diff --git a/changelog/770.feature.md b/changelog/770.feature.md
new file mode 100644
index 000000000..4ca92aab1
--- /dev/null
+++ b/changelog/770.feature.md
@@ -0,0 +1,7 @@
+The CI coupling gate now couples each regression baseline to its diagnostic's `Diagnostic.version`.
+A test case fails the gate when the diagnostic's in-code version no longer matches the version recorded
+when its baseline was minted, so an execution-affecting change can no longer slip through as a green replay
+against a stale committed bundle.
+The new author-declared `diagnostic_version` field lives in the test case `manifest.json` (schema version 2),
+and the new `ref test-cases migrate-manifests` command backfills it across existing baselines.
+A legitimate revert is still permitted: lower the diagnostic version and re-mint the baseline.
diff --git a/docs/background/regression-baselines.md b/docs/background/regression-baselines.md
index 8adff92fd..a5067a32b 100644
--- a/docs/background/regression-baselines.md
+++ b/docs/background/regression-baselines.md
@@ -27,14 +27,22 @@ A baseline is split into two layers with very different trust and portability pr
 
 The two layers are bound by a **`manifest.json`** alongside the bundle, which records:
 
-- `schema` — integer schema version for the manifest format itself (currently `1`).
+- `schema` — integer schema version for the manifest format itself (currently `2`).
   The loader rejects manifests whose `schema` does not match the current `SCHEMA_VERSION`,
   so format migrations are detected immediately rather than silently misread.
 - `test_case_version` — a monotonic, author-bumped integer that *authorises* a new baseline.
+- `diagnostic_version` — the author-declared `Diagnostic.version` captured at mint time,
+  coupling the baseline to the diagnostic code that produced it.
 - `committed` — sha256 digests of the committed JSON artefacts, over the exact placeholder-substituted bytes on disk.
 - `native` — sha256 + size of each curated native file (empty `{}` until minted).
 - `catalog_hash` — the hash of the test case's input `catalog.yaml`, coupling the baseline to the inputs that produced it.
 
+These give the manifest **two orthogonal version axes**:
+`test_case_version` is per-case and mint-authored (it authorises a new committed baseline),
+while `diagnostic_version` is per-diagnostic and author-authored (it declares that the
+diagnostic's *results* changed). `test_case_version` remains monotonic, and `diagnostic_version`
+may move backwards only for an authorised revert. The gate consults each for a different purpose.
+
 !!! note "An empty native set is a permanent, valid state"
     Fork contributors cannot mint
     (minting needs object-store write credentials that never run on untrusted pull-request code).
@@ -67,6 +75,7 @@ flowchart LR
 | `sync` | public read | Fetch the native blobs referenced by the manifest into the local store cache. |
 | `replay` | public read | Materialise the native baseline into a slot, re-run only `build_execution_result`, and tolerantly compare to the committed bundle. |
 | `check-store` | write | Preflight the writable native store (credentials + bucket) without uploading anything. Run this before a slow `mint` to confirm credentials are correct. |
+| `migrate-manifests` | none | One-shot, idempotent maintenance command that rewrites every committed `manifest.json` at the current `SCHEMA_VERSION`, stamping each case's `diagnostic_version` from the diagnostic's in-code `Diagnostic.version`. |
 
 ### Output slots
 
@@ -172,7 +181,7 @@ because an empty native set is legitimate, a missing native baseline downgrades
 - **`skip`** — nothing relevant to this case changed, or the case is not under regression management.
 - **`replay`** — cheap, anonymous re-check against the cached native baseline (only when native blobs exist). This also verifies a `test_case_version` bump that ships native blobs.
 - **`execute`** — full end-to-end re-run with tolerant compare; required when `test_case_version` was bumped to authorise a new baseline *and* no native baseline exists to replay against.
-- **`fail`** — an unauthorised or unverifiable change (committed bundle edited without a version bump, version moved backwards, bundle drifted from its manifest, or catalog changed without regenerating the baseline).
+- **`fail`** — an unauthorised or unverifiable change: the committed bundle or catalog changed without a version bump, a version moved backwards, the bundle drifted from its manifest, or the in-code `Diagnostic.version` no longer matches the recorded `diagnostic_version`.
 
 ### Decision flow
 
@@ -190,17 +199,24 @@ flowchart TD
     committedOk -->|yes| catalogOk{catalog.yaml<br/>matches manifest<br/>catalog_hash?}
     catalogOk -->|no| failCatalog[["FAIL<br/>inputs changed without<br/>regenerating baseline"]]
 
-    catalogOk -->|yes| seeding{newly added<br/>this branch?}
+    catalogOk -->|yes| staleVersion{code Diagnostic.version<br/>vs baseline<br/>diagnostic_version}
+    staleVersion -->|"code &gt; baseline"| failStale[["FAIL<br/>stale baseline<br/>re-mint required"]]
+    staleVersion -->|"code &lt; baseline"| failDowngrade[["FAIL<br/>illegal downgrade<br/>lower code AND re-mint"]]
+
+    staleVersion -->|equal| seeding{newly added<br/>this branch?}
     seeding -->|yes| seedNative{native<br/>non-empty?}
     seedNative -->|yes| replaySeed[["REPLAY<br/>seed against committed"]]
     seedNative -->|no| skipSeed[["SKIP<br/>committed-only baseline"]]
 
-    seeding -->|no| versionCmp{version vs base}
+    seeding -->|no| versionCmp{test_case_version<br/>vs base}
     versionCmp -->|decreased| failVersion[["FAIL<br/>version not monotonic"]]
-    versionCmp -->|bumped| bumpNative{native<br/>present?}
+    versionCmp -->|"unchanged or bumped"| diagVersionCmp{diagnostic_version<br/>decreased vs base?}
+    diagVersionCmp -->|"yes, committed unchanged"| failBareDowngrade[["FAIL<br/>bare downgrade<br/>re-mint required"]]
+    diagVersionCmp -->|"no, or committed re-minted"| versionBumped{test_case_version<br/>bumped?}
+    versionBumped -->|yes| bumpNative{native<br/>present?}
     bumpNative -->|yes| replayBump[["REPLAY<br/>verify new baseline<br/>reproduces from native"]]
     bumpNative -->|no| execute[["EXECUTE<br/>full re-run<br/>(no native to replay)"]]
-    versionCmp -->|unchanged| committedChanged{committed<br/>changed?}
+    versionBumped -->|no| committedChanged{committed<br/>changed?}
 
     committedChanged -->|yes| failUnauthorised[["FAIL<br/>baseline changed without<br/>version bump"]]
     committedChanged -->|no| nativeChanged{native<br/>changed?}
@@ -224,6 +240,16 @@ and maps the changed-file list onto each case:
 - **`extraction_changed`** is coarse and errs toward `replay` (cheap, credential-free):
   any change under the diagnostic's provider package,
   or under the core regression package, counts for every case in that provider.
+  It is a *path-based* heuristic, so it cannot tell an execution change from an extraction change.
+- **`diagnostic_version`** is the *author-declared* execution-change signal: when a diagnostic's
+  results change the author bumps `Diagnostic.version`, and the gate fails any baseline whose
+  recorded `diagnostic_version` no longer matches the in-code value until it is re-minted.
+  This closes the **replay blind-spot** that `extraction_changed` alone leaves open:
+  an execution-affecting change with no extraction-path edit (the #671 ECS case) would otherwise
+  route to a green replay against a stale bundle.
+  A `diagnostic_version` decrease is permitted only as an **authorised revert**: the author lowers
+  the code version *and* re-mints, so the committed bundle changes and the gate recognises the
+  revert structurally rather than via a flag.
 - **`committed_integrity_ok`** recomputes the committed digests from the working tree
   and compares them to `manifest.committed`.
 - **`catalog_integrity_ok`** recomputes the input catalog hash
diff --git a/packages/climate-ref-core/src/climate_ref_core/regression/gate.py b/packages/climate-ref-core/src/climate_ref_core/regression/gate.py
index 5c59dbc88..25741526f 100644
--- a/packages/climate-ref-core/src/climate_ref_core/regression/gate.py
+++ b/packages/climate-ref-core/src/climate_ref_core/regression/gate.py
@@ -1,22 +1,29 @@
 """
 CI coupling gate for test case regression bundles.
 
-For each test case, CI must decide *how* to verify the regression baseline in a pull request,
+For each test case, CI decides how to verify the regression baseline in a pull request,
 based on what changed relative to the base branch:
 
-- **EXECUTE** — re-run the diagnostic end-to-end and compare the regenerated committed
-    bundle to the in-repo copy (tolerant compare).
-    Required when the author has bumped ``test_case_version`` to authorise a new baseline
-    but no native baseline exists to replay against.
-- **REPLAY** — materialise the cached native baseline and re-run only
-    ``build_execution_result`` against it, comparing to the committed bundle.
-    Cheap and anonymous; used when extraction code changed but the committed bundle did
-    not, to seed a newly added manifest, and to verify a ``test_case_version`` bump that ships native blobs
-    — but only when native blobs exist to replay.
-- **FAIL** — the committed bundle (or its input catalog) changed without a
-    ``test_case_version`` bump (an unauthorised baseline change), or the version moved backwards.
-- **SKIP** — nothing relevant to this test case changed, or the case is not yet under
-    regression-baseline management.
+- **EXECUTE**: re-run the diagnostic end-to-end and compare the regenerated bundle
+    to the committed copy.
+    Used when ``test_case_version`` was bumped but no native baseline exists to replay.
+- **REPLAY**: re-run ``build_execution_result`` against the cached native baseline
+    and compare to the committed bundle.
+    Used when extraction code changed but the committed bundle did not,
+    to seed a newly added manifest,
+    and to verify a ``test_case_version`` bump that ships native blobs.
+- **FAIL**: the committed bundle or its catalog changed without a ``test_case_version`` bump,
+    a version moved backwards,
+    or the in-code ``Diagnostic.version`` no longer matches the recorded ``diagnostic_version``.
+- **SKIP**: nothing relevant changed, or the case is not under regression-baseline management.
+
+The gate tracks two orthogonal version axes:
+``test_case_version`` (per-case, mint-authored)
+and ``diagnostic_version`` (per-diagnostic, author-authored).
+``test_case_version`` is monotonic.
+``diagnostic_version`` may decrease only for an authorised revert:
+the code version is lowered and the baseline re-minted so the committed bundle changes,
+which the gate recognises structurally rather than via a flag.
 
 See [Regression Baselines](https://climate-ref.readthedocs.io/en/latest/background/regression-baselines/)
 for more information about the motivation and workflow for regression baselines.
@@ -59,13 +66,14 @@ class GateDecision:
     """A human-readable explanation, surfaced in CI logs."""
 
 
-def decide_coupling(  # noqa: PLR0911, PLR0912
+def decide_coupling(  # noqa: PLR0911, PLR0912, PLR0913
     manifest: Manifest | None,
     base_manifest: Manifest | None,
     *,
     extraction_changed: bool = False,
     committed_integrity_ok: bool = True,
     catalog_integrity_ok: bool = True,
+    code_diagnostic_version: int | None = None,
 ) -> GateDecision:
     """
     Decide how CI should verify a single test case's regression baseline.
@@ -118,6 +126,12 @@ def decide_coupling(  # noqa: PLR0911, PLR0912
         so the committed bundle no longer reflects its inputs — a hard failure.
 
         Always ``True`` when the manifest carries no ``catalog_hash``
+    code_diagnostic_version
+        The diagnostic's current in-code ``Diagnostic.version``, injected by the caller
+        (the pure function does no I/O). When provided, a code version that exceeds
+        ``manifest.diagnostic_version`` fails the case as a stale baseline that must be
+        re-minted, and a code version below it fails as an illegal downgrade with no re-mint.
+        ``None`` (the default) skips the staleness comparison entirely, preserving legacy behaviour.
 
     Returns
     -------
@@ -156,6 +170,28 @@ def decide_coupling(  # noqa: PLR0911, PLR0912
             "regenerate the baseline with `ref test-cases run` after changing the inputs",
         )
 
+    # Runs before seeding so a newly added manifest whose author bumped the code
+    # without re-minting still fails.
+    # Equality must fall through; only the > and < arms return.
+    if manifest is not None and code_diagnostic_version is not None:
+        if code_diagnostic_version > manifest.diagnostic_version:
+            return GateDecision(
+                Action.FAIL,
+                f"diagnostic Diagnostic.version is {code_diagnostic_version} but the baseline "
+                f"manifest records diagnostic_version {manifest.diagnostic_version}; the "
+                "diagnostic's results changed; re-mint this baseline (`ref test-cases mint`) "
+                "so the committed bundle reflects the new version",
+            )
+        if code_diagnostic_version < manifest.diagnostic_version:
+            return GateDecision(
+                Action.FAIL,
+                f"diagnostic Diagnostic.version ({code_diagnostic_version}) is below the "
+                f"baseline's diagnostic_version ({manifest.diagnostic_version}); "
+                "Diagnostic.version is append-only. To revert legitimately, lower the code "
+                "version AND re-mint (`ref test-cases mint`) so the bundle is re-authored at "
+                "the lower version.",
+            )
+
     if base_manifest is None:
         # Seeding a newly added manifest.
         # Replay only verifies something when native blobs exist
@@ -177,6 +213,20 @@ def decide_coupling(  # noqa: PLR0911, PLR0912
             f"{manifest.test_case_version}); version must be monotonic",
         )
 
+    # A diagnostic_version decrease only fails when the committed bundle is unchanged:
+    # a bare downgrade with no re-mint.
+    # A decrease that ships a re-minted bundle is an authorised revert and falls through,
+    # where the committed-changed logic below re-verifies it.
+    if manifest.diagnostic_version < base_manifest.diagnostic_version:
+        if manifest.committed == base_manifest.committed:
+            return GateDecision(
+                Action.FAIL,
+                f"diagnostic_version decreased ({base_manifest.diagnostic_version} -> "
+                f"{manifest.diagnostic_version}) with the committed bundle unchanged; "
+                "a bare downgrade is not permitted; re-mint to re-author the baseline at "
+                "the lower version, or restore the version",
+            )
+
     version_bumped = manifest.test_case_version > base_manifest.test_case_version
     committed_changed = manifest.committed != base_manifest.committed
     native_changed = manifest.native != base_manifest.native
diff --git a/packages/climate-ref-core/src/climate_ref_core/regression/manifest.py b/packages/climate-ref-core/src/climate_ref_core/regression/manifest.py
index 13a95cef2..56ae53ecc 100644
--- a/packages/climate-ref-core/src/climate_ref_core/regression/manifest.py
+++ b/packages/climate-ref-core/src/climate_ref_core/regression/manifest.py
@@ -6,6 +6,8 @@
 - ``schema``: the manifest schema version (``SCHEMA_VERSION``).
 - ``test_case_version``: a monotonic, author-bumped integer coupling the committed
   bundle to its native outputs.
+- ``diagnostic_version``: the author-declared ``Diagnostic.version`` captured at mint
+  time, coupling the baseline to the diagnostic code that produced it.
 - ``committed``: sha256 digests of the committed regression JSON artefacts,
   computed over the exact placeholder-substituted bytes as they sit on disk,
   so that a CI recompute is deterministic.
@@ -26,7 +28,7 @@
 
 from climate_ref_core.paths import safe_path
 
-SCHEMA_VERSION: int = 1
+SCHEMA_VERSION: int = 2
 """Current manifest schema version."""
 
