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* docs(cli): fix cluster apply semantics — converges graphs+schema, not config-only `cluster apply` creates graphs, applies schema updates (soft drops), writes stored-query/policy catalog resources, and executes approved graph deletes in one ordered run. Both the user docs and the shipped CLI help text still described it as a "Stage 3A" config-only (query/policy) subset that defers graph/schema changes "to a later stage" — wrong since the graph/schema executor landed. - docs/user/cli/reference.md: rewrite the cluster paragraph to describe apply's actual converge behavior; keep deferred for the genuinely-unsupported case (standalone schema deletes); drop the stale "Stage 3A" / "reserved for later stages" framing. - crates/omnigraph-cli/src/cli.rs: fix the `cluster apply` help text to match. Part of the docs/user coherence cleanup (docs/dev/docs-issues.md, P1). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FQ1Hf4eXLsJmeLUkTYBEw7 * docs(server): align stored-query exposure with cluster-only behavior server.md documented a per-query expose knob ("`mcp.expose` defaults to true; set `mcp: { expose: false }` to hide from the catalog") that does not exist in the only deployment mode. Cluster-only serving lists every stored query: the cluster registry has no expose field (`QueryConfig { file }`) and the boot bridge hardcodes `expose: true` for all cluster queries (omnigraph-server settings), and there is no GQ-level expose annotation. This contradicted clusters/config.md, which already states the correct behavior. Replace the knob bullet with the cluster truth (every applied query is listed; per-query exposure may become a Cedar-policy decision later) and drop the "`mcp.expose` stored queries" phrasing from the catalog description, the endpoint table, and the intro. The `mcp_expose` JSON catalog field is unchanged (still emitted, always true in cluster mode). Part of the docs/user coherence cleanup (docs/dev/docs-issues.md, P1). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FQ1Hf4eXLsJmeLUkTYBEw7 * docs(schema): split direct/embedded vs cluster-managed schema apply schema/index.md claimed `allow_data_loss` is "honored uniformly across transports" and listed HTTP `POST /schema/apply` among them. But that route is 409-disabled for cluster-backed serving (already documented in server.md), and cluster-managed graphs evolve only through `cluster apply` with soft drops — there is no cluster HTTP data-loss path. Scope the data-loss flag to the direct/embedded path (`schema apply --store`, SDK), and add a paragraph: cluster-managed graphs use `cluster apply` (soft drops only); HTTP `POST /schema/apply` is 409 for cluster serving; direct apply against a cluster-managed path is refused. Cross-refs server + cluster docs. Part of the docs/user coherence cleanup (docs/dev/docs-issues.md, P2). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FQ1Hf4eXLsJmeLUkTYBEw7 * docs(server): document /load as canonical in limits + admission prose The endpoint table already listed both `/load` (canonical) and `/ingest` (deprecated alias) at 32 MB, but the admission-control, body-limit, rate-limit, and manifest-conflict prose named only `/ingest` — and the constants page called the limit "Ingest body limit". Add `/load` alongside (or ahead of) `/ingest` everywhere, and rename the constant to "Load (bulk-write) body limit" noting the `/ingest` alias shares it. Part of the docs/user coherence cleanup (docs/dev/docs-issues.md, P2). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FQ1Hf4eXLsJmeLUkTYBEw7 * docs(cli): drop stale bearer-token keys + fix version string The "Bearer token resolution (CLI)" section still listed removed omnigraph.yaml keys (`graphs.<name>.bearer_token_env`, `auth.env_file`) — config surfaces that no longer exist and that implied plaintext tokens in config. Replace it with a pointer to the keyed-credential model documented above (`OMNIGRAPH_TOKEN_<NAME>` → `~/.omnigraph/credentials` → `OMNIGRAPH_BEARER_TOKEN`). Also fix the `version` row: the CLI prints 0.7.x, not 0.3.x. Part of the docs/user coherence cleanup (docs/dev/docs-issues.md, P2 + smaller). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FQ1Hf4eXLsJmeLUkTYBEw7 * docs: route-spelling note + drop stale stage/deferred crumbs - server.md: add a one-line note that the per-graph subsections name routes in shorthand (`GET /queries`, `POST /query`, `POST /mutate`, `POST /queries/{name}`) but every one is served under `/graphs/{id}/…` — the endpoint table is already fully-qualified. - clusters/config.md: redefine the `deferred` plan disposition as an unsupported change (e.g. a standalone schema delete) instead of "graph/schema change, later phase" (graph creates and schema updates apply now); drop the "Stage 2C" label from the lock-recovery note. - search/indexes.md: `ingest --mode merge` → canonical `load --mode merge`. Part of the docs/user coherence cleanup (docs/dev/docs-issues.md, P2 + smaller). