[fix.ci.ρ.D8+] align contracts, docs, and clean-schema vocabulary

The failed CI run exposed four independent drift classes: public error unions omitted the idempotency conflict, the route-hook test accidentally required NumPy, documentation and twin semantics still used retired registry fields, and app.object_kind lagged the canonical scientific vocabulary by thirty values. This commit closes each at its authoritative boundary and adds migration 048 rather than rewriting released history.

Author: ivanicu

ARCHITECTURE.md

@@ -20,7 +20,7 @@ Invocation kernel
         │                    │                │
         │                    │                └─ Inline / Thread / Process / Remote
         │                    └─ field cache + generic method-version result cache
-        └─ 28 executable scientific Methods
+        └─ 30 executable scientific Methods
                      │
           ┌──────────┼──────────┐
           ▼          ▼          ▼
@@ -90,7 +90,7 @@ PostgreSQL is the durable authority:
 - `app.command_trace` and `app.v_command_observation` retain semantic-command outcomes,
   latency, cache, actor and linked-Job evidence for the architecture twin.
 
-Migrations are forward-only and content-hash checked. Migrations 000–038 are the
+Migrations are forward-only and content-hash checked. Migrations 000–048 are the
 current schema history.
 
 ## Client application
@@ -101,12 +101,63 @@ the separate truth for connected scientific capability. `AppShell` owns routing
 `ScientificContextStore` owns Program, focus, selection and the application's only
 staleness generation; `SceneService` owns one mol* instance that survives navigation.
 
-Twelve of thirty Views currently expose connected modules across Programs, Design,
+Thirteen of thirty Views currently expose connected modules across Programs, Design,
 Structures, Campaigns, Synthesis, Experiments, Knowledge and Runs. Existing chemistry
 facets are modules over the shared scene and context. Molecule embedding, fields,
 surface MEP and torsion strain enter through semantic commands; long results return by
 Job and content-addressed artifacts.
 
+The browser has two explicit runtime tiers built from one shared ESM graph. `shell.ts`
+boots routing, context, commands, theme and human-facing Workspace projections without
+importing mol* or RDKit. The first in-app navigation to a Scene route dynamically imports
+the molecular runtime without replacing the document; later Workspace and Scene changes
+reuse that module and the single `SceneService` instance. Program, ML, voice and
+scientific-chart code remain route- or visibility-owned chunks. Both the RDKit JavaScript
+bootstrap and WASM binary are fetched only when a chemistry-dependent surface is opened.
+The module registry projects real facet surfaces directly—there is no module-host or
+view-state adapter between the registry and the DOM. Production bundles also omit the
+generated-command integrity walk: that invariant is enforced by build and test gates.
+
+Desktop navigation owns one browser-local expanded/collapsed preference through the
+`RailController`; the responsive mobile rail deliberately ignores that desktop geometry.
+This is presentation state only and never enters Program, scientific-context or evidence
+records.
+
+Background work is visibility-aware and single-owner. The shell coalesces Program
+refreshes and publishes one state event to Workspace and Compute projections; hidden
+legacy surfaces are not populated. Off-screen graphs, charts and Gantt views defer both
+their runtime download and rendering. The ML control-room refresh loop suspends in hidden
+tabs, refreshes volatile Jobs and attention every 15 seconds, refreshes capability
+metadata on a five-minute/manual cadence, and fingerprints snapshots before replacing
+the DOM. Palette updates subscribe to scene state instead of polling. Chemistry results
+have one generation-aware cache that is invalidated on molecule, ligand-target and
+cutoff changes, preventing both repeated WASM work and stale cross-molecule facets.
+
+Three cross-cutting human layers deepen the existing Views without creating new product
+surface area. The Journey Rail projects one durable Program and Work Item across
+Question, Understand, Design, Decide, Make, Test and Learn; it delegates its visible
+"next" action to the existing governed handoff controller rather than bypassing command
+preconditions. The lazily loaded Evidence Inspector classifies a selected record as
+observed, computed, inferred, proposed or unresolved, then reports missing identity,
+observation time, method version, frozen inputs, provenance, artifacts, digest declaration
+and evidence boundary without upgrading presence into validation. Program disclosures and
+the comfortable/compact density preference are browser-local reading state, never durable
+scientific state.
+
+The shell also carries one five-level reading contract across every Workspace and the ML
+control room: **Signal (1) → Visual (2) → Structured (3) → Explanation (4) → Audit (5)**.
+This is explicit component metadata rather than an inferred font-size heuristic. `Scan`
+prioritizes state and visual flow, `Work` balances canonical records with explanation, and
+`Audit` opens provenance and raw records. The preference is browser-local. No mode deletes,
+hides, reclassifies, or mutates scientific evidence; high-difficulty material remains
+keyboard reachable through progressive disclosure.
+
+The all-route performance gate covers the thirty routable Views. The 2026-08-13 local
+matrix verified a roughly 943 KB cold payload for non-scene routes, four font files per
+route, no eager RDKit payload, no eager scientific-visual payload on ordinary Workspace
+routes, and no initial long task on the Program overview. Scene routes deliberately pay
+the mol* runtime cost; that boundary is kept separate from the compact application shell.
+
 ## Runtime topology
 