 _DIGEST_RE = re.compile(r"^[0-9a-f]{64}$")
@@ -133,6 +135,14 @@ class Manifest:
     test_case_version: int
     """Monotonic, author-bumped version coupling the bundle to its native outputs."""
 
+    diagnostic_version: int
+    """Author-declared ``Diagnostic.version`` at mint time.
+
+    Monotonic and append-only (with an authorised-revert carve-out in the CI gate).
+    The gate fails a case whose in-code ``Diagnostic.version`` exceeds this value
+    (a stale baseline that must be re-minted).
+    """
+
     committed: dict[str, str]
     """Digests of committed regression JSON artefacts: ``{relpath: sha256}``."""
 
@@ -195,7 +205,11 @@ def loads(cls, text: str, *, source: str = "<string>") -> Manifest:
             (e.g. hand-edited or written by an incompatible version).
         """
         data = json.loads(text)
-        missing = [key for key in ("schema", "test_case_version", "committed", "native") if key not in data]
+        missing = [
+            key
+            for key in ("schema", "test_case_version", "diagnostic_version", "committed", "native")
+            if key not in data
+        ]
         if missing:
             raise ValueError(
                 f"Invalid manifest {source}: missing required keys {missing}. "
@@ -209,6 +223,16 @@ def loads(cls, text: str, *, source: str = "<string>") -> Manifest:
                 f"expected {SCHEMA_VERSION}. The manifest was written by an incompatible "
                 "version; regenerate it with `ref test-cases run --force-regen`."
             )
+        diagnostic_version = data["diagnostic_version"]
+        if (
+            isinstance(diagnostic_version, bool)
+            or not isinstance(diagnostic_version, int)
+            or diagnostic_version < 1
+        ):
+            raise ValueError(
+                f"Invalid manifest {source}: diagnostic_version {diagnostic_version!r} "
+                "is invalid; expected an integer >= 1."
+            )
         try:
             native = {
                 relpath: NativeEntry(sha256=entry["sha256"], size=entry["size"])
@@ -235,6 +259,7 @@ def loads(cls, text: str, *, source: str = "<string>") -> Manifest:
         return cls(
             schema=data["schema"],
             test_case_version=data["test_case_version"],
+            diagnostic_version=diagnostic_version,
             committed=dict(data["committed"]),
             native=native,
             # TODO: remove optonality when all manifests have this field.
@@ -256,6 +281,7 @@ def dump(self, path: Path) -> None:
         payload = {
             "schema": self.schema,
             "test_case_version": self.test_case_version,
+            "diagnostic_version": self.diagnostic_version,
             "catalog_hash": self.catalog_hash,
             "committed": self.committed,
             "native": {relpath: asdict(entry) for relpath, entry in self.native.items()},
@@ -264,7 +290,12 @@ def dump(self, path: Path) -> None:
         path.write_text(text, encoding="utf-8")
 
     @classmethod
-    def seed_v1(cls, committed_digests: dict[str, str], catalog_hash: str | None = None) -> Manifest:
+    def seed_v1(
+        cls,
+        committed_digests: dict[str, str],
+        catalog_hash: str | None = None,
+        diagnostic_version: int = 1,
+    ) -> Manifest:
         """
         Create an initial manifest at ``test_case_version == 1`` with no native outputs.
 
@@ -274,6 +305,9 @@ def seed_v1(cls, committed_digests: dict[str, str], catalog_hash: str | None = N
             Digests of the committed regression JSON artefacts.
         catalog_hash
             Hash of the input ``catalog.yaml`` that produced the baseline, if known.
+        diagnostic_version
+            Author-declared ``Diagnostic.version`` at seed time. Defaults to ``1``,
+            the version of a brand-new baseline.
 
         Returns
         -------
@@ -283,6 +317,7 @@ def seed_v1(cls, committed_digests: dict[str, str], catalog_hash: str | None = N
         return cls(
             schema=SCHEMA_VERSION,
             test_case_version=1,
+            diagnostic_version=diagnostic_version,
             committed=dict(committed_digests),
             catalog_hash=catalog_hash,
             native={},
diff --git a/packages/climate-ref-core/tests/unit/regression/test_gate.py b/packages/climate-ref-core/tests/unit/regression/test_gate.py
index c0fbea039..2a03eb26f 100644
--- a/packages/climate-ref-core/tests/unit/regression/test_gate.py
+++ b/packages/climate-ref-core/tests/unit/regression/test_gate.py
@@ -21,11 +21,13 @@ def make_manifest(
     version: int,
     committed: dict[str, str] | None = None,
     native: dict[str, NativeEntry] | None = None,
+    diagnostic_version: int = 1,
 ) -> Manifest:
     """Build a manifest with a given version and committed/native digests."""
     return Manifest(
         schema=SCHEMA_VERSION,
         test_case_version=version,
+        diagnostic_version=diagnostic_version,
         committed=committed if committed is not None else {"output.json": "a" * 64},
         native=native if native is not None else {},
     )
@@ -158,6 +160,84 @@ def test_no_change_skips(self) -> None:
         assert "nothing to verify" in decision.reason
 
 
+class TestDiagnosticVersionGate:
+    """The staleness (2a) and conditioned-monotonic (2b) diagnostic_version branches."""
+
+    def test_code_ahead_of_manifest_fails(self) -> None:
+        # The diagnostic was bumped but the baseline was not re-minted: stale -> FAIL.
+        manifest = make_manifest(1, diagnostic_version=1)
+        decision = decide_coupling(manifest, None, code_diagnostic_version=2)
+        assert decision.action is Action.FAIL
+        assert "re-mint" in decision.reason
+
+    def test_code_below_manifest_fails(self) -> None:
+        # The code version dropped below the recorded baseline with no re-mint: FAIL.
+        manifest = make_manifest(1, diagnostic_version=2)
+        decision = decide_coupling(manifest, None, code_diagnostic_version=1)
+        assert decision.action is Action.FAIL
+        assert "append-only" in decision.reason
+
+    def test_code_equals_manifest_falls_through(self) -> None:
+        # Equality must NOT early-return: a matched baseline proceeds to the normal logic.
+        manifest = make_manifest(1, native={"data.nc": NativeEntry("a" * 64, 10)}, diagnostic_version=2)
+        decision = decide_coupling(manifest, None, code_diagnostic_version=2)
+        assert decision.action is Action.REPLAY
+        assert "seeding" in decision.reason
+
+    def test_staleness_outranks_seeding(self) -> None:
+        # A newly added manifest (no base) whose code is ahead is stale -> FAIL, not REPLAY/SKIP.
+        manifest = make_manifest(1, native={"data.nc": NativeEntry("a" * 64, 10)}, diagnostic_version=1)
+        decision = decide_coupling(manifest, None, code_diagnostic_version=2)
+        assert decision.action is Action.FAIL
+
+    def test_staleness_below_integrity(self) -> None:
+        # An integrity failure outranks the staleness check.
+        manifest = make_manifest(1, diagnostic_version=1)
+        decision = decide_coupling(manifest, None, committed_integrity_ok=False, code_diagnostic_version=2)
+        assert decision.action is Action.FAIL
+        assert "does not match manifest.json digests" in decision.reason
+
+    def test_diagnostic_version_decrease_bare_downgrade_fails(self) -> None:
+        # A diagnostic_version decrease with the committed bundle unchanged is a bare downgrade.
+        base = make_manifest(1, {"output.json": "a" * 64}, diagnostic_version=2)
+        current = make_manifest(1, {"output.json": "a" * 64}, diagnostic_version=1)
+        decision = decide_coupling(current, base, code_diagnostic_version=1)
+        assert decision.action is Action.FAIL
+        assert "bare downgrade" in decision.reason
+
+    def test_diagnostic_version_decrease_with_reminted_bundle_falls_through(self) -> None:
+        # A decrease that ships a re-minted bundle (committed changed) + a tcv bump is authorised.
+        native = {"data.nc": NativeEntry("a" * 64, 10)}
+        base = make_manifest(1, {"output.json": "a" * 64}, native, diagnostic_version=2)
+        current = make_manifest(2, {"output.json": "b" * 64}, native, diagnostic_version=1)
+        decision = decide_coupling(current, base, code_diagnostic_version=1)
+        # 2b falls through; the tcv bump with native present routes to REPLAY.
+        assert decision.action is Action.REPLAY
+        assert "1 -> 2" in decision.reason
+
+    def test_diagnostic_version_increase_proceeds(self) -> None:
+        # An increase (with matching code) is not a 2b failure; normal logic applies.
+        base = make_manifest(1, {"output.json": "a" * 64}, diagnostic_version=1)
+        current = make_manifest(1, {"output.json": "a" * 64}, diagnostic_version=2)
+        decision = decide_coupling(current, base, code_diagnostic_version=2)
+        assert decision.action is Action.SKIP
+        assert "nothing to verify" in decision.reason
+
+    def test_legacy_none_skips_all_new_branches(self) -> None:
+        # code_diagnostic_version=None preserves legacy behaviour: no staleness check at all.
+        manifest = make_manifest(1, diagnostic_version=1)
+        decision = decide_coupling(manifest, None, code_diagnostic_version=None)
+        assert decision.action is Action.SKIP
+
+    def test_tcv_bump_with_matched_diagnostic_version_still_executes(self) -> None:
+        # A test_case_version bump with code == manifest.diagnostic_version behaves as before.
+        base = make_manifest(1, diagnostic_version=2)
+        current = make_manifest(2, diagnostic_version=2)
+        decision = decide_coupling(current, base, code_diagnostic_version=2)
+        assert decision.action is Action.EXECUTE
+        assert "1 -> 2" in decision.reason
+
+
 class TestPathsUnder:
     def test_file_directly_under_root_matches(self) -> None:
         assert paths_under(["pkg/src/mod.py"], ["pkg/src"])
diff --git a/packages/climate-ref-core/tests/unit/regression/test_manifest.py b/packages/climate-ref-core/tests/unit/regression/test_manifest.py
index 90700bcb6..33f3fe1df 100644
--- a/packages/climate-ref-core/tests/unit/regression/test_manifest.py
+++ b/packages/climate-ref-core/tests/unit/regression/test_manifest.py
@@ -83,6 +83,14 @@ def test_committed_digests_stored(self) -> None:
         m = Manifest.seed_v1(digests)
         assert m.committed == digests
 
+    def test_diagnostic_version_defaults_to_1(self) -> None:
+        m = Manifest.seed_v1({})
+        assert m.diagnostic_version == 1
+
+    def test_diagnostic_version_override(self) -> None:
+        m = Manifest.seed_v1({}, diagnostic_version=3)
+        assert m.diagnostic_version == 3
+
 
 class TestDumpLoad:
     """dump then load must be byte-identical and stable."""
@@ -91,6 +99,7 @@ def _make_manifest(self) -> Manifest:
         return Manifest(
             schema=SCHEMA_VERSION,
             test_case_version=2,
+            diagnostic_version=3,
             committed={"output.json": "cc" * 32, "series.json": "dd" * 32},
             native={"foo/bar.nc": NativeEntry(sha256="ee" * 32, size=1024)},
         )
@@ -102,6 +111,7 @@ def test_round_trip_values(self, tmp_path: Path) -> None:
         loaded = Manifest.load(p)
         assert loaded.schema == original.schema
         assert loaded.test_case_version == original.test_case_version
+        assert loaded.diagnostic_version == original.diagnostic_version
         assert loaded.committed == original.committed
         assert loaded.native == original.native
 
@@ -133,6 +143,7 @@ def test_native_entry_round_trip(self, tmp_path: Path) -> None:
         m = Manifest(
             schema=SCHEMA_VERSION,
             test_case_version=1,
+            diagnostic_version=1,
             committed={},
             native={"path/to/file.nc": entry},
         )
@@ -141,17 +152,67 @@ def test_native_entry_round_trip(self, tmp_path: Path) -> None:
         loaded = Manifest.load(p)
         assert loaded.native["path/to/file.nc"] == entry
 
