[codex] fix RFC-011 follow-up regressions (#258)

* fix rfc-011 follow-up regressions

* test(cli): remove served schema-apply tests obsoleted by the cluster 409

This PR disables server-side schema apply for cluster-backed serving (409 →
`omnigraph cluster apply`). Two system_local tests still drove *served* schema
apply against a spawned `--cluster` server and asserted the pre-409 behavior, so
they failed under `cargo test --workspace`:

- `local_cli_schema_apply_enforces_engine_layer_policy` — expected a per-actor
  policy `denied`/allow on the served route; the route now 409s for everyone
  before policy runs.
- `local_cli_schema_apply_rejects_stored_query_breakage_before_publish` —
  expected a served apply to reject a stored-query breakage; the route now 409s
  before any apply.

Both exercise a path the PR intentionally removed. Their surviving coverage:
the 409 itself is pinned by `schema_routes::schema_apply_route_refuses_cluster_backed_server_mode`
(asserts 409 + no mutation); stored-query-breakage-before-publish stays covered
by `schema_routes::schema_apply_route_rejects_stored_query_breakage_before_publish`
(single-mode); engine-layer schema_apply Cedar enforcement stays covered by
`policy_engine_chassis`. Remove the obsolete served versions.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

* fix(server): report the cluster-backed schema-apply 409 after the Cedar gate

The 409 ("schema apply is disabled for cluster-backed serving") fired at the top
of `server_schema_apply`, before `authorize_request`. An authenticated-but-
unauthorized actor therefore learned the server is cluster-backed (409) instead
of getting a normal 403 — leaking topology before authorization, against the
same posture that keeps `GET /graphs` default-deny.

Move the 409 below the Cedar gate so the route reports 401 → 403 → 409: an
unauthorized actor gets 403, and only an actor authorized for `schema_apply`
sees the actionable "use `omnigraph cluster apply`" 409. (An open/unauthenticated
server still 409s, as it has no topology to protect.)

Regression: `schema_apply_route_cluster_backed_denies_unauthorized_actor_before_409`
(POLICY_YAML grants no schema_apply → act-ragnor gets 403, not 409). Addresses the
bot-review finding on #258.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

docs/user/cli/index.md

@@ -59,10 +59,11 @@ omnigraph commit show --uri graph.omni <commit-id> --json
 
 ## Remote Server Mode
 
-Serve a graph:
+Serve a cluster-applied graph:
 
 ```bash
-omnigraph-server graph.omni --bind 127.0.0.1:8080
+omnigraph cluster apply --config ./company-brain
+omnigraph-server --cluster ./company-brain --bind 127.0.0.1:8080
 ```
 
 Read through the HTTP API — invoke a stored query by name from the catalog:

docs/user/cli/reference.md

@@ -2,7 +2,7 @@
 
 A reference for the `omnigraph` binary's command surface and the per-operator `~/.omnigraph/config.yaml` schema. For a quick-start guide, see [cli.md](index.md).
 
-Top-level command families and subcommands. Graph-targeting commands accept a positional `file://`/`s3://` URI, `--server <name|url>` (an operator-defined server from `~/.omnigraph/config.yaml` by name, or a literal `http(s)://` URL, optionally with `--graph <id>` for multi-graph servers; exclusive with a positional URI), `--store <uri>` (a single graph's storage directly), or `--profile <name>` / `$OMNIGRAPH_PROFILE` (a named scope bundle; see [Scopes & profiles](#scopes--profiles-rfc-011)); `cluster` commands use `--config <dir>`. A remote server is addressed only with `--server` — a positional `http(s)://` URI is rejected. **`query`/`mutate` are the exception**: their positional is a stored-query *name* (RFC-011 D3), not a graph URI, so they address the graph only via `--store`/`--server`/`--profile`/defaults.
+Top-level command families and subcommands. Graph-targeting commands accept a positional `file://`/`s3://` URI, `--server <name|url>` (an operator-defined server from `~/.omnigraph/config.yaml` by name, or a literal `http(s)://` URL, optionally with `--graph <id>` for multi-graph servers; exclusive with a positional URI), `--store <uri>` (a single graph's storage directly), or `--profile <name>` / `$OMNIGRAPH_PROFILE` (a named scope bundle; see [Scopes & profiles](#scopes--profiles-rfc-011)); `cluster` commands use `--config <dir>`, while `policy` and `queries` read a cluster's applied state via `--cluster <dir|uri>`. A remote server is addressed only with `--server` — a positional `http(s)://` URI is rejected. **`query`/`mutate` are the exception**: their positional is a stored-query *name* (RFC-011 D3), not a graph URI, so they address the graph only via `--store`/`--server`/`--profile`/defaults.
 
