diff --git a/docs/dev/index.md b/docs/dev/index.md
index 4bc1e6a..b23326b 100644
--- a/docs/dev/index.md
+++ b/docs/dev/index.md
@@ -76,6 +76,8 @@ Working documents for in-flight feature work. Removed when the work lands.
 | Future cluster control plane — declarative as-code config, JSON state ledger, reconciler | [cluster-config-specs.md](cluster-config-specs.md), [cluster-axioms.md](cluster-axioms.md), [cluster-config-implementation-spec.md](cluster-config-implementation-spec.md) |
 | Cluster graph & schema apply — Phase 4 sidecars, roll-forward recovery, approval artifacts | [rfc-004-cluster-graph-schema-apply.md](rfc-004-cluster-graph-schema-apply.md) |
 | Server boots from cluster state — Phase 5 mode switch, applied-revision serving | [rfc-005-server-cluster-boot.md](rfc-005-server-cluster-boot.md) |
+| Per-operator config — `~/.omnigraph/` identity, keyed credentials, named servers (the operator slice of RFC-002) | [rfc-007-operator-config.md](rfc-007-operator-config.md) |
+| Deprecate `omnigraph.yaml` — one concern per config surface; key-by-key migration map and staged retirement | [rfc-008-deprecate-omnigraph-yaml.md](rfc-008-deprecate-omnigraph-yaml.md) |
 
 ## Boundary
 
diff --git a/docs/dev/rfc-007-operator-config.md b/docs/dev/rfc-007-operator-config.md
new file mode 100644
index 0000000..52a446e
--- /dev/null
+++ b/docs/dev/rfc-007-operator-config.md
@@ -0,0 +1,292 @@
+# RFC: Per-Operator Config — the Operator Slice of RFC-002
+
+**Status:** Proposed
+**Date:** 2026-06-11
+**Builds on:** [rfc-002-config-cli-architecture.md](rfc-002-config-cli-architecture.md) (Proposed; implementation parked — PRs #139/#162 closed over review findings), [rfc-005-server-cluster-boot.md](rfc-005-server-cluster-boot.md) (Landed), RFC-006 storage roots (#186/#190/#194, landed). The #139 review record is a normative input: every design rule in §D6 traces to a confirmed finding.
+**Paired with:** [rfc-008-deprecate-omnigraph-yaml.md](rfc-008-deprecate-omnigraph-yaml.md) — together they define the two-surface architecture this RFC's operator half belongs to.
+**Target release:** unversioned (staged; see Sequencing).
+
+## Summary
+
+Give OmniGraph the operator half of the **two-surface config architecture**
+(RFC-008): **cluster config** (team-owned, in a repo — what the system *is*)
+and **operator config** (person-owned, in `$HOME` — who *I* am). This is
+Terraform's split: `~/.terraformrc` for the operator, the checkout for the
+declaration. OmniGraph today has neither half cleanly — `omnigraph.yaml`
+mixes both concerns (RFC-008 retires it), and there is no home-level config
+at all: identity and credentials get re-declared per working directory, in
+files that sit next to repo-committed config.
+
+This RFC introduces **`~/.omnigraph/config.yaml`** (the operator surface)
+and a **keyed credentials chain**, scoped deliberately small:
+
+1. **Operator identity** — a default actor for every `--as` cascade.
+2. **Credentials by server name** — no more inventing env-var names per
+   server; secrets never inline, never in any repo-committed file.
+3. **Named servers** — operator-owned endpoint definitions; nothing a
+   checkout supplies can redefine them.
+
+It is explicitly a **subset of RFC-002**, sequenced to land. RFC-002 settled
+the right long-term decisions (one `~/.omnigraph/` dir, credentials keyed by
+server name, `OMNIGRAPH_CONFIG`/`OMNIGRAPH_HOME` env precedence) but its
+implementation arrived as one 4,800-line PR mixing a crate extraction with
+behavior changes, and died over ten confirmed findings. This RFC adopts
+RFC-002's settled decisions verbatim where they apply, defers everything
+else (`GraphLocator`, multi-homing, `omnigraph use`, the State layer), and
+encodes the #139 findings as design rules so the same failures cannot recur.