+    def test_dump_emits_unconditional_null_catalog_hash(self, tmp_path: Path) -> None:
+        # dump always serialises catalog_hash (as null when unset) for byte-stability.
+        p = tmp_path / "manifest.json"
+        self._make_manifest().dump(p)
+        data = json.loads(p.read_text(encoding="utf-8"))
+        assert "catalog_hash" in data
+        assert data["catalog_hash"] is None
+        assert data["diagnostic_version"] == 3
+
     def test_load_missing_keys_raises_value_error(self, tmp_path: Path) -> None:
         p = tmp_path / "manifest.json"
         p.write_text(json.dumps({"schema": SCHEMA_VERSION, "committed": {}}), encoding="utf-8")
-        with pytest.raises(ValueError, match=r"missing required keys \['test_case_version', 'native'\]"):
+        with pytest.raises(
+            ValueError,
+            match=r"missing required keys \['test_case_version', 'diagnostic_version', 'native'\]",
+        ):
+            Manifest.load(p)
+
+    def test_load_missing_diagnostic_version_raises_value_error(self, tmp_path: Path) -> None:
+        # A schema-2 payload missing diagnostic_version is rejected post-bump.
+        p = tmp_path / "manifest.json"
+        payload = {
+            "schema": SCHEMA_VERSION,
+            "test_case_version": 1,
+            "committed": {},
+            "native": {},
+        }
+        p.write_text(json.dumps(payload), encoding="utf-8")
+        with pytest.raises(ValueError, match="missing required keys"):
             Manifest.load(p)
 
+    @pytest.mark.parametrize("bad_value", [0, -1, "1", True, 1.0])
+    def test_load_rejects_invalid_diagnostic_version(self, bad_value: object) -> None:
+        payload = {
+            "schema": SCHEMA_VERSION,
+            "test_case_version": 1,
+            "diagnostic_version": bad_value,
+            "committed": {},
+            "native": {},
+        }
+        with pytest.raises(ValueError, match="diagnostic_version"):
+            Manifest.loads(json.dumps(payload))
+
+    def test_load_rejects_schema_1_text(self) -> None:
+        # A schema-1 manifest carrying diagnostic_version is still rejected by the schema check.
+        payload = {
+            "schema": 1,
+            "test_case_version": 1,
+            "diagnostic_version": 1,
+            "committed": {},
+            "native": {},
+        }
+        with pytest.raises(ValueError, match="unsupported schema"):
+            Manifest.loads(json.dumps(payload))
+
     def test_load_malformed_native_entry_raises_value_error(self, tmp_path: Path) -> None:
         p = tmp_path / "manifest.json"
         payload = {
             "schema": SCHEMA_VERSION,
             "test_case_version": 1,
+            "diagnostic_version": 1,
             "committed": {},
             "native": {"file.nc": {"sha256": "aa" * 32}},  # missing "size"
         }
@@ -168,6 +229,7 @@ def test_load_rejects_unsafe_native_path(self, tmp_path: Path, bad_relpath: str)
         payload = {
             "schema": SCHEMA_VERSION,
             "test_case_version": 1,
+            "diagnostic_version": 1,
             "committed": {},
             "native": {bad_relpath: {"sha256": "aa" * 32, "size": 1}},
         }
@@ -184,6 +246,7 @@ def test_load_rejects_bad_native_digest(self, tmp_path: Path, bad_digest: str) -
         payload = {
             "schema": SCHEMA_VERSION,
             "test_case_version": 1,
+            "diagnostic_version": 1,
             "committed": {},
             "native": {"file.nc": {"sha256": bad_digest, "size": 1}},
         }
@@ -191,11 +254,12 @@ def test_load_rejects_bad_native_digest(self, tmp_path: Path, bad_digest: str) -
         with pytest.raises(ValueError, match="Invalid sha256 digest"):
             Manifest.load(p)
 
