feat!: delete the legacy OmnigraphConfig + config migrate; finish the omnigraph.yaml docs sweep (#252)

* refactor(cli): own ReadOutputFormat/TableCellLayout in the CLI

The two output-presentation enums lived in `omnigraph-server::config` and were
re-exported for the CLI, even though the server never used them. Move both
definitions into `omnigraph-cli/src/read_format.rs` (where the renderer already
lives) and drop them from the server's public re-export. This is a step toward
deleting the legacy `omnigraph-server::config` module entirely — a CLI
presentation concern has no business in the server crate.

No behavior change. The server keeps private copies in `config.rs` only for the
soon-to-be-deleted legacy `CliDefaults`.

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

* feat(cli)!: remove the `config migrate` command and migrate.rs

`config migrate` was the last CLI consumer of the legacy `omnigraph.yaml`
(`OmnigraphConfig` + `load_config`). With the excision complete there is no
legacy file to split, so the whole `omnigraph config` command group is removed
along with `migrate.rs`. The `OmnigraphConfig` type, `load_config`, and the
deprecation machinery are deleted next.

- Remove `Command::Config` / `ConfigCommand` from the clap surface and the
  dispatch arm; drop `mod migrate;` and the now-unused `load_config` import.
- Drop the `Command::Config` arms in `planes.rs`.
- Delete the `config_migrate_splits_legacy_config` integration test.

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

* feat(server)!: delete the legacy OmnigraphConfig type and load_config

With `config migrate` gone, nothing loads `omnigraph.yaml` anymore. Delete the
entire `omnigraph-server::config` module: the `OmnigraphConfig` type and its
sub-structs (`ProjectConfig`, `TargetConfig`, `CliDefaults`, `ServerDefaults`,
`AuthDefaults`, `QueryDefaults`, `AliasConfig`, `AliasCommand`, `PolicySettings`,
`QueryEntry`, `McpSettings`), `load_config`, and the RFC-008 deprecation
machinery (`OMNIGRAPH_CONFIG`, `OMNIGRAPH_NO_LEGACY_CONFIG`,
`OMNIGRAPH_SUPPRESS_YAML_DEPRECATION`, the deprecation map + warner).

- `QueryRegistry::load` (the only `OmnigraphConfig`/`QueryEntry` consumer; its
  only caller was its own test) is removed — server boot and the CLI both build
  registries via `QueryRegistry::from_specs`.
- `graph_resource_id_for_selection` (CLI-only) moves into the CLI
  (`helpers.rs`), with its unit test; the server no longer exports it.
- Drop the already-dead `format_registry_load_errors` helper (config-adjacent).

No behavior change — every deleted item was unreachable after the excision.

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

* docs: purge the legacy omnigraph.yaml surface from the docs

Finish the RFC-011 excision in the docs: the CLI no longer reads omnigraph.yaml
and the server boots cluster-only, so every doc that described the legacy file
as a live config is now wrong.

- AGENTS.md: rewrite the HTTP-server line to cluster-only boot (drop the
  single-graph/flat-route and omnigraph.yaml-boot framing); rewrite the CLI
  two-surface-config passage (drop `config migrate`, the deprecation env vars,
  and "Never extend omnigraph.yaml"); fix the topic table + capability rows.
- cli/reference.md: delete the entire "omnigraph.yaml schema (legacy combined
  file)" section and the `config migrate` row; re-home the `policy` row, the
  bearer-token chain, the actor/format/param-precedence references, and the
  `--config` mentions to the operator config + `--cluster`.
- cli/index.md: rewrite the multi-graph-server + add-graph paragraphs to
  cluster (`--cluster` + `cluster apply`); fix the policy examples to
  `--cluster`; replace the `## Config` omnigraph.yaml example with the
  operator/cluster two-surface model.
- operations/policy.md: rewrite per-graph-vs-server-level policy to the cluster
  `policies:`/`applies_to` model; re-home the actor + CLI tooling sections.
- clusters/config.md, clusters/index.md, deployment.md: server boots from the
  cluster only; per-operator facts come from ~/.omnigraph/config.yaml.
- architecture.md, testing.md: drop the stale omnigraph.yaml / deleted-test
  references.