+
+## Motivation
+
+Three concrete pains, all hit in real operation this cycle:
+
+- **Identity repetition.** The cluster actor cascade (#180) resolves
+  `--as` from the per-operator `omnigraph.yaml` — which means every
+  operator hand-maintains a copy in every working directory (the
+  `~/exp/intel` setup needed exactly this). A repo-committed
+  `omnigraph.yaml` cannot carry `as: act-andrew` without claiming every
+  contributor is Andrew.
+- **Credential ergonomics.** `bearer_token_env` forces three coordinated
+  steps per server (invent a var name, reference it in config, set it in
+  the secret store). The peer group — AWS profiles, `gh hosts`, kubeconfig
+  users — keys secrets by the server's *name*.
+- **Cluster-era working shape.** With clusters on object storage (RFC-006),
+  the project directory is a *declaration checkout* — operators run
+  `cluster apply --config ./checkout` from anywhere. The things that are
+  about the *operator* (who am I, which servers do I know, how do I like
+  output formatted) have no home that travels with them.
+
+## Non-Goals
+
+- **`GraphLocator` / multi-homed graph resolution** (RFC-002 §1) — the
+  biggest and riskiest part of config-v2; untouched here.
+- **`omnigraph use` / the State layer** (`~/.omnigraph/state/`) — deferred
+  with it (finding #2 showed its precedence interacts badly with scaffolds;
+  that problem belongs to the slice that introduces it).
+- **OS keychain integration** — the credentials *chain* (§D4) leaves a slot
+  for it; this RFC ships env + file sources only.
+- **Config-file walk-up.** Terraform does not walk up from subdirectories
+  and neither do we — `--config` (or running in the directory) stays the
+  explicit, deterministic story for cluster checkouts. Rejected, not
+  deferred: walk-up makes "which config am I using" a function of cwd
+  depth, the class of surprise this RFC exists to remove.
+- **Retiring `omnigraph.yaml`** — that is RFC-008's job, with its own
+  staging. This RFC builds the destination; during RFC-008's deprecation
+  window the legacy file keeps loading exactly as today.
+- **Renaming or removing anything.** No flag renames, no key renames, no
+  schema-version bumps (findings #1, #3, #10).
+
+## Background (verified against main)
+
+- **Project-config lookup today** (`crates/omnigraph-server/src/config.rs:529-553`,
+  shared by CLI and server): `--config <path>`, else `./omnigraph.yaml` in
+  cwd, else built-in defaults. Relative paths inside the file resolve
+  against the file's own directory (`base_dir`). No env var, no home file,
+  no walk-up.
+- **Side-effect on load** (`crates/omnigraph-cli/src/helpers.rs:102-108`):
+  `load_cli_config` also loads `auth.env_file` into the process env —
+  this is how `OMNIGRAPH_BEARER_TOKEN` reaches remote commands today.
+- **Actor resolution** (`helpers.rs:170`, #180): `--as` flag, else the
+  project config's actor — currently the end of the chain.
+- **Existing credential mechanism**: `TargetConfig.bearer_token_env` names
+  an env var; `auth.env_file` points at a git-ignored dotenv. Both keep
+  working indefinitely (RFC-002 already committed to this; finding #3
+  showed what happens otherwise).
+- **`OMNIGRAPH_CONFIG`** exists today only as the *container entrypoint's*
+  translation to the server's `--config`. The CLI does not read it.
+
+## Design
+
+### D1. Files and discovery
+
+```
+~/.omnigraph/config.yaml      # the operator surface (this RFC)
+~/.omnigraph/credentials      # keyed secrets, 0600, git-irrelevant (§D4)
+./cluster.yaml + checkout     # the team surface (unchanged; RFC-004..006)
+./omnigraph.yaml              # legacy, loads as today through RFC-008's window
+```
+
+Discovery order for the operator file: `$OMNIGRAPH_HOME/config.yaml` if
+`OMNIGRAPH_HOME` is set, else `~/.omnigraph/config.yaml`. Absent file =
+empty layer, never an error. `~` is expanded wherever paths are read
+(finding #9 — today a literal `./~/...` directory gets created).