-    @pytest.mark.parametrize("bad_schema", [2, 0, "1", True, 1.0])
+    @pytest.mark.parametrize("bad_schema", [3, 0, "1", True, 1.0])
     def test_load_rejects_unknown_schema(self, bad_schema: object) -> None:
         payload = {
             "schema": bad_schema,
             "test_case_version": 1,
+            "diagnostic_version": 1,
             "committed": {},
             "native": {},
         }
@@ -207,6 +271,7 @@ def test_load_rejects_invalid_native_size(self, bad_size: object) -> None:
         payload = {
             "schema": SCHEMA_VERSION,
             "test_case_version": 1,
+            "diagnostic_version": 1,
             "committed": {},
             "native": {"file.nc": {"sha256": "aa" * 32, "size": bad_size}},
         }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/climate-at-global-warming-levels/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/climate-at-global-warming-levels/cmip6/manifest.json
index 5391330fa..6cd9776ec 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/climate-at-global-warming-levels/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/climate-at-global-warming-levels/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "e0dd8f0902fcc0d6b032e6ef1e57b785c776aa18847ef60805d4b388166a2daa",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "20a2c7e604440a3e14b33de2306b0deee39187a7bebf626af2dab1cebdc6ab92",
@@ -103,6 +104,6 @@
       "size": 2
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/climate-drivers-for-fire/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/climate-drivers-for-fire/cmip6/manifest.json
index 38732230c..74f79e554 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/climate-drivers-for-fire/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/climate-drivers-for-fire/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "da1aeaaa1b0a99771b91fdddaefcd3769a8ef6d7183396cfd0d0f97eb7e359dd",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "e52b1e19e1ed5a2a046bb8aa01c004240305fabfe69c4ffb4e64898b1b6bbb84",
@@ -43,6 +44,6 @@
       "size": 2
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/climate-drivers-for-fire/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/climate-drivers-for-fire/cmip7/manifest.json
index 31bf2d55a..82323eb17 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/climate-drivers-for-fire/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/climate-drivers-for-fire/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "c7a2dd809d8e30636ec7b2410764b4f44a799c911bb10b4ee323a57f8c94b751",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {},
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/cloud-radiative-effects/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/cloud-radiative-effects/cmip6/manifest.json
index 617f68e09..e08cba786 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/cloud-radiative-effects/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/cloud-radiative-effects/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "4b9ebaf83c65b8e0718a84951502617a545fce6386cabe640de7ec406afe6509",
     "series.json": "4ec8ab11924089ef7cba8bd16de237ad8431399caaef74c0a66e81fefee69ef3"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "e52b1e19e1ed5a2a046bb8aa01c004240305fabfe69c4ffb4e64898b1b6bbb84",
@@ -79,6 +80,6 @@
       "size": 60160
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-cli-ta/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-cli-ta/cmip6/manifest.json
index e813145c7..7b06d2b2d 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-cli-ta/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-cli-ta/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "454335b7796afd5d5c214c24501fad57b9dbaf21c997177209da025d24b3b6aa",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "e52b1e19e1ed5a2a046bb8aa01c004240305fabfe69c4ffb4e64898b1b6bbb84",
@@ -43,6 +44,6 @@
       "size": 2
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clivi-lwcre/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clivi-lwcre/cmip6/manifest.json
index ef89dead6..ef499c2ed 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clivi-lwcre/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clivi-lwcre/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "312cf9003669edd2a808aa35983c77e987dba3a4f0ceb234b63345539e6a36a3",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "e52b1e19e1ed5a2a046bb8aa01c004240305fabfe69c4ffb4e64898b1b6bbb84",
@@ -43,6 +44,6 @@
       "size": 2
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clivi-lwcre/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clivi-lwcre/cmip7/manifest.json
index 906c842a3..4bc7cde6f 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clivi-lwcre/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clivi-lwcre/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "add694adb3b029792e8706dc1ec646e90978d30b0e5ff3be7ce86d67715a3368",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {},
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clt-swcre/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clt-swcre/cmip6/manifest.json
index 3e841cf4b..e4c700d20 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clt-swcre/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clt-swcre/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "cd6d53a6375230ea611d2938b3f8af535b24f3045ce8f520dd0edde98c54ec96",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "e52b1e19e1ed5a2a046bb8aa01c004240305fabfe69c4ffb4e64898b1b6bbb84",
@@ -43,6 +44,6 @@
       "size": 2
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clt-swcre/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clt-swcre/cmip7/manifest.json
index 35e09cf11..b872e914e 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clt-swcre/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clt-swcre/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "958937d8c54124c46bdada306cccec6401a7d6a8397b2b003151e278ee38f169",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {},
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clwvi-pr/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clwvi-pr/cmip6/manifest.json
index 089975392..e83045134 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clwvi-pr/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clwvi-pr/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "c95e6545f3873b3627b496aa9245e12c7b7e3834f073d89b6dfc9e0d553691af",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "e52b1e19e1ed5a2a046bb8aa01c004240305fabfe69c4ffb4e64898b1b6bbb84",
@@ -43,6 +44,6 @@
       "size": 2
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clwvi-pr/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clwvi-pr/cmip7/manifest.json
index 501b27344..6b6e5b7a2 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clwvi-pr/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/cloud-scatterplots-clwvi-pr/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "7342b55c0338ca15ab3fc43f366fe1be04a68922ee8566cd24f77b9fe2caf6bc",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {},
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/enso-basic-climatology/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/enso-basic-climatology/cmip6/manifest.json
index cf3e5eb44..eff37af87 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/enso-basic-climatology/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/enso-basic-climatology/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "f1a62fdcea7c346688eb476587778df31bec3e0b457b8fb5b4aeb7d57d2bb63e",
     "series.json": "2e7f6ee7162116378d21f0f405d639244ea8e53b74c2dfe2260ad0e1665b3ec9"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "e52b1e19e1ed5a2a046bb8aa01c004240305fabfe69c4ffb4e64898b1b6bbb84",
@@ -147,6 +148,6 @@
       "size": 93534
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/enso-characteristics/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/enso-characteristics/cmip6/manifest.json
index 7db55d5b2..9870c424b 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/enso-characteristics/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/enso-characteristics/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "334cac04275b2581ab1129356f1242164d3bb5eaade4fc3de27fb9b89772f1a5",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "63803d2c8776cb1a2d869405aaac5513e512a08d0c36a92d1e7eba4351091024",
@@ -59,6 +60,6 @@
       "size": 2
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/equilibrium-climate-sensitivity/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/equilibrium-climate-sensitivity/cmip6/manifest.json
index 657b6d01a..746042b56 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/equilibrium-climate-sensitivity/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/equilibrium-climate-sensitivity/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "dd8c208f2134be1289606e1b12be998d327f4ae329318a5a83cfd82ac2325219",
     "series.json": "cac18de7ea3575ad34111d4e3402545ba358959e2037e5bc8c48fdf22f264267"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "4253b68b6116fc9afc5970a9186b20c82be9975330842a8e61efe812b1c2d0aa",
@@ -43,6 +44,6 @@
       "size": 8877
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/global-mean-timeseries/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/global-mean-timeseries/cmip6/manifest.json
index 4e4a2c2af..c0b1136a5 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/global-mean-timeseries/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/global-mean-timeseries/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "ec46b24f66ebe4116471f65b6da7b1b141cd5fdc6683baba7b09c5f9579c207d",
     "series.json": "6e2a7bfbf5eb29f4380344a81b7022c772e2d5b22620266af47b739f6c92e5d6"
   },
+  "diagnostic_version": 1,
   "native": {
     "diagnostic.json": {
       "sha256": "e52b1e19e1ed5a2a046bb8aa01c004240305fabfe69c4ffb4e64898b1b6bbb84",
@@ -35,6 +36,6 @@
       "size": 9827
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/global-mean-timeseries/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/global-mean-timeseries/cmip7/manifest.json
index ed2b6bb45..a07b297ce 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/global-mean-timeseries/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/global-mean-timeseries/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "9a8ff885fbf13c06d1974834210da71f48f83fa1700f335fce5813bf5c0535b2",
     "series.json": "30b664467549cef4af8a5cb11736fa8aa7b8c1042ea0401192bf6d7c03a9ac0b"
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+  "diagnostic_version": 1,
   "native": {},
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/ozone-annual-cycle/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/ozone-annual-cycle/cmip6/manifest.json
index 6f7d01342..8ab2d212b 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/ozone-annual-cycle/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/ozone-annual-cycle/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "978fd3b10d7e7ff386b4c39dbdc1f33ef5509fcb3afd3759132eee6524fc1b60",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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@@ -43,6 +44,6 @@
       "size": 2
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/ozone-annual-cycle/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/ozone-annual-cycle/cmip7/manifest.json
index 08075cd11..def58c196 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/ozone-annual-cycle/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/ozone-annual-cycle/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "6f71c80892ecb575a43c0ee25a77769ad779162ae4da22fc1585ee869a1d3857",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
   "native": {},
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/ozone-lat-time/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/ozone-lat-time/cmip6/manifest.json
index 6764b53f4..a96abd484 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/ozone-lat-time/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/ozone-lat-time/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "806aec53b4c2ce0a9d9ec21cd2c0360d9b433ef2392f04053eead0f4e9e30a0e",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
   "native": {
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@@ -43,6 +44,6 @@
       "size": 2
     }
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/ozone-lat-time/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/ozone-lat-time/cmip7/manifest.json
index 85923cd86..509b065a8 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/ozone-lat-time/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/ozone-lat-time/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "758c03396e0b6b00a89ace6651712a6f9dc268f5d207fe3bbb35365351b68205",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {},
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/ozone-nh-mar/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/ozone-nh-mar/cmip6/manifest.json
index d0192fbc6..2001df54e 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/ozone-nh-mar/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/ozone-nh-mar/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "a8589880fc34c8a12ab98fdccf5c893dc58c8d6ba76a72338c8297eb375af1f4",
     "series.json": "9cd508338685d5054387550f19f9b008ddc8a255bd6f28ba4bc909cc242a43ec"
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+  "diagnostic_version": 1,
   "native": {
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@@ -35,6 +36,6 @@
       "size": 4422
     }
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/ozone-nh-mar/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/ozone-nh-mar/cmip7/manifest.json
index 65aae7f8d..5765aae25 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/ozone-nh-mar/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/ozone-nh-mar/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "a8589880fc34c8a12ab98fdccf5c893dc58c8d6ba76a72338c8297eb375af1f4",
     "series.json": "d8bf2a7bd65802c545927b8293bfda7ca47bc08c9160aa387291624b32c08571"
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+  "diagnostic_version": 1,
   "native": {},
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/ozone-sh-oct/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/ozone-sh-oct/cmip6/manifest.json
index cfbbed55c..0e8e4fb1d 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/ozone-sh-oct/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/ozone-sh-oct/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "7474e7e327a830c53b821d5320e05bff2f55c24068a4926fb49c76c484ed2c9a",
     "series.json": "4b803facd29ee24afb14f81e2de5d5ae5dc3997a28f58a61eec90d27525d7c1d"
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+  "diagnostic_version": 1,
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@@ -35,6 +36,6 @@
       "size": 4412
     }
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/ozone-sh-oct/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/ozone-sh-oct/cmip7/manifest.json
index b957db73a..e8cf34cc7 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/ozone-sh-oct/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/ozone-sh-oct/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "7474e7e327a830c53b821d5320e05bff2f55c24068a4926fb49c76c484ed2c9a",
     "series.json": "f40c1da8ac81e1ef2317fad9c17dbd78e04f336b226a9313307dbdfadbeb3fc0"
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+  "diagnostic_version": 1,
   "native": {},
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/ozone-zonal/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/ozone-zonal/cmip6/manifest.json
index 246376dbc..f5b2dc46b 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/ozone-zonal/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/ozone-zonal/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "c3ad14429dfae8653c4ee2a86e24c5c8b49fa7f5ec4e7b13f3183aaf719fb75a",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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@@ -43,6 +44,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-annual-cycle/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-annual-cycle/cmip6/manifest.json
index f4cc21678..2228236ac 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-annual-cycle/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-annual-cycle/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "4face38eb05e1815739e9dd290ddffbb13989edd30ae4483927b3902915abc31",
     "series.json": "f4da9c7dbf8f6fdcc0ac6dd86043e6163a788034c8076e865bf2cf9703626b63"
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+  "diagnostic_version": 1,
   "native": {
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@@ -2363,6 +2364,6 @@
       "size": 295674
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-annual-cycle/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-annual-cycle/cmip7/manifest.json
index be373c4c6..145aa7558 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-annual-cycle/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-annual-cycle/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "4face38eb05e1815739e9dd290ddffbb13989edd30ae4483927b3902915abc31",
     "series.json": "8442bce313fac12b2c0e1dd66e7ed6702455600d02aabf319986780731dbec78"
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+  "diagnostic_version": 1,
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-timeseries/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-timeseries/cmip6/manifest.json
index 42c5a0947..086d4c72d 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-timeseries/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-timeseries/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "f4161df1ae5efcf92d271fe6f6f50b65d04efd73b503659479b6a7b242254ca0",
     "series.json": "0882a4bc2e3007cc5451574124079b9621f4e1fe07b48f3bf952ec6e83c8aa48"
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+  "diagnostic_version": 1,
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@@ -135,6 +136,6 @@
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 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-timeseries/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-timeseries/cmip7/manifest.json
index 9367c0df8..70d1de404 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-timeseries/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-timeseries/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "f4161df1ae5efcf92d271fe6f6f50b65d04efd73b503659479b6a7b242254ca0",
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+  "diagnostic_version": 1,
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-  "schema": 1,
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 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-trend/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-trend/cmip6/manifest.json
index 9158b5f78..70b5e2f94 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-trend/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-trend/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "51aa6644a84d7632889f588d83bf8c7680caecdcae2c5af9c4f1f38a699f9e53",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
   "native": {
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@@ -83,6 +84,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-trend/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-trend/cmip7/manifest.json
index 7cb785d65..b9c994852 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-trend/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/regional-historical-trend/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "51aa6644a84d7632889f588d83bf8c7680caecdcae2c5af9c4f1f38a699f9e53",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-area-basic/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-area-basic/cmip6/manifest.json
index a901c5114..3a964ba37 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-area-basic/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-area-basic/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "ece9f19183b1bede25cda85779d3eb905f51bc24615559dbcc2ac6688835cd92",
     "series.json": "8ad040e4747b2fc954d9166da0e6a11749cf5f97efc51ea73e49b220b2062f8b"
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+  "diagnostic_version": 1,
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@@ -63,6 +64,6 @@
       "size": 17179
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+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-area-basic/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-area-basic/cmip7/manifest.json
index c12d51d00..e5f0e2ea6 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-area-basic/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-area-basic/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "ece9f19183b1bede25cda85779d3eb905f51bc24615559dbcc2ac6688835cd92",
     "series.json": "1535dab04428841a3ac32a30acaa7c78ce57d8035cd3671518c01ab1db9e52eb"
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+  "diagnostic_version": 1,
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-sensitivity/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-sensitivity/cmip6/manifest.json
index 599b24ffb..d64db0bcf 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-sensitivity/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-sensitivity/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "0addb1511d0f758554aa7caac92ee3c254d279e2cb7da71e326dcdc191169939",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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@@ -55,6 +56,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-sensitivity/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-sensitivity/cmip7/manifest.json
index f7cf844db..f237e17b1 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-sensitivity/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/sea-ice-sensitivity/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "0addb1511d0f758554aa7caac92ee3c254d279e2cb7da71e326dcdc191169939",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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-  "schema": 1,
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 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response-emissions/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response-emissions/cmip6/manifest.json
index 594529a10..98b884f3a 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response-emissions/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response-emissions/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "666d10cf64bf489e34d726b6cad954dbd05b92cff0cb61b054b3a06d036c7558",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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@@ -35,6 +36,6 @@
       "size": 2
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+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response-emissions/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response-emissions/cmip7/manifest.json
index f89855f77..7945b5bf5 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response-emissions/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response-emissions/cmip7/manifest.json
@@ -5,7 +5,8 @@
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     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response/cmip6/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response/cmip6/manifest.json
index 26ad6f8d2..0f8697103 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response/cmip6/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "fd052cef9fed3553114ac7840c1a3771f1e0e0c626fe439e5248739390278d69",
     "series.json": "1a798f01f18c15b28d20af2397d80304bbe116a7d4d8b83ba4a26baaad1732aa"
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+  "diagnostic_version": 1,
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@@ -39,6 +40,6 @@
       "size": 8670
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response/cmip7/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response/cmip7/manifest.json
index 6cfb0155d..e454ca0ea 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response/cmip7/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/transient-climate-response/cmip7/manifest.json
@@ -5,7 +5,8 @@
     "output.json": "fd052cef9fed3553114ac7840c1a3771f1e0e0c626fe439e5248739390278d69",
     "series.json": "222fba950bba928affc9ec3d4c0267e71e5dba9e2ce6edae04289cc693034d27"
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+  "diagnostic_version": 1,
   "native": {},
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/zero-emission-commitment/cmip6-1pctCO2-parent/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/zero-emission-commitment/cmip6-1pctCO2-parent/manifest.json
index 6125d8c18..bbe52567d 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/zero-emission-commitment/cmip6-1pctCO2-parent/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/zero-emission-commitment/cmip6-1pctCO2-parent/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "1ee3bdfdd9c227d6a61d02862d9c0d10c0534b7dda424faf9296fb7447fb47d5",
     "series.json": "b7be3eed74de5ab386270f0c741ffd6007908297d50670c20e14af0dcfcc1db6"
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+  "diagnostic_version": 1,
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@@ -43,6 +44,6 @@
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-esmvaltool/tests/test-data/zero-emission-commitment/cmip6-esm-1pctCO2-parent/manifest.json b/packages/climate-ref-esmvaltool/tests/test-data/zero-emission-commitment/cmip6-esm-1pctCO2-parent/manifest.json
index 46e024676..b7ba00667 100644
--- a/packages/climate-ref-esmvaltool/tests/test-data/zero-emission-commitment/cmip6-esm-1pctCO2-parent/manifest.json
+++ b/packages/climate-ref-esmvaltool/tests/test-data/zero-emission-commitment/cmip6-esm-1pctCO2-parent/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "1ee3bdfdd9c227d6a61d02862d9c0d10c0534b7dda424faf9296fb7447fb47d5",
     "series.json": "51756d25e3969e66d38e2371879c1f2241e0e31f2826a6e9a4f9d5075e3fa341"
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@@ -43,6 +44,6 @@
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-  "schema": 1,
+  "schema": 2,
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 }
diff --git a/packages/climate-ref-example/tests/test-data/global-mean-timeseries/cmip7/manifest.json b/packages/climate-ref-example/tests/test-data/global-mean-timeseries/cmip7/manifest.json
index 91d02cecf..ecbea23ef 100644
--- a/packages/climate-ref-example/tests/test-data/global-mean-timeseries/cmip7/manifest.json
+++ b/packages/climate-ref-example/tests/test-data/global-mean-timeseries/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "e937c8b787585d0c2f4025eb93a4effe8f4065ba4575285655d5be6cffa5db55",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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@@ -23,6 +24,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 2
 }
diff --git a/packages/climate-ref-example/tests/test-data/global-mean-timeseries/default/manifest.json b/packages/climate-ref-example/tests/test-data/global-mean-timeseries/default/manifest.json
