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

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* 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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@ -78,20 +78,26 @@ literal URL); a positional `http(s)://` URI is rejected. If the server requires
auth, set its bearer token and `omnigraph login <server>` (or
`OMNIGRAPH_BEARER_TOKEN`).
## Multi-graph servers (v0.6.0+)
## Multi-graph servers
Against a multi-graph server (started with `--config omnigraph.yaml` referencing a non-empty `graphs:` map), use `omnigraph graphs list` to enumerate the registered graphs. The server must configure bearer tokens and `server.policy.file` with a rule that allows `graph_list`; `/graphs` is closed by default even when the server runs with `--unauthenticated`.
A server boots from a cluster directory (`omnigraph-server --cluster <dir>`) and
serves every graph the cluster declares. Use `omnigraph graphs list` to enumerate
them. The cluster's server-level policy must allow `graph_list`; `/graphs` is
closed by default even when the server runs with `--unauthenticated`.
```bash
OMNIGRAPH_BEARER_TOKEN=admin-token \
omnigraph graphs list --uri http://server.example.com --json
omnigraph graphs list --server http://server.example.com --json
```
For config-driven clients, set the remote graph's `bearer_token_env` to an environment variable containing a token whose actor is authorized by `server.policy.file`.
For an operator-defined server, store its token with `omnigraph login <name>` (or
`OMNIGRAPH_TOKEN_<NAME>`); the actor must be authorized by the cluster's
server-level policy.
`list` rejects local URI targets — it's for remote multi-graph servers only.
`list` rejects local (`--store`) targets — it's for remote multi-graph servers only.
Runtime add/remove is **not** in v0.6.0. To add a graph, stop the server, add a `graphs.<id>` entry to `omnigraph.yaml`, then restart. To remove, stop the server, delete the entry, restart.
Runtime add/remove via API is not exposed. To add or remove a graph, edit the
cluster's `cluster.yaml`, run `omnigraph cluster apply`, then restart the server.
Per-graph addressing: select a graph on a multi-graph server with `--graph`:
@ -107,9 +113,9 @@ omnigraph check --query queries.gq graph.omni --json
omnigraph schema plan --schema next.pg graph.omni --json
omnigraph schema apply --schema next.pg graph.omni --json
omnigraph policy validate --config omnigraph.yaml
omnigraph policy test --config omnigraph.yaml
omnigraph policy explain --config omnigraph.yaml --actor act-alice --action read --branch main
omnigraph policy validate --cluster ./company-brain --graph knowledge
omnigraph policy test --cluster ./company-brain --graph knowledge --tests policy.tests.yaml
omnigraph policy explain --cluster ./company-brain --graph knowledge --actor act-alice --action read --branch main
omnigraph commit list graph.omni --json
omnigraph commit show --uri graph.omni <commit-id> --json
@ -123,34 +129,29 @@ also pass `--schema`.
## Config
`omnigraph.yaml` lets the CLI and server share named graphs, defaults, and
query roots:
Configuration has two surfaces with single owners (see the
[CLI reference](reference.md#config-surfaces) for the full schema):
- **`~/.omnigraph/config.yaml`** — your personal operator config: default actor
(`--as`), named servers + credentials, clusters, profiles, aliases, and
default scope (`defaults.server` / `defaults.store` / `default_graph`). It
decides *who you are* and *what you address by default*.
- **`cluster.yaml`** (a team-owned cluster directory) — declares *what the system
is*: graphs, schemas, stored queries, policies, and storage. A server boots
from it (`--cluster <dir>`); see the [cluster guide](../clusters/index.md).
```yaml
graphs:
local:
uri: demo.omni
# ~/.omnigraph/config.yaml
operator:
actor: act-andrew
servers:
dev:
uri: http://127.0.0.1:8080
bearer_token_env: OMNIGRAPH_BEARER_TOKEN
cli:
graph: local
branch: main
query:
roots:
- queries
- .
url: http://127.0.0.1:8080
defaults:
server: dev
default_graph: knowledge
```
The config file can also define:
- server bind defaults
- auth env files
- query aliases for common read and change commands
- `policy.file` for Cedar authorization rules
When policy is enabled, `schema apply` is authorized through the
`schema_apply` action and is typically limited to admins on protected `main`.
@ -168,6 +169,6 @@ one-line warning to stderr and otherwise behave identically.
| `omnigraph query lint` | `omnigraph lint` | Same flags. The argv-level shim rewrites `query lint` to `lint`. |
| `omnigraph query check` | `omnigraph check` | `check` is a visible alias of `omnigraph lint`. |
The `command:` field in `aliases.<name>` in `omnigraph.yaml` accepts both
`read` / `change` (legacy) and `query` / `mutate` (canonical); the two
The `command:` field in `aliases.<name>` in `~/.omnigraph/config.yaml` accepts
both `read` / `change` (legacy) and `query` / `mutate` (canonical); the two
spellings are interchangeable on the wire via serde aliases.