+
+`OMNIGRAPH_CONFIG=<path>` becomes a first-class override for the `--config`
+argument in the CLI (highest precedence below the flag itself), aligning the
+CLI with the container contract that already uses this variable for the
+server. One name, one meaning, both binaries — it points at whatever the
+command's `--config` would (a cluster checkout for cluster commands; the
+legacy file during RFC-008's window).
+
+Per RFC-002 §4 (adopted verbatim): `~/.omnigraph/` is the one canonical
+dir — cache/state subdirectories arrive with their own slices; XDG roots are
+not part of the mental model (`$XDG_CONFIG_HOME` may be honored as a
+fallback read location if set, but is never written to).
+
+### D2. The operator schema (v1 of this layer)
+
+```yaml
+# ~/.omnigraph/config.yaml — about the OPERATOR, never about the system
+operator:
+  actor: act-andrew          # default for every --as cascade
+
+servers:                     # operator-owned endpoint definitions
+  intel-dev:
+    url: http://127.0.0.1:8080
+  prod:
+    url: https://graph.modernrelay.ai
+    # No token here, ever. Resolution: §D4.
+
+aliases:                     # personal shorthand over CLUSTER-owned queries
+  triage:                    # (the query is the shared contract; the alias,
+    server: intel-dev        #  its defaults, and its name are mine — RFC-008)
+    graph: spike
+    query: weekly_triage
+
+defaults:
+  output: table              # read --format default
+```
+
+Unknown keys are a **warning, not an error** in this layer (an operator file
+written by a newer CLI must not brick an older one; contrast with
+`cluster.yaml`, where unknown keys are deliberately fatal because they
+change what a *plan* means).
+
+### D3. Precedence and the merge rule
+
+The end-state cascade is short, because the team surface (cluster config)
+deliberately carries **no operator-resolvable keys** — no actor, no tokens,
+no output preferences. Identity can never come from a checkout:
+
+```
+flag  >  env  >  operator config  >  built-in
+```
+
+During RFC-008's deprecation window, a legacy `omnigraph.yaml` slots in
+between env and operator config (its keys win over operator defaults,
+preserving today's behavior for unmigrated setups) — with the §D5
+credential inversion: **credentials and endpoint definitions never come
+from a legacy/checkout file when an operator-layer definition exists for
+the same server name.**
+
+Merging is **key-level**: scalars override per key; maps (`servers:`,
+`aliases:`) merge per *entry*, and entries merge per *field* (finding #13 —
+`merge_map` replacing whole entries silently dropped sibling fields).
+
+Concretely for the two flows this slice touches:
+
+- **Actor**: `--as` > legacy `cli.actor` (window only, unchanged semantics)
+  > `operator.actor` > none (commands that need an actor keep failing
+  loudly).
+- **Output format**: `--format` > legacy default (window only) >
+  `defaults.output` > `table`.
+
+### D4. Credentials: keyed by server name, by-reference always
+
+Adopted from RFC-002 §5 unchanged, minus the keychain (a later source in
+the same chain). For a server named `<name>`, the resolution chain is:
+
+1. `OMNIGRAPH_TOKEN_<NAME>` (uppercased, `-`→`_`) — explicit env, wins.
+2. `[<name>]` section in `~/.omnigraph/credentials` (INI-style, `0600`;
+   the loader refuses a group/world-readable file).
+3. The legacy pair — `bearer_token_env` + `auth.env_file` — exactly as
+   today, for configs that already use it.
+
+No inline secrets in any YAML file, anywhere (the existing invariant 12
+posture extended to disk). A future `omnigraph login <name>`
+writes/rotates one section of the credentials file via temp + rename
+(finding #7: every operator-layer write is atomic), creating it `0600`.