index 5ecb21bb3..573d1a904 100644
--- a/packages/climate-ref-example/tests/test-data/global-mean-timeseries/default/manifest.json
+++ b/packages/climate-ref-example/tests/test-data/global-mean-timeseries/default/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "e937c8b787585d0c2f4025eb93a4effe8f4065ba4575285655d5be6cffa5db55",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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@@ -23,6 +24,6 @@
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 2
 }
diff --git a/packages/climate-ref-example/tests/test-data/global-sst-bias/cmip7/manifest.json b/packages/climate-ref-example/tests/test-data/global-sst-bias/cmip7/manifest.json
index b2c31944e..a76c2898e 100644
--- a/packages/climate-ref-example/tests/test-data/global-sst-bias/cmip7/manifest.json
+++ b/packages/climate-ref-example/tests/test-data/global-sst-bias/cmip7/manifest.json
@@ -5,6 +5,7 @@
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@@ -31,6 +32,6 @@
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 }
diff --git a/packages/climate-ref-example/tests/test-data/global-sst-bias/default/manifest.json b/packages/climate-ref-example/tests/test-data/global-sst-bias/default/manifest.json
index 9080e509a..b2d31e00e 100644
--- a/packages/climate-ref-example/tests/test-data/global-sst-bias/default/manifest.json
+++ b/packages/climate-ref-example/tests/test-data/global-sst-bias/default/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "3fe2b84a2d7c0b7c5332657ccd49b6dfdbb6634d8d48902e883da35cd74ad9d4",
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@@ -31,6 +32,6 @@
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/burntfractionall-gfed/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/burntfractionall-gfed/cmip6/manifest.json
index 4e0ae0049..07fc3a894 100644
--- a/packages/climate-ref-ilamb/tests/test-data/burntfractionall-gfed/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/burntfractionall-gfed/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "bea6d4be3d825f3ebca24eb6a164409d05cbce234eeab4378ad21c57a9d199d1",
     "series.json": "bfc11736e025968323c015e182d4473fc1e03726d7d2d2a241fcd8f0002cdc71"
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+  "diagnostic_version": 2,
   "native": {
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@@ -99,6 +100,6 @@
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/burntfractionall-gfed/cmip7/manifest.json b/packages/climate-ref-ilamb/tests/test-data/burntfractionall-gfed/cmip7/manifest.json
index 7b2c7be14..d21466cdc 100644
--- a/packages/climate-ref-ilamb/tests/test-data/burntfractionall-gfed/cmip7/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/burntfractionall-gfed/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "35453fd1efc52369b562391777b76c794c5a568a5b44054b006721bbec626412",
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+  "diagnostic_version": 2,
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@@ -99,6 +100,6 @@
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+  "schema": 2,
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/csoil-hwsd2/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/csoil-hwsd2/cmip6/manifest.json
index 38ebb13fa..96065d4f2 100644
--- a/packages/climate-ref-ilamb/tests/test-data/csoil-hwsd2/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/csoil-hwsd2/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "012cc1766c43d0ee125a4ae63af7b286d087a8590546fdcf83e312a5e7623c7f",
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+  "diagnostic_version": 2,
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@@ -75,6 +76,6 @@
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/csoil-hwsd2/cmip7/manifest.json b/packages/climate-ref-ilamb/tests/test-data/csoil-hwsd2/cmip7/manifest.json
index b716ba321..21a73b14b 100644
--- a/packages/climate-ref-ilamb/tests/test-data/csoil-hwsd2/cmip7/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/csoil-hwsd2/cmip7/manifest.json
@@ -5,6 +5,7 @@
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@@ -75,6 +76,6 @@
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/emp-gleamgpcp2.3/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/emp-gleamgpcp2.3/cmip6/manifest.json
index 9f2ad698f..4da728c26 100644
--- a/packages/climate-ref-ilamb/tests/test-data/emp-gleamgpcp2.3/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/emp-gleamgpcp2.3/cmip6/manifest.json
@@ -5,6 +5,7 @@
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@@ -99,6 +100,6 @@
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/gpp-fluxnet2015/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/gpp-fluxnet2015/cmip6/manifest.json
index 14d514b64..5a7a7a110 100644
--- a/packages/climate-ref-ilamb/tests/test-data/gpp-fluxnet2015/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/gpp-fluxnet2015/cmip6/manifest.json
@@ -5,6 +5,7 @@
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@@ -99,6 +100,6 @@
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/gpp-wecann/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/gpp-wecann/cmip6/manifest.json
index 243881ca0..0711db279 100644
--- a/packages/climate-ref-ilamb/tests/test-data/gpp-wecann/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/gpp-wecann/cmip6/manifest.json
@@ -5,6 +5,7 @@
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@@ -147,6 +148,6 @@
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/lai-avh15c1/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/lai-avh15c1/cmip6/manifest.json
index 412960f53..4476f8df2 100644
--- a/packages/climate-ref-ilamb/tests/test-data/lai-avh15c1/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/lai-avh15c1/cmip6/manifest.json
@@ -5,6 +5,7 @@
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@@ -99,6 +100,6 @@
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/lai-avh15c1/cmip7/manifest.json b/packages/climate-ref-ilamb/tests/test-data/lai-avh15c1/cmip7/manifest.json
index 094a2d8dd..875105ca1 100644
--- a/packages/climate-ref-ilamb/tests/test-data/lai-avh15c1/cmip7/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/lai-avh15c1/cmip7/manifest.json
@@ -5,6 +5,7 @@
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@@ -99,6 +100,6 @@
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/mrro-lora/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/mrro-lora/cmip6/manifest.json
index 2871eb2bb..a783c3816 100644
--- a/packages/climate-ref-ilamb/tests/test-data/mrro-lora/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/mrro-lora/cmip6/manifest.json
@@ -5,6 +5,7 @@
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@@ -107,6 +108,6 @@
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/mrro-lora/cmip7/manifest.json b/packages/climate-ref-ilamb/tests/test-data/mrro-lora/cmip7/manifest.json
index 79ffda5cf..116572712 100644
--- a/packages/climate-ref-ilamb/tests/test-data/mrro-lora/cmip7/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/mrro-lora/cmip7/manifest.json
@@ -5,6 +5,7 @@
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@@ -107,6 +108,6 @@
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diff --git a/packages/climate-ref-ilamb/tests/test-data/mrsos-wangmao/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/mrsos-wangmao/cmip6/manifest.json
index e7b78d815..c9dd6d0ee 100644
--- a/packages/climate-ref-ilamb/tests/test-data/mrsos-wangmao/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/mrsos-wangmao/cmip6/manifest.json
@@ -5,6 +5,7 @@
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@@ -99,6 +100,6 @@
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 3
 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/nbp-hoffman/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/nbp-hoffman/cmip6/manifest.json
index def687610..04cd8e8a1 100644
--- a/packages/climate-ref-ilamb/tests/test-data/nbp-hoffman/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/nbp-hoffman/cmip6/manifest.json
@@ -5,6 +5,7 @@
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+  "diagnostic_version": 2,
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@@ -43,6 +44,6 @@
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/nbp-hoffman/cmip7/manifest.json b/packages/climate-ref-ilamb/tests/test-data/nbp-hoffman/cmip7/manifest.json
index 819c6f3e6..96905c31a 100644
--- a/packages/climate-ref-ilamb/tests/test-data/nbp-hoffman/cmip7/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/nbp-hoffman/cmip7/manifest.json
@@ -5,6 +5,7 @@
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     "series.json": "4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945"
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+  "diagnostic_version": 2,
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@@ -43,6 +44,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/snc-esacci/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/snc-esacci/cmip6/manifest.json
index 041d75310..042963fff 100644
--- a/packages/climate-ref-ilamb/tests/test-data/snc-esacci/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/snc-esacci/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "d8da1405ed69e80bacc72e5c6d5321b6a127d3fbc07a0f1d018358ab7f4af751",
     "series.json": "87dc060af17150527b07f6694ad31b9ea8101c1886bd56adf9c5eb9e90c22444"
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+  "diagnostic_version": 2,
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@@ -99,6 +100,6 @@
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/snc-esacci/cmip7/manifest.json b/packages/climate-ref-ilamb/tests/test-data/snc-esacci/cmip7/manifest.json
index 8d61fc1b3..cf7339af5 100644
--- a/packages/climate-ref-ilamb/tests/test-data/snc-esacci/cmip7/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/snc-esacci/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "b9bd57f224a6a7a1847bceb0ca31ee70d9c6da56b7f9424f65ce210ce2a6efc0",
     "series.json": "e4014a3532f46ec3e3d93ec5d814aec685d5208b2c77a26812e84f188d33a8c9"
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+  "diagnostic_version": 2,
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@@ -99,6 +100,6 @@
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-  "schema": 1,
+  "schema": 2,
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 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/so-woa2023-surface/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/so-woa2023-surface/cmip6/manifest.json
index 908e3a108..4a52aec40 100644
--- a/packages/climate-ref-ilamb/tests/test-data/so-woa2023-surface/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/so-woa2023-surface/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "ab674e556c95adf33dcc6b8235d7eb1cc38a2a5927f25fd096dc9b5250f82dd1",
     "series.json": "4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945"
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+  "diagnostic_version": 2,
   "native": {
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@@ -55,6 +56,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/so-woa2023-surface/cmip7/manifest.json b/packages/climate-ref-ilamb/tests/test-data/so-woa2023-surface/cmip7/manifest.json
index e81ac0229..bebbd7714 100644
--- a/packages/climate-ref-ilamb/tests/test-data/so-woa2023-surface/cmip7/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/so-woa2023-surface/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "6005ba9d11745d6ecbe4dcf0f8085639522a67ec7d06f375854b665f705b258c",
     "series.json": "4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945"
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+  "diagnostic_version": 2,
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@@ -55,6 +56,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/thetao-woa2023-surface/cmip6/manifest.json b/packages/climate-ref-ilamb/tests/test-data/thetao-woa2023-surface/cmip6/manifest.json
index 3564f8c19..355c32ee7 100644
--- a/packages/climate-ref-ilamb/tests/test-data/thetao-woa2023-surface/cmip6/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/thetao-woa2023-surface/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "ab674e556c95adf33dcc6b8235d7eb1cc38a2a5927f25fd096dc9b5250f82dd1",
     "series.json": "4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945"
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+  "diagnostic_version": 2,
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@@ -55,6 +56,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-ilamb/tests/test-data/thetao-woa2023-surface/cmip7/manifest.json b/packages/climate-ref-ilamb/tests/test-data/thetao-woa2023-surface/cmip7/manifest.json
index 7adcfa94c..ac4027aef 100644
--- a/packages/climate-ref-ilamb/tests/test-data/thetao-woa2023-surface/cmip7/manifest.json
+++ b/packages/climate-ref-ilamb/tests/test-data/thetao-woa2023-surface/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "6005ba9d11745d6ecbe4dcf0f8085639522a67ec7d06f375854b665f705b258c",
     "series.json": "4f53cda18c2baa0c0354bb5f9a3ecbe5ed12ab4d8e11ba873c2f11161202b945"
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+  "diagnostic_version": 2,
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@@ -55,6 +56,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
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 }
diff --git a/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip6-pr/manifest.json b/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip6-pr/manifest.json
index 1774f62a8..727d29c3a 100644
--- a/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip6-pr/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip6-pr/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "62f8d92c40e3a93b6f4feb4b4de84784a5feff3faf3279e4f5decb661543674a",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 2,
   "native": {
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@@ -63,6 +64,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip6-ts/manifest.json b/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip6-ts/manifest.json
index a8f25382f..adedae40b 100644
--- a/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip6-ts/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip6-ts/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "e46ca7fa84827e863165dc002b50f0a4a476fdc2ae4c228cbaeddbad86c5d9f7",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 2,
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@@ -43,6 +44,6 @@
       "size": 12567
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip7-ts/manifest.json b/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip7-ts/manifest.json
index ee24e8442..804f83009 100644
--- a/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip7-ts/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/annual-cycle/cmip7-ts/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "e46ca7fa84827e863165dc002b50f0a4a476fdc2ae4c228cbaeddbad86c5d9f7",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 2,
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@@ -43,6 +44,6 @@
       "size": 12567
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-  "schema": 1,
+  "schema": 2,
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 }
diff --git a/packages/climate-ref-pmp/tests/test-data/enso_proc/cmip6/manifest.json b/packages/climate-ref-pmp/tests/test-data/enso_proc/cmip6/manifest.json
index 8cf705dc4..50ef7fe84 100644
--- a/packages/climate-ref-pmp/tests/test-data/enso_proc/cmip6/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/enso_proc/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "e5f199fbf35da8f9f4e2608474e8c711e93a8b2b429abfafc9e3c5b04a221efd",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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@@ -143,6 +144,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/enso_proc/cmip7/manifest.json b/packages/climate-ref-pmp/tests/test-data/enso_proc/cmip7/manifest.json
index e219b523c..2a56a5f5a 100644
--- a/packages/climate-ref-pmp/tests/test-data/enso_proc/cmip7/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/enso_proc/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "e5f199fbf35da8f9f4e2608474e8c711e93a8b2b429abfafc9e3c5b04a221efd",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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@@ -143,6 +144,6 @@
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-  "schema": 1,
+  "schema": 2,
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 }
diff --git a/packages/climate-ref-pmp/tests/test-data/enso_tel/cmip6/manifest.json b/packages/climate-ref-pmp/tests/test-data/enso_tel/cmip6/manifest.json
index 74fc7e002..59a54632b 100644
--- a/packages/climate-ref-pmp/tests/test-data/enso_tel/cmip6/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/enso_tel/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "c62a83a4a1fd9a05e038666a26220d0f8dbaa25bd24d31445073fd21e01706d8",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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@@ -187,6 +188,6 @@
       "size": 2
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-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/enso_tel/cmip7/manifest.json b/packages/climate-ref-pmp/tests/test-data/enso_tel/cmip7/manifest.json
index 15b0a59cf..76ed63bc8 100644
--- a/packages/climate-ref-pmp/tests/test-data/enso_tel/cmip7/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/enso_tel/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "c62a83a4a1fd9a05e038666a26220d0f8dbaa25bd24d31445073fd21e01706d8",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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@@ -187,6 +188,6 @@
       "size": 2
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+  "schema": 2,
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 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nam/cmip6/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nam/cmip6/manifest.json
index 515865e16..f582ff6d6 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nam/cmip6/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nam/cmip6/manifest.json
@@ -5,6 +5,7 @@
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     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
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+  "diagnostic_version": 1,
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@@ -215,6 +216,6 @@
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 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nam/cmip7/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nam/cmip7/manifest.json
index 717292fcb..ffbb3d9af 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nam/cmip7/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nam/cmip7/manifest.json
@@ -5,6 +5,7 @@
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@@ -215,6 +216,6 @@
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 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nao/cmip6/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nao/cmip6/manifest.json
index ed7694db8..f9ee6e7ea 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nao/cmip6/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nao/cmip6/manifest.json
@@ -5,6 +5,7 @@
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+  "diagnostic_version": 1,
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@@ -215,6 +216,6 @@
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 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nao/cmip7/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nao/cmip7/manifest.json
index 669e952ab..a35d5c27a 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nao/cmip7/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-nao/cmip7/manifest.json
@@ -5,6 +5,7 @@
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@@ -215,6 +216,6 @@
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   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npgo/cmip6/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npgo/cmip6/manifest.json
index 92d7c1e20..890a7dc2e 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npgo/cmip6/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npgo/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "e36bf1d06d3635f2047609530f9da8d0dc048f352df424f0168d5bb913145079",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "EG_Spec_North_test_NPGO_monthly_HadISST-1-1_1900-2005.png": {
       "sha256": "f7e720e3115fd6cd39e57144a4aaf3cc427944c761436b87e96f752a351c9ddc",
@@ -83,6 +84,6 @@
       "size": 5457
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npgo/cmip7/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npgo/cmip7/manifest.json
index 40e1b0b37..32f02faf7 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npgo/cmip7/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npgo/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "000fe71a4613185d864720121db10eaadb1a312e5e20199346421223a804999e",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "EG_Spec_North_test_NPGO_monthly_HadISST-1-1_1900-2005.png": {
       "sha256": "f7e720e3115fd6cd39e57144a4aaf3cc427944c761436b87e96f752a351c9ddc",
@@ -83,6 +84,6 @@
       "size": 5456
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npo/cmip6/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npo/cmip6/manifest.json
index 3e1b67f82..f8ab355f8 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npo/cmip6/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npo/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "bf0dedc8a6242551d92ae91c1bcc8424341c46cec150edb7600f58783ec49108",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "EG_Spec_North_test_NPO_DJF_20CR_1900-2005.png": {
       "sha256": "cd7d18a767f9e3563783b655ab9a248b6d61bc3ac25e7a075bb631fca29d75bf",
@@ -263,6 +264,6 @@
       "size": 16243
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npo/cmip7/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npo/cmip7/manifest.json
index a93f62a40..83f01f96c 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npo/cmip7/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-npo/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "de79a3ddc42c9739cc69e39a77348f8d119b871ac46a161e199663f8280a501e",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "EG_Spec_North_test_NPO_DJF_20CR_1900-2005.png": {
       "sha256": "cd7d18a767f9e3563783b655ab9a248b6d61bc3ac25e7a075bb631fca29d75bf",
@@ -263,6 +264,6 @@
       "size": 16243
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pdo/cmip6/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pdo/cmip6/manifest.json
index 189f23bc0..fa1f08bd8 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pdo/cmip6/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pdo/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "a882dd976926ecf89e7fc7efbea9e0fd2ddd2280c45760a4cff284d6bbe73f62",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "EG_Spec_North_test_PDO_monthly_HadISST-1-1_1900-2005.png": {
       "sha256": "b39032778d59e47a7c3269e66aed9aadab04c887de0c19de65317350df53fe19",
@@ -71,6 +72,6 @@
       "size": 4464
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pdo/cmip7/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pdo/cmip7/manifest.json
index 75bff0902..0b40b1c06 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pdo/cmip7/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pdo/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "37f0eed421f73813e27df652aeab97a28a142adda89d3f5e26862b345c92168c",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "EG_Spec_North_test_PDO_monthly_HadISST-1-1_1900-2005.png": {
       "sha256": "b39032778d59e47a7c3269e66aed9aadab04c887de0c19de65317350df53fe19",
@@ -71,6 +72,6 @@
       "size": 4459
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pna/cmip6/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pna/cmip6/manifest.json
index 63c27adc1..1de10b91c 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pna/cmip6/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pna/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "e20535bfc6e337eb4f36b90f75494a192878dc04b6a83cc334bc7595aafb05b4",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "EG_Spec_North_test_PNA_DJF_20CR_1900-2005.png": {
       "sha256": "507f5faee65bd25a8d517604e236fae5c6fa0759c040dbfa96d1be6a1275a88b",
@@ -215,6 +216,6 @@
       "size": 12338
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pna/cmip7/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pna/cmip7/manifest.json
index a7f3f246a..6794bbce2 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pna/cmip7/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-pna/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "341b4e6788ae59388c9bd54805e5340e72358b0491b825a7f0d93518f3725eb6",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "EG_Spec_North_test_PNA_DJF_20CR_1900-2005.png": {
       "sha256": "507f5faee65bd25a8d517604e236fae5c6fa0759c040dbfa96d1be6a1275a88b",
@@ -215,6 +216,6 @@
       "size": 12338
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-sam/cmip6/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-sam/cmip6/manifest.json
index 0d8a2509c..779a02bc3 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-sam/cmip6/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-sam/cmip6/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "e12259f127181727494f357ae5480074a7c3bff706bacc087fd6c53b02641587",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "EG_Spec_North_test_SAM_DJF_20CR_1950-2005.png": {
       "sha256": "c7ef152390fa88c2cd263a03855103fe895e10e1be04497faf284e7ce93d4220",
@@ -215,6 +216,6 @@
       "size": 12341
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-sam/cmip7/manifest.json b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-sam/cmip7/manifest.json
index 7a5c7a7e5..67c3b5a18 100644
--- a/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-sam/cmip7/manifest.json
+++ b/packages/climate-ref-pmp/tests/test-data/extratropical-modes-of-variability-sam/cmip7/manifest.json
@@ -5,6 +5,7 @@
     "output.json": "9eeab48e41a1de571f02f399dc4bd66e4f8e6406b498c108e3baaa99041a6486",
     "series.json": "37517e5f3dc66819f61f5a7bb8ace1921282415f10551d2defa5c3eb0985b570"
   },
+  "diagnostic_version": 1,
   "native": {
     "EG_Spec_North_test_SAM_DJF_20CR_1950-2005.png": {
       "sha256": "c7ef152390fa88c2cd263a03855103fe895e10e1be04497faf284e7ce93d4220",
@@ -215,6 +216,6 @@
       "size": 12341
     }
   },
-  "schema": 1,
+  "schema": 2,
   "test_case_version": 1
 }
diff --git a/packages/climate-ref/src/climate_ref/cli/test_cases/__init__.py b/packages/climate-ref/src/climate_ref/cli/test_cases/__init__.py
index 06d14cdde..2f65a199f 100644
--- a/packages/climate-ref/src/climate_ref/cli/test_cases/__init__.py
+++ b/packages/climate-ref/src/climate_ref/cli/test_cases/__init__.py
@@ -11,6 +11,7 @@
 - :mod:`~climate_ref.cli.test_cases.baselines` -- ``replay`` / ``mint`` / ``build``
 - :mod:`~climate_ref.cli.test_cases.store` -- ``sync`` / ``check-store``
 - :mod:`~climate_ref.cli.test_cases.ci_gate` -- ``ci-gate``
+- :mod:`~climate_ref.cli.test_cases.migrate` -- ``migrate-manifests``
 """
 