 ## Top-level commands
 
@@ -13,7 +13,7 @@ Top-level command families and subcommands. Graph-targeting commands accept a po
 | `ingest` | deprecated alias of `load --from <base>` (defaults: `--from main --mode merge`); prints a one-line warning to stderr |
 | `query <name>` (alias: `read`) | run a read query. **Catalog lane** (default): `<name>` is a stored query invoked **by name** from the served catalog (served-only — address with `--server`/`--profile`; the verb asserts the query is a read). **Ad-hoc lane**: with `--query <path>` or `-e`/`--query-string <GQ>`, runs that source (the positional `<name>` then selects which query in it). No positional graph URI — address via `--store`/`--server`/`--profile`. `read` is the deprecated previous name (one-line stderr warning) |
 | `mutate <name>` (alias: `change`) | run a mutation query; same catalog (by-name, served-only, verb asserts mutation) / ad-hoc (`--query`/`-e`) lanes as `query`. `change` is the deprecated previous name (one-line stderr warning) |
-| `alias <name> [args]` | invoke an operator alias — a personal binding (under `aliases:` in `~/.omnigraph/config.yaml`) to a stored query on a named server (RFC-011 D4; replaces the removed `--alias` flag) |
+| `alias <name> [args]` | invoke an operator alias — a read-only personal binding (under `aliases:` in `~/.omnigraph/config.yaml`) to a stored query on a named server (RFC-011 D4; replaces the removed `--alias` flag; stored mutations are rejected before execution) |
 | `snapshot` | print current snapshot (per-table version + row count) |
 | `export` | dump to JSONL on stdout (`--type T`, `--table K` filters) |
 | `branch create \| list \| delete \| merge` | branching ops |
@@ -26,7 +26,7 @@ Top-level command families and subcommands. Graph-targeting commands accept a po
 | `cleanup --keep N --older-than 7d --confirm` | destructive version GC (`--confirm` to execute; also needs `--yes` against a non-local `s3://` target — see *Write diagnostics & destructive confirmation*) |
 | `embed` | offline JSONL embedding pipeline |
 | `policy validate \| test \| explain` | Cedar tooling against a cluster's applied policies (`--cluster <dir>`; `--graph <id>` picks a graph's bundle when several apply). `test` takes `--tests <file>`; `explain` takes `--actor`/`--action`/`--branch`/`--target-branch` |
-| `profile list \| show [<name>]` | read-only inspection of `~/.omnigraph/config.yaml` profiles. `list` shows each profile's binding (server/cluster/store) + default graph and marks the `$OMNIGRAPH_PROFILE`-active one; `show` resolves one profile's scope (endpoint + default graph), defaulting to the active profile, else the flat operator defaults |
+| `profile list \| show [<name>]` | read-only inspection of `~/.omnigraph/config.yaml` profiles. `list` shows each profile's binding (server/cluster/store) + default graph and marks the `$OMNIGRAPH_PROFILE`-active one; JSON keeps `binding` and adds `scope_kind`, `target`, `valid`, and `error`; `show` resolves one profile's scope (endpoint + default graph), defaulting to the active profile, else the flat operator defaults |
 | `version` / `-v` | print `omnigraph 0.3.x` |
 
 ## Command capabilities
@@ -35,13 +35,13 @@ Every command declares the **capability** it needs — what it requires to reach
 