+
+### D5. The trust boundary (the security findings, made structural)
+
+Findings #4, #5, #6 share one root cause: a file that arrives with a
+*repo checkout* could redirect where requests go and what secrets they
+carry. In the end state this is closed by construction — cluster config has
+no server/credential keys at all, and the operator surface never comes from
+a checkout. The rules below therefore govern the **RFC-008 window** (while
+legacy `omnigraph.yaml` still loads) and stand as the permanent law for any
+future checkout-supplied surface:
+
+1. **A checkout-supplied file may *reference* a server by name; it may not
+   *redefine* an operator-defined server.** If a legacy `./omnigraph.yaml`
+   declares `servers.prod.url` and `~/.omnigraph/config.yaml` also defines
+   `prod`, the operator definition wins and the CLI warns about the
+   shadowed entry. A legacy-only server name keeps working (compat), but
+   the keyed-credentials chain (§D4 steps 1–2) never resolves for it —
+   only the legacy explicit `bearer_token_env` does. Net effect: a
+   malicious checkout cannot point `prod` at an attacker host and harvest
+   the operator's `prod` token.
+2. **`auth.env_file` keeps auto-loading (compat), but checkout-layer
+   env-files cannot *override* variables already set in the process or by
+   the operator layer** — first-set-wins, operator-before-checkout (the
+   existing real-env-wins rule, extended one layer down). Finding #5's
+   injection becomes a no-op against any var the operator actually uses.
+3. **A token is sent only to the server it is keyed to.** The legacy
+   single `OMNIGRAPH_BEARER_TOKEN` fallback keeps working for the
+   single-server shape, but when a request resolves through a *named*
+   server, only that name's chain applies (finding #6's broadcast).
+
+### D6. Compatibility rules (the #139 findings as law)
+
+| Rule | Source finding |
+|---|---|
+| No flag or key is removed or renamed; new behavior is additive | #1, #3 |
+| A config that loads today loads identically after this RFC; new validation applies only to new keys | #3, #8, #10 |
+| Every operator-layer file write is temp + rename, never in-place | #7 |
+| `~` expands wherever a path is read | #9 |
+| Map merges are per-entry, per-field — never wholesale replace | #13 |
+| One resolution path per concern — the actor chain and the token chain each have exactly one implementation, called by CLI and server alike | #11, #12 |
+| Each slice lands as its own PR with the workspace gate green; no slice mixes mechanical moves with behavior changes | #139's disposition |
+
+## Sequencing
+
+Three PRs, each independently useful, each landable without the next:
+
+1. **PR 1 — the operator file + identity.** Loader for
+   `~/.omnigraph/config.yaml` (+ `OMNIGRAPH_HOME`, `~`-expansion, warn-only
+   unknown keys), `operator.actor` joining the `--as` cascade,
+   `defaults.output` joining the format cascade, `OMNIGRAPH_CONFIG` env for
+   the CLI's `--config`. Docs: `cli-reference.md` gains the two-surface
+   table.
+2. **PR 2 — keyed credentials.** `servers:` in the operator layer, the
+   §D4 chain (env + credentials file), the §D5 trust rules, and
+   `omnigraph login <name>` (atomic write, `0600`). Legacy mechanisms
+   untouched and tested-as-untouched.
+3. **PR 3 — operator targeting.** `--server <name>` on remote-capable
+   commands and `aliases:` in the operator layer (server + graph + query +
+   default params), resolving through operator-defined servers. This is
+   the *bridge* toward RFC-002's locator — multi-server addressing in a
+   safe, minimal form without the `GraphLocator` rework — and the
+   replacement RFC-008 needs before legacy aliases can migrate.
+
+RFC-008's deprecation stages begin only after PRs 1–2 are on main: the
+operator surface must exist before `config migrate` has somewhere to move
+keys to.
+
+## Open questions
+
+- Should `operator.actor` apply to *local* (embedded-engine) writes too, or
+  only where a server/cluster boundary exists? Leaning yes-everywhere: one
+  identity chain (§D6 one-path rule), and local audit rows get better.