 from importlib import import_module
@@ -26,7 +27,7 @@
 # Import each command module for its registration side effect on ``app``.
 # The sequence below is the order the verbs appear in ``ref test-cases --help``
 # a dynamic import keeps it explicit, where a plain ``import`` block would be alphabetised by ruff.
-for _command_module in ("discovery", "run", "baselines", "store", "ci_gate"):
+for _command_module in ("discovery", "run", "baselines", "store", "ci_gate", "migrate"):
     import_module(f"{__name__}.{_command_module}")
 
 __all__ = [
diff --git a/packages/climate-ref/src/climate_ref/cli/test_cases/_common.py b/packages/climate-ref/src/climate_ref/cli/test_cases/_common.py
index 8dbddb538..2c05a0b50 100644
--- a/packages/climate-ref/src/climate_ref/cli/test_cases/_common.py
+++ b/packages/climate-ref/src/climate_ref/cli/test_cases/_common.py
@@ -100,10 +100,11 @@ def _validate_requested_filters(
             raise typer.Exit(code=1)
 
 
-def _write_test_case_manifest(
+def _write_test_case_manifest(  # noqa: PLR0913
     paths: TestCasePaths,
     *,
     test_case_version: int,
+    diagnostic_version: int,
     committed: dict[str, str],
     native: dict[str, NativeEntry],
     schema: int | None = None,
@@ -114,6 +115,8 @@ def _write_test_case_manifest(
     Shared by ``run`` (which preserves the existing version and native block) and
     ``mint`` (which authors the native block and may bump the version); the two
     callers differ only in the ``test_case_version`` and ``native`` they supply.
+    Only ``mint`` advances ``diagnostic_version`` to the diagnostic's current
+    ``Diagnostic.version``; ``run`` / ``build`` preserve the value already recorded.
     The ``catalog_hash`` is always (re)derived from the current ``catalog.yaml`` so
     the manifest stays coupled to the inputs that produced the committed bundle.
     """
@@ -123,6 +126,7 @@ def _write_test_case_manifest(
     manifest = Manifest(
         schema=SCHEMA_VERSION if schema is None else schema,
         test_case_version=test_case_version,
+        diagnostic_version=diagnostic_version,
         committed=dict(committed),
         native=native,
         catalog_hash=get_catalog_hash(paths.catalog),
diff --git a/packages/climate-ref/src/climate_ref/cli/test_cases/baselines.py b/packages/climate-ref/src/climate_ref/cli/test_cases/baselines.py
index 2e52c4798..891604ed5 100644
--- a/packages/climate-ref/src/climate_ref/cli/test_cases/baselines.py
+++ b/packages/climate-ref/src/climate_ref/cli/test_cases/baselines.py
@@ -384,7 +384,13 @@ def mint_native(  # noqa: PLR0912, PLR0913, PLR0915
             version = previous.test_case_version + 1 if bump_version else previous.test_case_version
         else:
             version = 1
-        _write_test_case_manifest(paths, test_case_version=version, committed=committed, native=native)
+        _write_test_case_manifest(
+            paths,
+            test_case_version=version,
+            diagnostic_version=diag.version,
+            committed=committed,
+            native=native,
+        )
         write_source_stamp(slot, label=label, verb="mint", source=source_kind, test_case_version=version)
 
         minted += 1
@@ -497,6 +503,7 @@ def build_test_case(  # noqa: PLR0912, PLR0913, PLR0915
                 _write_test_case_manifest(
                     paths,
                     test_case_version=previous.test_case_version,
+                    diagnostic_version=previous.diagnostic_version,
                     committed=committed,
                     native=previous.native,
                     schema=previous.schema,
@@ -507,7 +514,13 @@ def build_test_case(  # noqa: PLR0912, PLR0913, PLR0915
                         "re-mint with `ref test-cases mint`"
                     )
             else:
-                _write_test_case_manifest(paths, test_case_version=1, committed=committed, native={})
+                _write_test_case_manifest(
+                    paths,
+                    test_case_version=1,
+                    diagnostic_version=diag.version,
+                    committed=committed,
+                    native={},
+                )
             logger.info(f"Promoted rebuilt bundle to regression baseline: {paths.regression}")
         else:
             logger.info(
diff --git a/packages/climate-ref/src/climate_ref/cli/test_cases/ci_gate.py b/packages/climate-ref/src/climate_ref/cli/test_cases/ci_gate.py
index b914fa875..d0f2f5161 100644
--- a/packages/climate-ref/src/climate_ref/cli/test_cases/ci_gate.py
+++ b/packages/climate-ref/src/climate_ref/cli/test_cases/ci_gate.py
@@ -275,6 +275,7 @@ def record(case: str, action: Action, reason: str) -> None:
             extraction_changed=extraction_changed,
             committed_integrity_ok=committed_integrity_ok,
             catalog_integrity_ok=catalog_integrity_ok,
+            code_diagnostic_version=diag.version,
         )
         record(case_id, decision.action, decision.reason)
 
diff --git a/packages/climate-ref/src/climate_ref/cli/test_cases/migrate.py b/packages/climate-ref/src/climate_ref/cli/test_cases/migrate.py
new file mode 100644
index 000000000..c057ba47c
--- /dev/null
+++ b/packages/climate-ref/src/climate_ref/cli/test_cases/migrate.py
@@ -0,0 +1,118 @@
+"""
+``ref test-cases migrate-manifests``.
+
+A one-shot, idempotent maintenance command that backfills every committed
+``manifest.json`` to the current ``SCHEMA_VERSION``, stamping each case's
+``diagnostic_version`` from the diagnostic's in-code ``Diagnostic.version`` only
+when the field is absent. An already-recorded ``diagnostic_version`` is preserved,
+so re-running never re-stamps a stale bundle and subverts the gate's staleness check.
+
+It iterates the same ``_iter_test_cases`` the CI gate uses, so its coverage is
+definitionally aligned with the gate (iterator parity). A pre-bump manifest is
+schema-1 and ``Manifest.load`` would reject it, so the raw JSON is read directly
+and re-serialised through ``Manifest(...).dump`` to keep the output byte-identical
+to what a later ``mint`` would write.
+"""
+
+from __future__ import annotations
+
+import json
+from typing import TYPE_CHECKING, Annotated
+
+import typer
+from loguru import logger
+
+from climate_ref.cli.test_cases._app import app
+from climate_ref.cli.test_cases._common import (
+    _iter_test_cases,
+    _validate_provider_in_registry,
+    _validate_requested_filters,
+)
+from climate_ref.config import Config
+
+if TYPE_CHECKING:
+    from rich.console import Console
+
+
+@app.command(name="migrate-manifests")
+def migrate_manifests(
+    ctx: typer.Context,
+    provider: Annotated[
+        str | None,
+        typer.Option(help="Limit the migration to a single provider slug"),
+    ] = None,
+    diagnostic: Annotated[
+        str | None,
+        typer.Option(help="Limit the migration to a single diagnostic slug"),
+    ] = None,
+    test_case: Annotated[
+        str | None,
+        typer.Option(help="Limit the migration to a single test case name"),
+    ] = None,
+) -> None:
+    """
+    Backfill every committed ``manifest.json`` to the current schema.
+
+    For each test case with an existing manifest, backfills ``diagnostic_version``
+    from the diagnostic's in-code ``Diagnostic.version`` when it is absent (an
+    already-recorded value is preserved) and rewrites the manifest at the current
+    ``SCHEMA_VERSION``. The operation is idempotent: re-running on an already-migrated
+    manifest preserves the recorded value and produces identical bytes.
+
+    Examples
+    --------
+        ref test-cases migrate-manifests
+        ref test-cases migrate-manifests --provider ilamb
+    """
+    from climate_ref.provider_registry import ProviderRegistry
+    from climate_ref_core.regression.manifest import SCHEMA_VERSION, Manifest, NativeEntry
+    from climate_ref_core.testing import TestCasePaths
+
+    config: Config = ctx.obj.config
+    db = ctx.obj.database
+    console: Console = ctx.obj.console
+
+    registry = ProviderRegistry.build_from_config(config, db)
+    _validate_provider_in_registry(registry, provider)
+    _validate_requested_filters(registry, provider=provider, diagnostic=diagnostic, test_case=test_case)
+    cases = list(_iter_test_cases(registry, provider=provider, diagnostic=diagnostic, test_case=test_case))
+
+    migrated = 0
+    skipped = 0
+
+    for diag, tc in cases:
+        case_id = f"{diag.provider.slug}/{diag.slug}/{tc.name}"
+        paths = TestCasePaths.from_diagnostic(diag, tc.name)
+        if paths is None or not paths.manifest.exists():
+            skipped += 1
+            continue
+
+        # Manifest.load rejects a schema-1 manifest, so read raw JSON and re-construct.
+        data = json.loads(paths.manifest.read_text(encoding="utf-8"))
+        native = {
+            relpath: NativeEntry(sha256=entry["sha256"], size=entry["size"])
+            for relpath, entry in data["native"].items()
+        }
+        # Preserve an already-recorded value so this stays a pure backfill.
+        # After an authorised bump the manifest lags the in-code version until a re-mint,
+        # and re-stamping it would mask the gate's staleness check.
+        diagnostic_version = data.get("diagnostic_version", diag.version)
+        manifest = Manifest(
+            schema=SCHEMA_VERSION,
+            test_case_version=data["test_case_version"],
+            diagnostic_version=diagnostic_version,
+            committed=dict(data["committed"]),
+            native=native,
+            catalog_hash=data.get("catalog_hash"),
+        )
+        # Serialise via dump so the bytes (sort_keys + unconditional `catalog_hash: null`)
+        # match exactly what a later mint would write.
+        manifest.dump(paths.manifest)
+        migrated += 1
+        logger.info(f"Migrated {case_id} -> schema {SCHEMA_VERSION}, diagnostic_version {diagnostic_version}")
+
+    console.print()
+    console.print(
+        f"[green]Migrated {migrated} manifest(s)[/green]"
+        + (f"; skipped {skipped} case(s) with no manifest" if skipped else "")
+    )
diff --git a/packages/climate-ref/src/climate_ref/cli/test_cases/run.py b/packages/climate-ref/src/climate_ref/cli/test_cases/run.py
index bcb22cfa8..7cf3dcf7e 100644
--- a/packages/climate-ref/src/climate_ref/cli/test_cases/run.py
+++ b/packages/climate-ref/src/climate_ref/cli/test_cases/run.py
@@ -222,6 +222,7 @@ def _run_single_test_case(  # noqa: PLR0911, PLR0912, PLR0913, PLR0915
             _write_test_case_manifest(
                 paths,
                 test_case_version=previous.test_case_version,
+                diagnostic_version=previous.diagnostic_version,
                 committed=committed,
                 native=previous.native,
                 schema=previous.schema,
@@ -232,7 +233,13 @@ def _run_single_test_case(  # noqa: PLR0911, PLR0912, PLR0913, PLR0915
                     "re-mint with `ref test-cases mint` (or `mint --from-replay`)"
                 )
         else:
-            _write_test_case_manifest(paths, test_case_version=1, committed=committed, native={})
+            _write_test_case_manifest(
+                paths,
+                test_case_version=1,
+                diagnostic_version=diag.version,
+                committed=committed,
+                native={},
+            )
         logger.info(f"Updated regression baseline: {paths.regression}")
         _print_regression_summary(console, paths.regression, size_threshold)
     else:
diff --git a/packages/climate-ref/tests/integration/test_native_roundtrip.py b/packages/climate-ref/tests/integration/test_native_roundtrip.py
index 84c032719..7e03c4d29 100644
--- a/packages/climate-ref/tests/integration/test_native_roundtrip.py
+++ b/packages/climate-ref/tests/integration/test_native_roundtrip.py
@@ -28,7 +28,9 @@
 import pandas as pd
 import pytest
 