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FQ1Hf4eXLsJmeLUkTYBEw7 * docs(dev): track user-docs coherence ledger; mark 2026-06-20 findings resolved Convert the scratch review notes into a tracked living ledger and link it from the dev index. All ten findings from the 2026-06-20 docs/user sweep are validated and fixed in this branch (P1 cluster-apply semantics + stored-query exposure; P2 schema-apply paths, /load canonical, bearer-token keys, route shorthand; plus version/ingest/deferred/stage crumbs). The verification grep checklist is retained for future audits. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FQ1Hf4eXLsJmeLUkTYBEw7 * docs(api): align GET /queries OpenAPI contract with cluster-only behavior Greptile P1 on #293: the prose fix in server.md left the OpenAPI surface stale. The utoipa annotations (handlers.rs, omnigraph-api-types QueriesCatalogOutput) still described the catalog as "the `mcp.expose == true` subset", and those drive the checked-in openapi.json — so SDK consumers read a contract the cluster-only server does not honor (it lists every stored query). Update the three Rust doc-comment/annotation strings to "every stored query" and regenerate openapi.json (OMNIGRAPH_UPDATE_OPENAPI=1; drift test green) in the same change, per AGENTS.md rule 4. Ledger updated: this finding resolved, plus the cross-repo drift it surfaced (omnigraph-ts generated spec/types and omnigraph-cookbooks best-practices bearer_token_env) tracked as open follow-ups. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FQ1Hf4eXLsJmeLUkTYBEw7 --------- Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Constants & Tunables (cheat sheet)
| Name | Value | Area |
|---|---|---|
MANIFEST_DIR |
__manifest |
manifest layout |
| Commit graph dir | _graph_commits.lance |
commit graph |
| Run registry dir (legacy, removed) | _graph_runs.lance |
inert post-v0.4.0; bytes remain until a prefix-delete primitive lands |
| Run branch prefix (legacy, removed) | __run__ |
swept off __manifest by the internal schema migration; no longer a reserved name |
| Schema apply lock | __schema_apply_lock__ |
schema apply |
| Manifest publisher retry budget | PUBLISHER_RETRY_BUDGET = 5 |
manifest publish |
| Internal manifest schema version | INTERNAL_MANIFEST_SCHEMA_VERSION = 3 |
manifest migrations |
| Merge stage batch | MERGE_STAGE_BATCH_ROWS = 8192 |
merge execution |
| Maintenance concurrency | OMNIGRAPH_MAINTENANCE_CONCURRENCY=8 |
optimize/cleanup |
| Lance blob compaction support | LANCE_SUPPORTS_BLOB_COMPACTION = false |
optimize |
| Graph index cache size | 8 (LRU) |
runtime cache |
| Expand indexed-path frontier ceiling | OMNIGRAPH_EXPAND_INDEXED_MAX_FRONTIER=1024 |
traversal |
| Expand indexed-path hop ceiling | OMNIGRAPH_EXPAND_INDEXED_MAX_HOPS=6 |
traversal |
| Expand CSR-build cost factor | CSR_BUILD_FACTOR = 1.5 |
traversal |
| Expand mode override | OMNIGRAPH_TRAVERSAL_MODE (indexed|csr; unset = cost-based auto) |
traversal |
| Default body limit | 1 MB |
HTTP server |
| Load (bulk-write) body limit | 32 MB |
HTTP server (/load; shared by the deprecated /ingest alias) |
| Default embed provider/model | openai-compatible / openai/text-embedding-3-large |
engine embedding |
| OpenAI-direct embed model | text-embedding-3-large |
engine embedding |
| Gemini-direct embed model | gemini-embedding-2 |
engine embedding |
| Embed deadline | OMNIGRAPH_EMBED_DEADLINE_MS=60000 |
engine embedding |
| Embed timeout | OMNIGRAPH_EMBED_TIMEOUT_MS=30000 |
engine embedding |
| Embed retries | OMNIGRAPH_EMBED_RETRY_ATTEMPTS=4 |
engine embedding |
| Embed retry backoff | OMNIGRAPH_EMBED_RETRY_BACKOFF_MS=200 |
engine embedding |
| LANCE memory pool default | 1 GB (raised in v0.3.0) |
runtime |
Expand traversal dispatch. With OMNIGRAPH_TRAVERSAL_MODE unset, the engine
chooses the indexed (per-hop BTREE) vs CSR (whole-graph in-memory) path with a
cost model over cheap manifest counts (frontier size, |E|, source-vertex count,
hops) plus the index-coverage signal: the indexed path is preferred when its
frontier-relative work beats building the CSR (≈ when hops × frontier is a
small fraction of the source-vertex set), and CSR is preferred for dense/deep
traversals or when the BTREE coverage is degraded and a full scan would be paid
per hop. The two ceilings bound the initial dispatch frontier/hops (beyond
them CSR is always used); they are not a hard per-hop bound — the cost model
estimates total indexed work as ~hops × frontier × fanout, so dense fan-out is
priced toward CSR rather than capped mid-traversal. The override flag forces a path (the auto result is identical either way;
only the path differs).