+- Does `defaults.output` belong in slice 1, or is identity-only an even
+  cleaner first PR? (Cost of including it is one cascade hop; value is
+  immediate.)
+- `omnigraph config view --resolved` (RFC-002 had it; #139 shipped a
+  version) — slice 1 or slice 2? It materially helps debugging precedence,
+  which argues early.
+
+## Relationship to RFC-002 and RFC-008
+
+**RFC-008 is the other half of this design**: this RFC builds the operator
+surface; RFC-008 retires the mixed-ownership file
+([rfc-008-deprecate-omnigraph-yaml.md](rfc-008-deprecate-omnigraph-yaml.md)),
+leaving exactly two config surfaces — cluster (team) and operator (person).
+Every mention of `omnigraph.yaml` in this RFC describes the deprecation
+window only. Sequencing couples them: RFC-007 PRs 1–2 land first, then
+RFC-008's migration stages run against them.
+
+RFC-002 remains the umbrella architecture. This RFC implements its §2
+(layered config, global-first), §4 (file naming / one dir), and §5
+(credentials) in their minimal load-bearing form, and explicitly defers §1
+(`GraphLocator`/targets), §3 (roles), and the State layer. If/when the
+locator work resumes, it builds on these layers rather than re-landing
+them. RFC-002's header should gain a pointer here once this merges.
diff --git a/docs/dev/rfc-008-deprecate-omnigraph-yaml.md b/docs/dev/rfc-008-deprecate-omnigraph-yaml.md
new file mode 100644
index 0000000..49e2c4b
--- /dev/null
+++ b/docs/dev/rfc-008-deprecate-omnigraph-yaml.md
@@ -0,0 +1,174 @@
+# RFC: Deprecate `omnigraph.yaml` — One Concern per Config Surface
+
+**Status:** Proposed
+**Date:** 2026-06-11
+**Builds on:** [rfc-007-operator-config.md](rfc-007-operator-config.md) (the
+operator layer that absorbs the identity/credential keys),
+[rfc-005-server-cluster-boot.md](rfc-005-server-cluster-boot.md) (Landed —
+cluster-booted serving), RFC-006 storage roots (landed: #186/#190/#194).
+**Supersedes in part:** RFC-007's "project layer" framing (§Relationship
+below) and [rfc-002-config-cli-architecture.md](rfc-002-config-cli-architecture.md)'s
+assumption that `omnigraph.yaml` remains the project manifest.
+**Target release:** staged; final removal at the next major (see Sequencing).
+
+## Summary
+
+Retire `omnigraph.yaml`. It is three unrelated concerns wearing one
+filename — server deployment config, project/CLI conveniences, and operator
+identity — and the mixture is not a cosmetic wart but the root cause of a
+recurring class of problems: operators keeping personal copies of "project"
+files, repo checkouts able to carry credential-adjacent keys (the #139
+security findings), `omnigraph init` scaffolding config into unrelated
+directories, and every config discussion needing a paragraph to establish
+which of the three files is meant.
+
+The end state is **two config surfaces with single owners**:
+
+| Surface | Owner | Declares |
+|---|---|---|
+| **Cluster config** (`cluster.yaml` + catalog) | the team, in a repo | what the system *is*: graphs, schemas, queries, policies, storage |
+| **Operator config** (`~/.omnigraph/`) | one person, in `$HOME` | who *I* am: identity, credentials, known servers, ergonomics |
+
+plus **flags/env** for the zero-config tier (one graph, one server, no
+control plane) — which already works today with no file at all.
+
+`omnigraph.yaml` has no role left once every key has a better home. This
+RFC gives each key that home, and stages the retirement so that no working
+setup breaks without a loud warning, a migration command, and a full
+deprecation cycle first.