+from climate_ref.cli.test_cases._common import _iter_test_cases
 from climate_ref.config import Config
+from climate_ref.provider_registry import ProviderRegistry
 from climate_ref.testing import TEST_DATA_DIR, TestCaseRunner
 from climate_ref_core.datasets import (
     DatasetCollection,
@@ -54,6 +56,8 @@
     capture_execution,
     materialise_native,
 )
+from climate_ref_core.regression.gate import Action, decide_coupling
+from climate_ref_core.regression.manifest import SCHEMA_VERSION
 from climate_ref_core.testing import (
     TestCase,
     TestCasePaths,
@@ -368,8 +372,9 @@ def test_run_mint_sync_replay(self, tmp_path: Path) -> None:
             assert digest == entry.sha256, "store digest must equal the captured digest"
 
         manifest = Manifest(
-            schema=1,
+            schema=2,
             test_case_version=1,
+            diagnostic_version=1,
             committed=committed_digests,
             native=native,
         )
@@ -575,8 +580,9 @@ def test_example_roundtrip(self, tmp_path: Path) -> None:  # noqa: PLR0915
             assert digest == entry.sha256
 
         manifest = Manifest(
-            schema=1,
+            schema=2,
             test_case_version=1,
+            diagnostic_version=1,
             committed=committed_digests,
             native=native,
         )
@@ -723,8 +729,9 @@ def _mint(self, tmp_path: Path) -> tuple[LocalFilesystemStore, Manifest, dict[st
             store.put(base_dir / relpath)
 
         manifest = Manifest(
-            schema=1,
+            schema=2,
             test_case_version=1,
+            diagnostic_version=1,
             committed=committed_digests,
             native=native,
         )
@@ -1141,3 +1148,63 @@ def test_replay_fails_when_reconstruction_input_not_captured(self, tmp_path: Pat
         )
         with pytest.raises((FileNotFoundError, OSError)):
             diag.build_execution_result(replay_definition)
+
+
+class TestManifestSchemaMigration:
+    """Every committed manifest is migrated to the current schema and stamped correctly."""
+
+    def test_all_committed_manifests_are_schema_2(self, config, db) -> None:
+        """For every iterated case with a manifest, it parses at schema 2 with the code's version.
+
+        The case universe is derived from the same ``_iter_test_cases`` the gate and the
+        migration verb use (iterator parity), never a hardcoded count. A schema-1 manifest left
+        behind by a partial backfill would raise on load and red this test.
+        """
+        registry = ProviderRegistry.build_from_config(config, db)
+        checked = 0
+        for diag, tc in _iter_test_cases(registry):
+            paths = TestCasePaths.from_diagnostic(diag, tc.name)
+            if paths is None or not paths.manifest.exists():
+                continue
+            manifest = Manifest.load(paths.manifest)
+            assert manifest.schema == SCHEMA_VERSION, (
+                f"{diag.provider.slug}/{diag.slug}/{tc.name} is not at schema {SCHEMA_VERSION}"
+            )
+            assert manifest.diagnostic_version == diag.version, (
+                f"{diag.provider.slug}/{diag.slug}/{tc.name} records diagnostic_version "
+                f"{manifest.diagnostic_version} but the code declares {diag.version}"
+            )
+            checked += 1
+        # The branch ships committed manifests, so the iterator must have reached at least one.
+        assert checked > 0
+
+    def test_schema_1_base_manifest_is_treated_as_seeding(self) -> None:
+        """A schema-1 base manifest is rejected by ``loads`` and falls back to seeding.
+
+        This pins the one-cycle transition window: the schema-2 ``loads`` deliberately
+        rejects the base-branch copy (suppressed via the ci_gate ``try/except``), so the case
+        is treated as newly added rather than crashing the gate.
+        """
+        # A full schema-1 base manifest text (no diagnostic_version) is rejected by loads().
+        schema_1_text = json.dumps(
+            {
+                "schema": 1,
+                "test_case_version": 1,
+                "committed": {"output.json": "a" * 64},
+                "native": {},
+            }
+        )
+        with pytest.raises(ValueError):
+            Manifest.loads(schema_1_text)
+
+        # The ci_gate path catches that ValueError and passes base_manifest=None (seeding).
+        current = Manifest(
+            schema=2,
+            test_case_version=1,
+            diagnostic_version=1,
+            committed={"output.json": "a" * 64},
+            native={"data.nc": NativeEntry("a" * 64, 10)},
+        )
+        decision = decide_coupling(current, None, code_diagnostic_version=1)
+        assert decision.action is Action.REPLAY
+        assert "seeding" in decision.reason
diff --git a/packages/climate-ref/tests/unit/cli/test_test_cases.py b/packages/climate-ref/tests/unit/cli/test_test_cases.py
index 221bba311..2a7fd8796 100644
--- a/packages/climate-ref/tests/unit/cli/test_test_cases.py
+++ b/packages/climate-ref/tests/unit/cli/test_test_cases.py
@@ -818,6 +818,7 @@ def test_run_with_force_regen(self, invoke_cli, mocker, tmp_path):
         mock_spec = MagicMock()
         mock_spec.test_cases = [mock_tc]
         mock_diag = MagicMock(slug="test-diag", test_data_spec=mock_spec)
+        mock_diag.version = 1
         mock_diag.provider = MagicMock(slug="example")
         mock_provider = MagicMock(slug="example")
         mock_provider.diagnostics.return_value = [mock_diag]
@@ -1042,6 +1043,7 @@ def test_run_warns_when_native_stale(self, invoke_cli, mocker, tmp_path):
         Manifest(
             schema=SCHEMA_VERSION,
             test_case_version=3,
+            diagnostic_version=4,
             committed={},
             native={"diagnostic.json": NativeEntry(sha256="00" * 32, size=1)},
         ).dump(paths.manifest)
@@ -1054,6 +1056,8 @@ def test_run_warns_when_native_stale(self, invoke_cli, mocker, tmp_path):
         # run preserves the mint-owned native block and version (it never authors native).
         manifest = Manifest.load(paths.manifest)
         assert manifest.test_case_version == 3
+        # run preserves the recorded diagnostic_version (only mint advances it).
+        assert manifest.diagnostic_version == 4
         assert set(manifest.native) == {"diagnostic.json"}
 
 
@@ -1400,6 +1404,7 @@ def _make_case_mocks():
     spec = MagicMock()
     spec.test_cases = [tc]
     diag = MagicMock(slug="test-diag", test_data_spec=spec)
+    diag.version = 1
     diag.provider = MagicMock(slug="example")
     provider = MagicMock(slug="example")
     provider.diagnostics.return_value = [diag]
@@ -1515,8 +1520,9 @@ def test_sync_fetches_missing_blob(self, invoke_cli, mocker, tmp_path):
         case_dir.mkdir(parents=True)
         paths = TestCasePaths(root=case_dir)
         Manifest(
-            schema=1,
+            schema=2,
             test_case_version=1,
+            diagnostic_version=1,
             committed={},
             native={"out.nc": NativeEntry(sha256=digest, size=len(b"native-data"))},
         ).dump(paths.manifest)
@@ -1543,8 +1549,9 @@ def test_sync_hard_fails_on_unservable_blob(self, invoke_cli, mocker, tmp_path):
         case_dir.mkdir(parents=True)
         paths = TestCasePaths(root=case_dir)
         Manifest(
-            schema=1,
+            schema=2,
             test_case_version=1,
+            diagnostic_version=1,
             committed={},
             native={"out.nc": NativeEntry(sha256="ab" * 32, size=1)},
         ).dump(paths.manifest)
@@ -1779,7 +1786,9 @@ def test_replay_empty_native_is_hard_failure(self, invoke_cli, mocker, tmp_path)
         (regression_dir / "diagnostic.json").write_text("{}")
         digests = compute_committed_digests(regression_dir)
         paths = TestCasePaths(root=case_dir)
-        Manifest(schema=1, test_case_version=1, committed=digests, native={}).dump(paths.manifest)
+        Manifest(schema=2, test_case_version=1, diagnostic_version=1, committed=digests, native={}).dump(
+            paths.manifest
+        )
 
         store = LocalFilesystemStore(root=tmp_path / "store")
         mocker.patch(
@@ -1864,8 +1873,9 @@ def test_replay_integrity_mismatch_warns_and_continues(self, invoke_cli, mocker,
         paths = TestCasePaths(root=case_dir)
         # Committed digest deliberately wrong -> integrity mismatch (now a warning, not a gate).
         Manifest(
-            schema=1,
+            schema=2,
             test_case_version=1,
+            diagnostic_version=1,
             committed={"diagnostic.json": "00" * 32},
             native={},
         ).dump(paths.manifest)
@@ -1915,8 +1925,9 @@ def test_replay_reconciles_integrity_mismatch_within_tolerance(self, invoke_cli,
         paths = TestCasePaths(root=case_dir)
         # Wrong committed digest -> integrity warns; native present -> passes the mint guard.
         Manifest(
-            schema=1,
+            schema=2,
             test_case_version=1,
+            diagnostic_version=1,
             committed={"series.json": "00" * 32},
             native={"out.nc": NativeEntry(sha256="ab" * 32, size=1)},
         ).dump(paths.manifest)
@@ -2126,6 +2137,8 @@ def test_mint_writes_blobs_and_manifest(self, invoke_cli, mocker, tmp_path):
 
         manifest = Manifest.load(paths.manifest)
         assert manifest.test_case_version == 1
+        # mint stamps the diagnostic's in-code Diagnostic.version.
+        assert manifest.diagnostic_version == 1
         # mint authored the native block from the captured snapshot.
         assert set(manifest.native) == {"diagnostic.json", "output.json", "series.json"}
         # Each native blob was PUT into the store.
@@ -2198,8 +2211,9 @@ def test_mint_from_replay_preserves_stored_native(self, invoke_cli, mocker, tmp_
         paths = TestCasePaths(root=case_dir)
         stored_native = {"output.json": NativeEntry(sha256="aa" * 32, size=10)}
         Manifest(
-            schema=1,
+            schema=2,
             test_case_version=1,
+            diagnostic_version=1,
             committed={"diagnostic.json": "00" * 32},
             native=stored_native,
         ).dump(paths.manifest)
@@ -2239,6 +2253,60 @@ def test_mint_from_replay_preserves_stored_native(self, invoke_cli, mocker, tmp_
         # The from-replay path must not snapshot the hydrated slot at all.
         snapshot.assert_not_called()
 
