install a permit-all policy without a new constructor.
- `app_for_loaded_repo_with_auth(token)` and
  `app_for_loaded_repo_with_auth_tokens(tokens)` test helpers now
  install a permit-all policy alongside tokens — they previously
  represented the "tokens but no policy" state that MR-723 makes
  default-deny, and tests that don't care about policy were
  inadvertently coupled to the loophole.

Tests:

- `classify_*` unit tests (3) — every cell of the matrix.
- `default_deny_mode_allows_read_for_authenticated_actor` — GET
  /snapshot succeeds with bearer token + no policy.
- `default_deny_mode_rejects_change_with_forbidden` — POST /change
  rejected with 403 + "default-deny" message.
- `default_deny_mode_rejects_schema_apply_with_forbidden` — POST
  /schema/apply rejected with 403 + "default-deny" message.
- New `app_for_repo_with_auth_tokens_only(schema, tokens)` helper
  builds the State-2 fixture without policy. The pre-MR-723 helpers
  `app_for_loaded_repo_with_auth*` shift semantics to "tokens +
  permit-all" so existing tests retain their original intent.

docs/user/policy.md: new "Server runtime states (MR-723)" section
documents the matrix and the explicit `--unauthenticated` opt-in.

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
2026-05-18 17:02:26 +03:00
Andrew Altshuler
a275306a15
policy: CLI policy injection — local writes go through engine enforce (MR-722) (#104)
Closes the CLI side of the policy chassis fan-out. Before this commit,
CLI direct-engine writes bypassed Cedar entirely because the CLI never
called `Omnigraph::with_policy(...)` for non-`policy validate|test|explain`
subcommands. After this commit, every CLI direct-engine writer
(change, load, ingest, branch create/delete/merge, schema apply) opens
the engine via a new `open_local_db_with_policy(uri, &config)` helper
that installs the configured `PolicyEngine` when `policy.file` is set,
and threads the resolved actor through to the `_as` writer methods.

Actor identity resolution:

- New top-level `--as <ACTOR>` global flag on the CLI overrides config.
- New `cli.actor` field in `omnigraph.yaml` provides a default actor.
- Precedence: `--as` > `cli.actor` > None.
- When policy is configured and neither is set, the engine-layer
  footgun guard fires and the write is denied — silent bypass via
  "I forgot the actor" is exactly what the guard prevents.
- Remote HTTP writes ignore both — bearer-token-resolved server-side.

Helpers added in main.rs:

- `open_local_db_with_policy(uri, &config) -> Result<Omnigraph>` —
  opens the DB and installs the PolicyEngine when configured. Without
  policy this is identical to a bare `Omnigraph::open`.
- `resolve_cli_actor(cli_as, &config) -> Option<&str>` — implements
  the flag > config > None precedence.

Engine: added `load_file_as` to the loader as the actor-aware mirror of
`load_file`, so CLI file-path loads flow through the same enforce gate
as in-memory `load_as` calls.

Test rewrite: `local_cli_policy_tooling_is_end_to_end_while_local_writes_stay_unenforced`
was the explicit assertion of the pre-chassis hole. Renamed and split:

- `local_cli_policy_tooling_is_end_to_end` — sanity for the read-only
  policy CLI surfaces (validate/test/explain), unchanged behavior.
- `local_cli_change_enforces_engine_layer_policy` — the new assertion:
  policy installed + no actor → footgun-guard denial; `--as act-bruno`
  on protected main → Cedar denial; `--as act-ragnor` (admins-write
  rule) on main → permit, write committed.

POLICY_E2E_YAML gains an `admins-write` rule so the permit case has
a non-trivial actor to exercise.

docs/user/policy.md updated with `cli.actor` + `--as <ACTOR>` usage.

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
2026-05-18 04:06:21 +03:00
Andrew Altshuler
da42beec41
policy: chassis fan-out — _as variants on the remaining 6 writers (MR-722) (#103)
PR #102 wired apply_schema_as. This PR completes the chassis-side
coverage so every public mutating engine entry point hits the same
Omnigraph::enforce(action, scope, actor) gate regardless of transport:

- mutate_as → enforce(Change, Branch(branch), actor)
- load_as → enforce(Change, Branch(branch), actor)
- ingest_as → enforce(Change, Branch(branch), actor); also threads
  actor through the implicit branch_create_from_as so fresh-branch
  ingest correctly hits BranchCreate too
- branch_create_as → enforce(BranchCreate, TargetBranch(name), actor)
- branch_create_from_as → enforce(BranchCreate,
  BranchTransition { source, target }, actor)
- branch_delete_as → enforce(BranchDelete, TargetBranch(name), actor)
- branch_merge_as → enforce(BranchMerge,
  BranchTransition { source, target }, actor)

Three new _as variants for branch ops (create, create_from, delete)
that had no actor surface before; existing actor-less variants delegate
with actor=None so the no-policy path is a strict no-op.