+
+## Motivation
+
+- **It breaks the ownership logic.** A config file must have one owner. A
+  file that carries `graphs:` (team-owned, reviewable) next to `cli.actor`
+  (one person's identity) and `auth.env_file` (credential loading) can be
+  neither safely committed nor sensibly personal. Every real deployment
+  this cycle tripped on it: per-operator copies in `~/exp/intel`,
+  graph-scoped alias URIs that only make sense per-person, the #139
+  findings where a checkout-supplied file could redirect tokens.
+- **The cluster made it redundant.** Since RFC-005/006, a cluster
+  deployment serves from the applied catalog — `--cluster` mode does not
+  read `omnigraph.yaml` *at all*. Stored queries, policies, bindings, and
+  graph addressing all have authoritative homes. What remains in
+  `omnigraph.yaml` for cluster users is dead weight that can silently
+  disagree with what is actually serving.
+- **Two declarative dialects is one too many.** `cluster.yaml` and
+  `omnigraph.yaml` both declare graphs/queries/policies with different
+  schemas, different validation strictness, and different lifecycle
+  guarantees. Maintaining, documenting, and testing both — and explaining
+  when each applies — is a permanent tax (the "programming integrated over
+  time" lens says: this forks on every config-surface change).
+
+## Non-Goals
+
+- **Breaking anyone now.** Every `omnigraph.yaml` that works today keeps
+  working through the entire deprecation window, with warnings.
+- **Retiring the zero-config tier.** `omnigraph-server s3://bucket/g.omni
+  --bind …` plus env vars stays first-class forever — that tier needs *no*
+  file, which is the point.
+- **Forcing the control plane on single-graph users.** The migration target
+  for a multi-graph yaml deployment is a *minimal* cluster (file-rooted,
+  no bucket required, `cluster.yaml` barely longer than the `graphs:` map
+  it replaces) — but a single graph never needs even that.
+- **Touching `cluster.yaml`** — its schema and strictness are unchanged.
+
+## Where every key goes (the complete migration map)
+
+The full `OmnigraphConfig` surface (verified against
+`crates/omnigraph-server/src/config.rs:182-207`):
+
+| `omnigraph.yaml` key | Concern | New home |
+|---|---|---|
+| `graphs.<name>.uri` | what exists / where | `cluster.yaml` `graphs:` (storage-root-derived) — or a flag/env for the zero-config tier |
+| `graphs.<name>.queries`, top-level `queries:` | what exists | cluster catalog (`.gq` discovery, RFC-004/#183) |
+| `graphs.<name>.policy.file`, top-level `policy.file`, `server.policy.file` | what's enforced | `cluster.yaml` `policies:` + `applies_to` bindings |
+| `server.bind` | deployment runtime | `--bind` / env (already authoritative; the key is a default) |
+| `server.graph` | deployment runtime | `--target`-style flag / env in the zero-config tier; meaningless under cluster boot |
+| `graphs.<name>.bearer_token_env`, `auth.env_file` | credentials | operator credentials chain (RFC-007 §D4) |
+| `cli.actor` | identity | `operator.actor` (RFC-007 §D3) |
+| `cli.output_format`, `cli.table_*` | personal ergonomics | `defaults:` in operator config (RFC-007 §D2) |
+| `cli.graph`, `cli.branch` | personal targeting | operator config: named servers + a per-operator default target (RFC-007 PR 3) |
+| `aliases.<name>` | personal ergonomics over shared queries | operator config `aliases:` — the *queries* they invoke are cluster-owned; the *shorthand* is personal |
+| `query.roots` | discovery convenience | obsolete — cluster query discovery (#183) replaced it |
+| `project.name` | label | dropped (the cluster's `metadata.name` is the deployment label) |
+
+Two placements worth defending:
+
+- **Aliases are operator config, not cluster config.** The stored query is
+  the shared contract (catalog-owned, digest-pinned); an alias is one
+  person's shorthand with their favorite default params and target. Putting
+  aliases in the cluster would force team review on personal ergonomics;
+  leaving them per-directory recreates today's problem. Per-operator,
+  keyed by server/graph name, is the AWS-profile shape.
