* 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>
Document the optional @embed model kwarg, the query-time same-space rejection, model-string strictness, and the loud schema-apply refusal on model change. Mark RFC-012 phases 1-4 implemented.
openai-alias host (Cursor): OMNIGRAPH_EMBED_PROVIDER=openai now defaults its base URL to https://api.openai.com/v1 (model text-embedding-3-large), while openai-compatible/unset keep the OpenRouter gateway default. The default is derived from the alias rather than the Provider enum, so an operator's stated intent can no longer be silently routed to OpenRouter; an explicit OMNIGRAPH_EMBED_BASE_URL still wins. New test from_env_openai_alias_uses_openai_host_not_openrouter.
single model source of truth (Cursor): remove the EmbedSpec.model field. The provider config is authoritative for the model, so a spec can no longer declare a model that is silently ignored while the API uses another (the wrong-space-vectors footgun); the embed summary reports the model actually resolved. Correct by construction rather than a truthful-echo patch.
stale @embed docs (Codex): docs/user/schema/index.md and docs/dev/execution.md still claimed @embed embeds at ingest; corrected to the real contract (catalog annotation; vectors supplied or pre-filled by 'omnigraph embed'). Also documented the openai-vs-OpenRouter base default in embeddings.md.
Greptile's RFC-status note is declined: the repo lifecycle keeps an RFC Status: Proposed while its PR is open and flips to Accepted on merge.
Remove developer-only scaffolding that leaked into the public user/operator
docs, while preserving every user-facing behavior, command, flag, endpoint,
constant, and env var. No behavior changes.
Removed across 18 files:
- internal ticket / sequencing refs (MR-NNN, RFC-NNN, "Phase N");
- source-code paths (crates/**/*.rs, *.pest) and internal struct/function
dumps (e.g. the QueryIR / GraphCommit / SchemaMigrationPlan Rust types,
internal fn names like fork_branch_from_state, optimize_all_tables);
- Lance-internal blocker prose (upstream issue numbers, blob-decode cause,
sidecar Phase-B/C mechanics) — keeping the user-visible behavior (e.g.
"optimize skips Blob-column tables; reads/writes unaffected");
- pre-v0.4.0 Run-state-machine archaeology.
Internal IR/lowering/recovery-internals sections were either trimmed to a
brief user-facing note (e.g. "Traversal execution", "interrupted writes
recover automatically; recovery commits are recorded under actor
omnigraph:recovery") or removed.
Kept: all language syntax, lint codes, Cedar actions/scopes, endpoints,
error taxonomy, every constant and env var (verified none dropped from the
constants cheat-sheet), and the operator-facing explanations of on-disk
artifacts. Residual "legacy" mentions are all user-facing (the deprecated
omnigraph.yaml, the legacy token chain, old command names).
Verified: zero internal-scaffolding leaks (MR/RFC/Phase/.rs/.pest = 0) across
docs/user; zero broken links; check-agents-md.sh green.
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
Move the 23 flat docs/user/*.md files into topic subdirectories so the
user guide is organized by area (schema, queries, search, branching, cli,
operations, clusters, concepts, reference) instead of a flat list. This is
a pure structural move — whole files relocated, every cross-doc link
recomputed, no prose rewrites or content splits (those follow in Phase 2).
- 19 `git mv`s (install.md, deployment.md stay top-level); history preserved
(renames detected at 92–100% similarity).
- All intra-doc links, AGENTS.md's topic table (52 pointers), and the
docs/dev + docs/releases back-links recomputed via relpath from each
file's new location.
- docs/user/index.md rewritten as a sectioned nav hub.
- Fixed 5 doc-path references in Rust (comments + two user-facing server
settings error strings) to point at the new locations.
Verified: zero broken .md links across tracked docs; check-agents-md.sh
green (with the untracked scratch docs set aside); touched crates build.
Note: the public site (omnigraph-web) imports docs/ via a flat-only script;
its import-docs.mjs needs a subdir-aware update before the next re-sync.
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