 - **`any`** — `query`, `mutate`, `load`, `ingest`, `branch *`, `snapshot`, `export`, `commit *`, `schema show`, `schema apply`. Run against a graph **served (via a server) or embedded (direct against a store)**: accept a positional `file://`/`s3://` URI, `--server <name|url>` (+ `--graph <id>` for multi-graph servers), `--store <uri>`, or `--profile <name>`. A remote server is addressed with `--server` — a positional `http(s)://` URI does **not** dispatch to one.
 - **`served`** — `graphs list`. Requires a server (accepts `--server` / `--profile`).
-- **`direct`** — `init`, `optimize`, `repair`, `cleanup`, `schema plan`, `queries validate`, `lint`. Need **direct storage access** (`file://` / `s3://`), never through a server. They accept a positional `URI`, but **not** `--server`, and a remote (`http(s)://`) URI is rejected. `optimize` / `repair` / `cleanup` additionally accept **`--cluster <dir|s3://…> --graph <id>`** (`--cluster` is a cluster directory or storage-root URI, named via `clusters:` in `~/.omnigraph/config.yaml` or a literal root), which resolves the graph's storage URI from the served cluster state (so you needn't know the `<storage>/graphs/<id>.omni` layout). `--graph` is the one graph selector across all scopes — on these three verbs it picks the cluster graph; on the other `direct` verbs it does not apply.
-- **`control`** — `cluster *`. Operates on a cluster directory via `--config <dir>`.
-- **`local`** — `policy *`, `embed`, `login`, `logout`, `config`, `version`, `queries list`. Address no graph.
+- **`direct`** — `init`, `optimize`, `repair`, `cleanup`, `schema plan`, `lint`. Need **direct storage access** (`file://` / `s3://`), never through a server. They accept a positional `URI`, but **not** `--server`, and a remote (`http(s)://`) URI is rejected. `optimize` / `repair` / `cleanup` additionally accept **`--cluster <dir|s3://…> --graph <id>`** (`--cluster` is a cluster directory or storage-root URI, named via `clusters:` in `~/.omnigraph/config.yaml` or a literal root), which resolves the graph's storage URI from the served cluster state (so you needn't know the `<storage>/graphs/<id>.omni` layout). `--graph` is the one graph selector across all scopes — on these three verbs it picks the cluster graph; on the other `direct` verbs it does not apply.
+- **`control`** — `cluster *` via `--config <dir>`; `policy *` and `queries *` via `--cluster <dir|uri>` or a cluster profile.
+- **`local`** — `alias`, `embed`, `login`, `logout`, `profile`, `version`. Address no explicit graph scope.
 
 These restrictions are enforced and reported, not silent:
 
-- A scope flag on a verb that can't consume it fails loudly rather than being silently dropped — `--server` outside a served scope, `--cluster` outside the maintenance verbs, or `--graph` where no multi-graph scope applies, e.g.: ``optimize is a direct (storage-native) command; --server addresses a served graph and does not apply. Pass a storage URI, or --cluster <dir> --graph <id>.``
+- A scope flag on a verb that can't consume it fails loudly rather than being silently dropped — `--server` outside a served scope, `--cluster` outside cluster-scoped verbs, or `--graph` where no multi-graph scope applies, e.g.: ``optimize is a direct (storage-native) command; --server addresses a served graph and does not apply. Pass a storage URI, or --cluster <dir> --graph <id>.``
 - A `direct` verb pointed at a remote URI fails loudly, e.g.: ``optimize is a direct (storage-native) command and needs direct storage access; the resolved target is a remote server (https://…). Pass the graph's file:// or s3:// URI.``
 - A data verb pointed at a positional `http(s)://` URI fails loudly: ``a remote graph must be addressed with --server <url> — a positional (or --uri) http(s):// URL no longer dispatches to a server.``
 - `init` into an **established cluster's** storage layout (`<root>/graphs/<id>.omni` where `<root>` holds `__cluster/state.json`) is refused — graphs in a cluster are created by `cluster apply` (which records ledger / recovery / approvals), not `init`.