+- **Multi-graph serving without a control plane migrates to a minimal
+  cluster, not to a new file.** The honest cost: `cluster import` + `apply`
+  once, on a `file://` root next to the graphs. The honest benefit: one
+  declarative dialect, one validation path, one serving source — and the
+  upgrade path to buckets/approvals is a one-line `storage:` change instead
+  of a re-platform.
+
+## Deprecation mechanics
+
+Per Hyrum's Law (the repo's own deny-list: shipped observable behavior is
+contract), retirement is staged, loud, and tooled:
+
+1. **Warn.** Loading `omnigraph.yaml` emits a one-line deprecation notice
+   naming the replacement for each key actually present in the file (not a
+   generic banner — the migration map above, applied to *your* file).
+   Suppressible per-process (`OMNIGRAPH_SUPPRESS_YAML_DEPRECATION=1`) for
+   CI logs during the window.
+2. **Migrate.** `omnigraph config migrate` reads an existing
+   `omnigraph.yaml` and writes the split: the team half as a ready-to-review
+   `cluster.yaml` (+ moves query/policy files into the checkout layout),
+   the personal half merged into `~/.omnigraph/config.yaml` — printing a
+   diff-style summary and touching nothing without `--write`. The command
+   is the test of the migration map's completeness: any key it cannot
+   place is a bug in this RFC.
+3. **Stop scaffolding.** `omnigraph init` stops generating
+   `omnigraph.yaml` (it currently scaffolds one into cwd — the source of
+   the test-pollution bug). `omnigraph cluster init` (new, small) scaffolds
+   a minimal `cluster.yaml` instead.
+4. **Opt-in strict.** `OMNIGRAPH_NO_LEGACY_CONFIG=1` turns the warning into
+   an error — for teams that finished migrating and want regressions caught.
+5. **Remove at the next major.** Loading the file becomes an error pointing
+   at `config migrate`. The `OmnigraphConfig` code path, the dual
+   query-registry loaders, and the yaml-mode server boot source are deleted
+   — the payoff that makes the whole exercise worth it.
+
+Stages 1–3 can land in one release once RFC-007 PRs 1–2 exist (the operator
+layer must exist before anything can migrate *to* it). Stage 4 the release
+after. Stage 5 at the major, with the removal listed in release notes from
+stage 1 onward.
+
+## What this deletes, eventually
+
+- The `OmnigraphConfig` struct and its 12-key surface, the
+  `load_config`/`load_cli_config` pair and its env-side-effect, the
+  scaffolder, and the legacy resolution paths (`resolve_cli_graph`'s dual
+  modes — finding #11's root cause).
+- The yaml-mode multi-graph server boot (`ServerConfigMode::Multi` keeps
+  existing — cluster boot constructs it — but its `omnigraph.yaml` source
+  goes).
+- An entire class of documentation ("which file does X go in?") and the
+  #139 security surface (a checkout cannot hijack what no longer loads).
+
+## Relationship to RFC-007 and RFC-002
+
+RFC-007 ships the operator layer this RFC migrates *to*; its "project
+layer" language should be read as transitional — after this RFC, the
+project layer **is** the cluster checkout, and RFC-007's PR 3 (project
+`server:` references) applies to `cluster.yaml`-adjacent operator targeting
+rather than to `omnigraph.yaml`. RFC-002's locator/state-layer work, if
+resumed, targets the two-surface world directly. RFC-002's file-naming
+decisions (`~/.omnigraph/` as the one dir) are unaffected.
+
+## Open questions
+
+- **Window length**: one minor release between warn (stage 1) and strict
+  (stage 4), or two? Cookbooks, skills, and the deployment docs all need
+  the same pass; the migration command makes a short window defensible.
+- **`omnigraph login` vs `config migrate` ordering** — both write
+  `~/.omnigraph/`; whichever lands first establishes the file-locking and
+  atomic-write helpers the other reuses.
+- **Does the MCP server config** (RFC-003) reference `omnigraph.yaml`
+  anywhere that needs the same treatment? To be audited in stage 1.