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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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2
docs/dev/architecture.md
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@ -1,6 +1,6 @@
# Architecture
OmniGraph is a typed property-graph engine built as a coordination layer over many Lance datasets, with Git-style branches and commits across the whole graph, multi-modal querying (vector + FTS + BM25 + RRF + graph traversal) in one runtime, an HTTP server with Cedar policy, and a CLI driven by a single `omnigraph.yaml`.
OmniGraph is a typed property-graph engine built as a coordination layer over many Lance datasets, with Git-style branches and commits across the whole graph, multi-modal querying (vector + FTS + BM25 + RRF + graph traversal) in one runtime, an HTTP server with Cedar policy, and a CLI driven by a per-operator `~/.omnigraph/config.yaml` plus team-owned cluster directories.
## Reading guide

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docs/dev/testing.md
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@ -7,7 +7,7 @@ This file is the always-on map of the test surface. **Consult it before every ta
| Crate | Path | Style |
|---|---|---|
| `omnigraph` (engine) | `crates/omnigraph/tests/` | Integration tests (28 files), fixture-driven, share `tests/helpers/mod.rs` |
| `omnigraph-cli` | `crates/omnigraph-cli/tests/` | Per-area suites (post-modularization): `cli_cluster.rs` (cluster command surface + operator-actor cascade), `cli_cluster_e2e.rs` (spawned-binary lifecycle compositions — lost-state re-import recovery, out-of-band drift, graph-root destruction, multi-graph mixed-disposition convergence), `cli_data.rs` (load/read/change/branch/commit/export/snapshot/policy/embed/maintenance + operator format cascade), `cli_schema_config.rs` (init/config, schema plan/apply, RFC-008 deprecation warnings + `config migrate` + strict mode), `cli_queries.rs`, `parity_matrix.rs` (RFC-009 Phase 1: the embedded-vs-remote referee — every forked verb run against both arms with matched Cedar policy and the same actor, scrubbed-JSON + exit-code equality; divergences are pinned in its `KNOWN_DIVERGENCES` ledger, never silently repaired), `system_local.rs` (full-cycle cluster lifecycle with a spawned `--cluster` server, applied-policy enforcement over HTTP, keyed-credential auth, operator aliases), `system_remote.rs`; share `tests/support/mod.rs` (hermetic `OMNIGRAPH_HOME` by default) |
| `omnigraph-cli` | `crates/omnigraph-cli/tests/` | Per-area suites (post-modularization): `cli_cluster.rs` (cluster command surface + operator-actor cascade), `cli_cluster_e2e.rs` (spawned-binary lifecycle compositions — lost-state re-import recovery, out-of-band drift, graph-root destruction, multi-graph mixed-disposition convergence), `cli_data.rs` (load/read/change/branch/commit/export/snapshot/policy/embed/maintenance + operator format cascade), `cli_schema_config.rs` (init/config, schema plan/apply), `cli_queries.rs`, `parity_matrix.rs` (RFC-009 Phase 1: the embedded-vs-remote referee — every forked verb run against both arms with matched Cedar policy and the same actor, scrubbed-JSON + exit-code equality; divergences are pinned in its `KNOWN_DIVERGENCES` ledger, never silently repaired), `system_local.rs` (full-cycle cluster lifecycle with a spawned `--cluster` server, applied-policy enforcement over HTTP, keyed-credential auth, operator aliases), `system_remote.rs`; share `tests/support/mod.rs` (hermetic `OMNIGRAPH_HOME` by default) |
| `omnigraph-cluster` | mostly in-source `#[cfg(test)] mod tests`; `tests/failpoints.rs` (feature-gated); `tests/s3_cluster.rs` (bucket-gated full lifecycle on object storage) | Cluster config parser, local JSON state diff, state CAS/lock handling/recovery, read-only validate/plan/status plus explicit refresh/import graph observations, config-only apply (content-addressed payload publish, disposition gating, composite-digest convergence, idempotent re-apply), catalog payload verification (status read-only, refresh drift + self-heal), failpoint crash-mid-apply / CAS-race coverage, Stage 4A graph creation (create executor, recovery sidecars + sweep rows, create crash windows), Stage 4B schema apply (migration previews in plan, schema executor, schema-apply sweep classification, schema crash windows), Stage 4C gated deletes (digest-bound approvals, delete executor + tombstones, delete sweep rows, delete crash windows), and 5A policy binding metadata (applies_to in the applied revision, binding-change diffing + convergence, pre-5A backfill), and the 5B serving-snapshot read API (converged read, refusal rows) |
| `omnigraph-server` | `crates/omnigraph-server/tests/` | Per-area suites (post-modularization): `auth_policy.rs`, `data_routes.rs`, `schema_routes.rs`, `stored_queries.rs`, `multi_graph.rs` (cluster-mode boot — converged serving, policy binding wiring, boot refusals — + the concurrent branch-ops matrix), `boot_settings.rs` (mode inference, PolicySource), `s3.rs` (bucket-gated: single-graph serving + config-free `--cluster s3://` boot), `openapi.rs` (OpenAPI drift / regeneration); share `tests/support/mod.rs` |
| `omnigraph-compiler` | mostly in-source `#[cfg(test)] mod tests` | Parser, type-checker, IR lowering, lint |