+    def test_mint_from_replay_advances_diagnostic_version(self, invoke_cli, mocker, tmp_path):
+        """`mint --from-replay` re-stamps the manifest's diagnostic_version from the code version.
+
+        A version bump followed by `mint --from-replay` re-couples the unchanged native bundle to
+        the new declared Diagnostic.version even though the native blobs are reused verbatim.
+        """
+        from climate_ref_core.regression.manifest import Manifest, NativeEntry
+        from climate_ref_core.testing import TestCasePaths
+
+        registry, diag, _tc = _make_case_mocks()
+        # The diagnostic code has been bumped past the recorded baseline.
+        diag.version = 2
+
+        case_dir = tmp_path / "td" / "test-diag" / "default"
+        case_dir.mkdir(parents=True)
+        (case_dir / "catalog.yaml").touch()
+        paths = TestCasePaths(root=case_dir)
+        stored_native = {"output.json": NativeEntry(sha256="aa" * 32, size=10)}
+        Manifest(
+            schema=2,
+            test_case_version=1,
+            diagnostic_version=1,
+            committed={"diagnostic.json": "00" * 32},
+            native=stored_native,
+        ).dump(paths.manifest)
+
+        store = MagicMock()
+        store.has.return_value = True
+        mocker.patch(
+            "climate_ref.provider_registry.ProviderRegistry.build_from_config",
+            return_value=registry,
+        )
+        mocker.patch("climate_ref_core.testing.TestCasePaths.from_diagnostic", return_value=paths)
+        mocker.patch("climate_ref_core.testing.get_catalog_hash", return_value=None)
+        mocker.patch("climate_ref_core.regression.store.build_native_store", return_value=store)
+        mocker.patch("climate_ref.cli.test_cases.baselines.stage_materialise")
+        mocker.patch(
+            "climate_ref.cli.test_cases.baselines.stage_build",
+            return_value={"diagnostic.json": "00" * 32},
+        )
+        mocker.patch("climate_ref.cli.test_cases.baselines.promote_to_baseline")
+
+        result = invoke_cli(
+            ["test-cases", "mint", "--provider", "example", "--diagnostic", "test-diag", "--from-replay"]
+        )
+        assert result.exit_code == 0
+
+        written = Manifest.load(paths.manifest)
+        # The native is preserved, but diagnostic_version advances to the in-code version.
+        assert {k: v.sha256 for k, v in written.native.items()} == {
+            k: v.sha256 for k, v in stored_native.items()
+        }
+        assert written.diagnostic_version == 2
+
     def test_mint_from_replay_requires_minted_manifest(self, invoke_cli, mocker, tmp_path):
         """`mint --from-replay` fails when there is no existing minted native to replay from."""
         from climate_ref_core.regression.store import LocalFilesystemStore
@@ -2403,6 +2471,8 @@ def _setup(
         current_version=None,
         committed_content=None,
         native=None,
+        diagnostic_version=1,
+        code_diagnostic_version=1,
     ):
         """
         Wire a single example test case for the gate.
@@ -2444,6 +2514,7 @@ def _setup(
         mock_tc.name = "default"
         mock_spec = MagicMock(test_cases=[mock_tc])
         mock_diag = MagicMock(slug="test-diag", test_data_spec=mock_spec)
+        mock_diag.version = code_diagnostic_version
         mock_diag.provider = MagicMock(slug="example")
         mock_provider = MagicMock(slug="example")
         mock_provider.diagnostics.return_value = [mock_diag]
@@ -2463,6 +2534,7 @@ def _setup(
             Manifest(
                 schema=SCHEMA_VERSION,
                 test_case_version=current_version,
+                diagnostic_version=diagnostic_version,
                 committed=committed_digests,
                 native=native or {},
             ).dump(paths.manifest)
@@ -2482,7 +2554,7 @@ def _setup(
         return repo, paths, committed_digests
 
     @staticmethod
-    def _set_base(repo, version, committed, native=None):
+    def _set_base(repo, version, committed, native=None, diagnostic_version=1):
         """Configure ``repo.git.show`` to return a base manifest with these fields."""
         import json as _json
 
@@ -2493,6 +2565,7 @@ def _set_base(repo, version, committed, native=None):
         payload = {
             "schema": SCHEMA_VERSION,
             "test_case_version": version,
+            "diagnostic_version": diagnostic_version,
             "committed": committed,
             "native": {relpath: asdict(entry) for relpath, entry in (native or {}).items()},
         }
@@ -2679,6 +2752,28 @@ def test_corrupt_base_manifest_treated_as_seeding(self, invoke_cli, mocker, tmp_
         assert result.exit_code == 0
         assert "replay" in result.output
 
+    def test_schema_1_base_manifest_treated_as_seeding(self, invoke_cli, mocker, tmp_path):
+        # The transition window: git show returns a *valid-JSON* schema-1 base manifest (no
+        # diagnostic_version). The schema-2 loader rejects it, and the real ci_gate try/except
+        # must convert that into base_manifest=None (seeding) rather than crashing the gate.
+        import json as _json
+
+        from climate_ref_core.regression.manifest import NativeEntry
+
+        repo, _, digests = self._setup(
+            mocker, tmp_path, current_version=1, native={"data.nc": NativeEntry("a" * 64, 10)}
+        )
+        repo.git.show.side_effect = None
+        repo.git.show.return_value = _json.dumps(
+            {"schema": 1, "test_case_version": 1, "committed": digests, "native": {}},
+            indent=2,
+            sort_keys=True,
+        )
+
+        result = invoke_cli(["test-cases", "ci-gate"])
+        assert result.exit_code == 0
+        assert "replay" in result.output
+
     def test_catalog_drift_fails(self, invoke_cli, mocker, tmp_path):
         # The manifest records a catalog_hash that the on-disk catalog no longer matches.
         from climate_ref_core.regression.manifest import Manifest
@@ -2688,6 +2783,7 @@ def test_catalog_drift_fails(self, invoke_cli, mocker, tmp_path):
         Manifest(
             schema=manifest.schema,
             test_case_version=manifest.test_case_version,
+            diagnostic_version=manifest.diagnostic_version,
             committed=manifest.committed,
             native=manifest.native,
             catalog_hash="expected_hash",
@@ -2697,3 +2793,202 @@ def test_catalog_drift_fails(self, invoke_cli, mocker, tmp_path):
         result = invoke_cli(["test-cases", "ci-gate"], expected_exit_code=1)
         assert result.exit_code == 1
         assert "fail" in result.output
+
+    def test_stale_diagnostic_version_fails(self, invoke_cli, mocker, tmp_path):
+        # The in-code Diagnostic.version is ahead of the recorded baseline: stale -> FAIL.
+        repo, _, digests = self._setup(
+            mocker, tmp_path, current_version=1, diagnostic_version=1, code_diagnostic_version=2
+        )
+        self._set_base(repo, 1, digests, diagnostic_version=1)
+
+        result = invoke_cli(["test-cases", "ci-gate"], expected_exit_code=1)
+        assert result.exit_code == 1
+        assert "fail" in result.output
+
+    def test_matched_diagnostic_version_does_not_fail(self, invoke_cli, mocker, tmp_path):
+        # code == manifest.diagnostic_version: no new failure, falls through to normal logic.
+        repo, _, digests = self._setup(
+            mocker, tmp_path, current_version=1, diagnostic_version=2, code_diagnostic_version=2
+        )
+        self._set_base(repo, 1, digests, diagnostic_version=2)
+
+        result = invoke_cli(["test-cases", "ci-gate"])
+        assert result.exit_code == 0
+        assert "skip" in result.output
+
+    def test_ecs_blind_spot_closed_then_remint_recovers(self, invoke_cli, mocker, tmp_path):
+        """#671: an execution change (code version bumped) FAILs until the baseline is re-minted."""
+        from climate_ref_core.regression.manifest import Manifest, NativeEntry
+
+        native = {"data.nc": NativeEntry("a" * 64, 10)}
+
+        # Code bumped to 2, baseline still records 1: stale -> FAIL.
+        repo, paths, digests = self._setup(
+            mocker,
+            tmp_path,
+            current_version=1,
+            diagnostic_version=1,
+            code_diagnostic_version=2,
+            native=native,
+        )
+        self._set_base(repo, 1, digests, diagnostic_version=1, native=native)
+        stale = invoke_cli(["test-cases", "ci-gate"], expected_exit_code=1)
+        assert stale.exit_code == 1
+        assert "fail" in stale.output
+
+        # Simulate the re-mint: rewrite the HEAD manifest at diagnostic_version 2 (== code).
+        current = Manifest.load(paths.manifest)
+        Manifest(
+            schema=current.schema,
+            test_case_version=current.test_case_version,
+            diagnostic_version=2,
+            committed=current.committed,
+            native=current.native,
+            catalog_hash=current.catalog_hash,
+        ).dump(paths.manifest)
+        recovered = invoke_cli(["test-cases", "ci-gate"])
+        assert recovered.exit_code == 0
+        assert "fail" not in recovered.output
+
+    def test_revert_green_path(self, invoke_cli, mocker, tmp_path):
+        """A legitimate revert (code v2->v1 + re-mint + tcv bump) has a GREEN gate exit."""
+        from climate_ref_core.regression.manifest import NativeEntry
+
+        native = {"data.nc": NativeEntry("a" * 64, 10)}
+        # HEAD: re-minted at diagnostic_version 1, tcv bumped to 2, committed re-authored.
+        repo, _, _ = self._setup(
+            mocker,
+            tmp_path,
+            current_version=2,
+            diagnostic_version=1,
+            code_diagnostic_version=1,
+            committed_content={"output.json": '{"reauthored": 1}\n'},
+            native=native,
+        )
+        # Base: the pre-revert baseline at diagnostic_version 2 with the old committed bundle.
+        self._set_base(repo, 1, {"output.json": "f" * 64}, native=native, diagnostic_version=2)
+
+        result = invoke_cli(["test-cases", "ci-gate"])
+        assert result.exit_code == 0
+        # 2a passes on equality, 2b's carve-out lets the decrease through, the tcv bump REPLAYs.
+        assert "replay" in result.output
+        assert "fail" not in result.output
+
+
+class TestMigrateManifestsCommand:
+    """Tests for the ``ref test-cases migrate-manifests`` verb."""
+
+    def _wire(self, mocker, tmp_path, *, code_version=1):
+        from climate_ref_core.testing import TestCasePaths
+
+        registry, diag, _tc = _make_case_mocks()
+        diag.version = code_version
+
+        case_dir = tmp_path / "td" / "test-diag" / "default"
+        case_dir.mkdir(parents=True)
+        paths = TestCasePaths(root=case_dir)
+
+        mocker.patch(
+            "climate_ref.provider_registry.ProviderRegistry.build_from_config",
+            return_value=registry,
+        )
+        mocker.patch("climate_ref_core.testing.TestCasePaths.from_diagnostic", return_value=paths)
+        return paths
+
+    def test_migrate_help(self, invoke_cli):
+        result = invoke_cli(["test-cases", "migrate-manifests", "--help"])
+        assert "diagnostic_version" in result.output or "schema" in result.output
+
+    def test_migrate_stamps_code_version_and_bumps_schema(self, invoke_cli, mocker, tmp_path):
+        import json as _json
+
+        paths = self._wire(mocker, tmp_path, code_version=2)
+        # A schema-1 manifest (no diagnostic_version) on disk, as it would exist pre-migration.
+        paths.manifest.write_text(
+            _json.dumps(
+                {
+                    "schema": 1,
+                    "test_case_version": 3,
+                    "catalog_hash": "abc",
+                    "committed": {"output.json": "a" * 64},
+                    "native": {},
+                },
+                indent=2,
+                sort_keys=True,
+            )
+            + "\n",
+            encoding="utf-8",
+        )
+
+        result = invoke_cli(["test-cases", "migrate-manifests", "--provider", "example"])
+        assert result.exit_code == 0
+
+        from climate_ref_core.regression.manifest import Manifest
+
+        migrated = Manifest.load(paths.manifest)
+        assert migrated.schema == 2
+        assert migrated.diagnostic_version == 2  # stamped from diag.version
+        assert migrated.test_case_version == 3
+        assert migrated.catalog_hash == "abc"
+        assert migrated.committed == {"output.json": "a" * 64}
+
+    def test_migrate_preserves_recorded_diagnostic_version(self, invoke_cli, mocker, tmp_path):
+        import json as _json
+
+        # Code has advanced to version 3 but the committed manifest still records version 2:
+        # an authorised bump not yet re-minted, which the gate's staleness check fails until
+        # a re-mint. migrate-manifests must not paper over that by re-stamping the recorded
+        # value to the in-code version.
+        paths = self._wire(mocker, tmp_path, code_version=3)
+        paths.manifest.write_text(
+            _json.dumps(
+                {
+                    "schema": 2,
+                    "test_case_version": 1,
+                    "diagnostic_version": 2,
+                    "catalog_hash": None,
+                    "committed": {"output.json": "a" * 64},
+                    "native": {},
+                },
+                indent=2,
+                sort_keys=True,
+            )
+            + "\n",
+            encoding="utf-8",
+        )
+
+        result = invoke_cli(["test-cases", "migrate-manifests", "--provider", "example"])
+        assert result.exit_code == 0
+
+        from climate_ref_core.regression.manifest import Manifest
+
+        migrated = Manifest.load(paths.manifest)
+        assert migrated.diagnostic_version == 2  # preserved, NOT re-stamped to 3
+
+    def test_migrate_is_idempotent_and_byte_stable(self, invoke_cli, mocker, tmp_path):
+        import json as _json
+
+        paths = self._wire(mocker, tmp_path, code_version=1)
+        paths.manifest.write_text(
+            _json.dumps(
+                {
+                    "schema": 1,
+                    "test_case_version": 1,
+                    "committed": {},
+                    "native": {},
+                },
+                indent=2,
+                sort_keys=True,
+            )
+            + "\n",
+            encoding="utf-8",
+        )
+
+        first = invoke_cli(["test-cases", "migrate-manifests", "--provider", "example"])
+        assert first.exit_code == 0
+        after_first = paths.manifest.read_bytes()
+
+        # Re-running on an already-migrated manifest is a no-op (byte-identical).
+        second = invoke_cli(["test-cases", "migrate-manifests", "--provider", "example"])
+        assert second.exit_code == 0
+        assert paths.manifest.read_bytes() == after_first