HTTP handlers updated to thread the resolved actor into the new _as
variants for branch_create and branch_delete (was previously dropped).

14 new SDK chassis tests (one allow + one deny pair per wired writer);
the existing 4 apply_schema_as tests stay. All 18 pass.

docs/user/policy.md updated to describe engine-wide enforcement and the
coarse-vs-fine layer split (engine = action gate, query layer per-row =
MR-725 future). AGENTS.md capability matrix updated to match.

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
2026-05-18 03:38:18 +03:00
Andrew Altshuler
7a86f654d4
policy: codify signed-token-claim-only actor identity (MR-731) (#101)
Warm-up commit for the policy chassis epic (MR-722). PR #1 of the
chassis series — same role as schema-lint v1's commit #1 baseline.
Zero behavioral change; establishes the regression test, the
load-bearing doc comment, and the user-doc paragraph for an
invariant already true in code.

Server auth already resolves `actor_id` from the matched bearer
token at `omnigraph-server/src/lib.rs:692-694`, overwriting whatever
the handler put in the PolicyRequest. The principle is named in
docs/dev/invariants.md Hard Invariant 11 ("clients cannot set actor
identity directly"). What was missing: a regression test, a
load-bearing doc comment at the resolution site, and a user-facing
documentation paragraph. This commit adds all three.

Why first. The actor-identity invariant is the foundation every
other policy decision stands on. If `actor_id` can be spoofed, every
chassis primitive (per-row scope, audit log, two-person rule)
becomes ungated. Pinning the invariant first means PR #2 (the
chassis core) doesn't have to re-prove this assertion.

Changes:

* crates/omnigraph-server/tests/server.rs — new regression test
  actor_id_resolves_from_bearer_token_ignoring_client_supplied_headers
  with three sub-assertions:
  - spoof-up: bearer for denied actor + X-Actor-Id naming allowed
    actor → 403 (header doesn't promote)
  - spoof-down: bearer for allowed actor + X-Actor-Id naming denied
    actor → 200 (header doesn't demote)
  - empty-string spoof: empty X-Actor-Id doesn't clear resolved actor
  Cross-link to MR-777 (auth boundary cases — actor-id collision +
  malformed bearer) noted in the test docstring.

* crates/omnigraph-server/src/lib.rs — expanded doc comment at
  the actor-resolution site explaining the SECURITY INVARIANT,
  citing Hard Invariant 11, the Supabase RLS history footgun, and
  the regression test that pins the contract. Reader thinking "I
  should let clients override actor_id for impersonation" hits
  this comment first.

* docs/user/policy.md — new "Actor identity (signed-claim-only)"
  section near the existing Server enforcement section. Closes the
  user-facing doc gap MR-731's "Done when" requires.

Architectural decisions for PR #2+ pinned this session (not
implemented here, recorded so future implementers don't re-litigate):
- PolicyEngine moves to new `omnigraph-policy` workspace crate so
  both engine and server can depend on it (Q2).
- `enforce(action, scope, actor)` will take a new `ResourceScope`
  enum, leaving room for MR-725's per-type and per-row variants (Q3).
- `PolicyAction::Admin` is kept and wired (Option A) — meta-action
  for policy-management surfaces (hot reload, audit log query,
  approvals list) as those consumer features land (Q4).

Test results:
- cargo test -p omnigraph-server --test server: 45 pass (44 existing
  + 1 new); no regressions
- scripts/check-agents-md.sh: passes (34 links / 33 docs OK)

Out of scope (PR #2+):
- Omnigraph::with_policy() + enforce() method
- omnigraph-policy crate creation
- ResourceScope enum
- CLI policy injection into Omnigraph
- HTTP-layer redundant-check removal
- MR-724 Admin action wiring (PR #2)
- MR-723 default-deny 3-state (PR #4)
- MR-736 severity warn/deny (PR #5)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
2026-05-17 02:51:34 +03:00
Andrew Altshuler
60eee78465
docs: split user and developer docs (#93) 2026-05-15 03:45:22 +03:00