docs/user/operations/server.md

@@ -40,16 +40,16 @@ graph id from the cluster's applied revision:
 | GET | `/openapi.json` | none | — (strips security if auth disabled; emits the nested cluster paths with `cluster_` operation-id prefix) |
 | GET | `/graphs/{id}/snapshot?branch=` | bearer + `read` | snapshot of branch |
 | POST | `/graphs/{id}/query` | bearer + `read` | inline read query (canonical; clean field names `query`/`name`; mutations → 400) |
-| POST | `/graphs/{id}/read` | bearer + `read` | **deprecated** alias of `/query` (legacy field names `query_source`/`query_name`, byte-stable response; carries `Deprecation: true` + `Link: </query>; rel="successor-version"`) |
+| POST | `/graphs/{id}/read` | bearer + `read` | **deprecated** alias of `/query` (legacy field names `query_source`/`query_name`, byte-stable response; carries `Deprecation: true` + `Link: <query>; rel="successor-version"`) |
 | POST | `/graphs/{id}/export` | bearer + `export` | NDJSON stream |
 | POST | `/graphs/{id}/mutate` | bearer + `change` | mutation (canonical; `query`/`name`; accepts legacy `query_source`/`query_name` as serde aliases) |
-| POST | `/graphs/{id}/change` | bearer + `change` | **deprecated** alias of `/mutate` (carries `Deprecation: true` + `Link: </mutate>; rel="successor-version"`) |
+| POST | `/graphs/{id}/change` | bearer + `change` | **deprecated** alias of `/mutate` (carries `Deprecation: true` + `Link: <mutate>; rel="successor-version"`) |
 | GET | `/graphs/{id}/queries` | bearer + `read` | list the `mcp.expose` stored queries as a typed tool catalog |
 | POST | `/graphs/{id}/queries/{name}` | bearer + `invoke_query` (+ `change` for a stored mutation) | invoke a named query from the `queries:` registry; deny == 404 |
 | GET | `/graphs/{id}/schema` | bearer + `read` | get current `.pg` source |
-| POST | `/graphs/{id}/schema/apply` | bearer + `schema_apply` (target=`main`) | migrate |
+| POST | `/graphs/{id}/schema/apply` | bearer + `schema_apply` (target=`main`) | disabled for cluster-backed serving; returns 409 and points operators at `omnigraph cluster apply` + restart |
 | POST | `/graphs/{id}/load` | bearer + `branch_create` (only when `from` is set and the branch is created) + `change` | bulk load (canonical); branch creation is opt-in via `from` — without it a missing `branch` is a 404, never an implicit fork (32 MB body limit) |
-| POST | `/graphs/{id}/ingest` | bearer + `branch_create` (only when `from` is set and the branch is created) + `change` | **deprecated** alias of `/load` (carries `Deprecation: true` + `Link: </load>; rel="successor-version"`) (32 MB body limit) |
+| POST | `/graphs/{id}/ingest` | bearer + `branch_create` (only when `from` is set and the branch is created) + `change` | **deprecated** alias of `/load` (carries `Deprecation: true` + `Link: <load>; rel="successor-version"`) (32 MB body limit) |
 | GET | `/graphs/{id}/branches` | bearer + `read` | list branches |
 | POST | `/graphs/{id}/branches` | bearer + `branch_create` | create |
 | DELETE | `/graphs/{id}/branches/{branch}` | bearer + `branch_delete` | delete |
@@ -131,8 +131,8 @@ channels:
 - **Response headers (RFC 9745)**: every response carries `Deprecation: true`.
 - **Response headers (RFC 8288)**: every response carries a `Link` header
   pointing at the canonical successor:
-  `Link: </query>; rel="successor-version"` for `/read`, and
-  `Link: </mutate>; rel="successor-version"` for `/change`. SDKs and HTTP
+  `Link: <query>; rel="successor-version"` for `/read`, and
+  `Link: <mutate>; rel="successor-version"` for `/change`. SDKs and HTTP
   proxies can pick the successor up automatically.
 
 Migration is purely cosmetic on the client side — swap the URL path, leave