RFCs, design specs, and prior release notes are left as historical records.

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

---------

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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@ -20,7 +20,7 @@ Server-scoped action (v0.6.0+; binds to `Omnigraph::Server::"root"`):
10. `graph_list``GET /graphs` registry enumeration (multi-graph mode)
Server-scoped actions cannot use `branch_scope` or `target_branch_scope` — they operate on the registry, not on a graph's branches. A rule cannot mix server-scoped and per-graph actions; split into separate rules. (Runtime `graph_create` / `graph_delete` are reserved but not shipped in v0.6.0; operators add/remove graphs by editing `omnigraph.yaml` and restarting.)
Server-scoped actions cannot use `branch_scope` or `target_branch_scope` — they operate on the registry, not on a graph's branches. A rule cannot mix server-scoped and per-graph actions; split into separate rules. (Runtime `graph_create` / `graph_delete` over HTTP are reserved but not shipped; operators add/remove graphs by editing the cluster's `cluster.yaml`, running `omnigraph cluster apply`, and restarting the server.)
## Scope kinds
@ -28,38 +28,34 @@ Server-scoped actions cannot use `branch_scope` or `target_branch_scope` — the
- `target_branch_scope` — applied to destination (`schema_apply`, branch ops, run ops)
- `protected_branches` — named list with special rules; rule scopes are `any | protected | unprotected`
## Per-graph vs. server-level policy (multi-graph mode)
## Per-graph vs. server-level policy
In multi mode (`omnigraph.yaml` with a non-empty `graphs:` map), policy files attach at two levels:
A server boots from a cluster (`--cluster <dir>`), and the cluster's
`cluster.yaml` declares its policy bundles in a `policies:` section. Each bundle
names the scopes it `applies_to`: a graph id (per-graph rules — `read`, `change`,
`branch_*`, `schema_apply`) or the literal `cluster` (server-level rules —
`graph_list`).
```yaml
server:
policy:
file: server-policy.yaml # server-level: graph_list
graphs:
# cluster.yaml
policies:
base:
file: base.policy.yaml
applies_to: [cluster, knowledge] # cluster-level + the `knowledge` graph
alpha:
uri: s3://tenant-bucket/alpha
policy:
file: policies/alpha.yaml # per-graph: read, change, branch_*, schema_apply
beta:
uri: s3://tenant-bucket/beta
# no per-graph policy → no engine-layer Cedar enforcement on beta
file: policies/alpha.yaml
applies_to: [alpha] # per-graph: alpha only
```
**Config follows graph identity, not server mode.** A graph served by **name**
(`--target <name>` or `server.graph`) uses its own `graphs.<name>.policy.file`,
exactly as in multi-graph mode. Top-level `policy.file` applies only to an
**anonymous** graph — one served by a bare `<URI>` with no `graphs:` entry.
Serving a **named** graph (single- or multi-graph mode) while top-level
`policy.file` (or `queries:`) is populated **refuses boot**, naming the block,
since the top-level value would otherwise be silently shadowed by the per-graph
block. Move per-graph rules to `graphs.<graph_id>.policy.file` and `graph_list`
rules to `server.policy.file`.
A graph with no bundle bound to it has no engine-layer Cedar enforcement. Each
graph's HTTP request flows through its bound bundle; the management endpoint
(`GET /graphs`) flows through the `cluster`-scoped bundle. When no bundle binds
`cluster`, `GET /graphs` is denied in every runtime state, including
`--unauthenticated`; with bearer tokens configured it returns 403 after admission
control because `graph_list` is not a `read`-equivalent action. The operator must
bind a `cluster`-scoped bundle granting `graph_list` to expose `/graphs`.
Each graph's HTTP request flows through its own per-graph policy. The management endpoint (`GET /graphs`) flows through the server-level policy. When `server.policy.file` is unset, `GET /graphs` is denied in every runtime state, including `--unauthenticated`; with bearer tokens configured, it returns 403 after admission control because `graph_list` is not a `read`-equivalent action. The operator must explicitly authorize via `server-policy.yaml` to expose `/graphs`.
Example server-level policy:
Example `cluster`-scoped bundle:
```yaml
version: 1
@ -72,38 +68,26 @@ rules:
actions: [graph_list]
```
## Configuration
Each per-graph rule may use at most one of `branch_scope` or
`target_branch_scope`. Server-scoped rules (`graph_list`) take neither — they
have no branch context.
`omnigraph.yaml`:
## Actor for direct-engine writes
```yaml
policy:
file: policy.yaml # Cedar rules + groups
tests: policy.tests.yaml # declarative test cases
cli:
actor: act-andrew # default actor for CLI direct-engine writes
```
Each per-graph rule may use at most one of `branch_scope` or `target_branch_scope`. Server-scoped rules (`graph_list`) take neither — they have no branch context.
`cli.actor` is the default actor identity for CLI direct-engine writes
when `policy.file` is configured. Override per-invocation with `--as
<ACTOR>` (top-level flag) — `--as` wins, otherwise `cli.actor` is used,
otherwise no actor. With policy configured and neither set, the
engine-layer footgun guard intentionally denies the write (silent bypass
via "I forgot the actor" is exactly what the guard prevents). Remote
HTTP writes ignore both — they resolve their actor server-side from the
bearer token.
The default actor identity for CLI direct-engine (`--store`) writes is
`operator.actor` in `~/.omnigraph/config.yaml`. Override per-invocation with
`--as <ACTOR>``--as` wins, otherwise `operator.actor`, otherwise no actor.
Remote HTTP writes ignore both — they resolve their actor server-side from the
bearer token. (Direct-store access carries no Cedar policy under RFC-011; policy
lives in the cluster/server.)
## CLI
Policy tooling resolves its graph like server single-mode policy: `cli.graph`
wins, otherwise `server.graph` is used, otherwise the top-level `policy.file`
is validated/tested/explained as the anonymous policy.
Policy tooling reads a cluster's applied policy bundles: pass `--cluster <dir>`,
and `--graph <id>` to pick a graph's bundle when several apply.
- `omnigraph policy validate` — parse + count actors, exit 1 on parse error.
- `omnigraph policy test` — run cases in `policy.tests.yaml`, exit 1 on any expectation mismatch.
- `omnigraph policy test --tests <file>` — run the declarative cases in `<file>` against the selected bundle, exit 1 on any expectation mismatch.
- `omnigraph policy explain --actor … --action … [--branch …] [--target-branch …]` — show decision and matched rule.
- `omnigraph --as <ACTOR> <subcommand>` — set the actor for the duration of one invocation. Effective for `change`, `load` (and its deprecated `ingest` alias), `branch create|delete|merge`, and `schema apply` against a direct (`--store`) graph. **Rejected** on a served write (`--server`): the actor is bearer-token-resolved server-side, so `--as` can't set it there.
@ -132,7 +116,7 @@ reaches the authorization gate without a matching policy permit.
|---|---|---|---|
| **Open** | no | no | Every request is permitted. Refuses to start unless `--unauthenticated` or `OMNIGRAPH_UNAUTHENTICATED=1` is set — the operator must explicitly opt in. |
| **DefaultDeny** | yes | no | Every authenticated request for an action other than `read` is rejected with HTTP 403. Closes the "tokens but forgot the policy file" trap — an operator who sets up auth and forgot to point at a policy file used to ship the illusion of protection. |
| **PolicyEnabled** | yes | yes | Authenticated requests that reach a configured policy engine are evaluated by Cedar. Server-scoped actions still require `server.policy.file`. |
| **PolicyEnabled** | yes | yes | Authenticated requests that reach a configured policy engine are evaluated by Cedar. Server-scoped actions still require a `cluster`-scoped policy bundle. |
The server refuses to start for the "no tokens, no policy, no flag" cell
and for "policy file, no tokens" — instead of silently shipping an open