 - `dirac-fields.service` on `:8901` is the one application/scientific control plane.
@@ -148,7 +199,7 @@ rebuilds. The model can therefore calibrate observed command latency and outcome
 addition to detecting drift, ranking static hotspots and estimating dependency radius.
 It still cannot predict unseen inputs or autonomously change the architecture; that is
 the L4 boundary. The platform substrate is complete against its approved DoD; the
-product capability is explicitly partial (currently 8/8 Workspaces represented and 12/30 Views connected)
+product capability is explicitly partial (currently 8/8 Workspaces represented and 13/30 Views connected)
 even though the navigable product shell is complete at 8/8 and 30/30.
 
 `scripts/digital_twin_scope.json` is the ownership boundary. The watcher recursively

README.md

@@ -82,9 +82,9 @@ parts of one scientific decision system rather than separate tools.
 
 ## Construction status
 
-Dirac currently defines 8 stable Workspaces and 30 routable Views, of which 12 are
-connected to working modules. The contract layer contains 79 versioned semantic Commands
-over 83 canonical ObjectKinds and 28 scientific Method manifests behind one invocation
+Dirac currently defines 8 stable Workspaces and 30 routable Views, of which 13 are
+connected to working modules. The contract layer contains 92 versioned semantic Commands
+over 83 canonical ObjectKinds and 30 scientific Method manifests behind one invocation
 path. PostgreSQL owns Programs, Jobs, attempts, artifacts, relations, provenance and
 execution control.
 
@@ -148,8 +148,11 @@ npm run build:dirac
 node_modules/.bin/http-server build/dirac -p 1360 -g -c-1 -a 0.0.0.0 -P http://127.0.0.1:1360?
 ```
 
-Open <http://localhost:1360/>. The first load fetches the vendored RDKit WASM bundle;
-after that the browser cache supplies it.
+Open <http://localhost:1360/>. Workspace, Knowledge, Runs and ML routes load the compact
+application shell only. Molecular scene routes load mol*; the RDKit JavaScript bootstrap
+and WASM binary are fetched only when a chemistry-dependent surface or semantic layer is
+opened. Program, ML, voice and scientific visual runtimes are split and loaded only by
+the route or visible surface that owns them.
 
 On the canonical workstation, **do not run that server command**: `dirac-web.service`
 already owns the one allowed web port, 1360. Rebuild with `npm run build:dirac` and reload

STATUS.md

@@ -11,11 +11,11 @@ validation. A green contract or transport gate does not validate a scientific mo
 | Capability | Current evidence |
 |---|---|
 | Canonical domain | 83 ObjectKinds and 27 controlled relation kinds; ObjectRef types generated for Python and TypeScript |
-| Semantic Commands | 79 registered Commands with schemas, actor identity, mutation policy, required-Job policy and typed errors |
-| Scientific Methods | 28 Method manifests behind one InvocationService |
-| Durable schema | 39 forward-only migrations, `000` through `038` |
+| Semantic Commands | 92 registered Commands with schemas, actor identity, mutation policy, required-Job policy and typed errors |
+| Scientific Methods | 30 Method manifests behind one InvocationService |
+| Durable schema | 49 forward-only migrations, `000` through `048` |
 | Product shell | 8 Workspaces and 30 routable Views |
-| Connected UI | 12 of 30 Views connected to 15 composable modules; the remaining 18 are explicit shells |
+| Connected UI | 13 of 30 Views connected to 17 composable modules; the remaining 17 are explicit shells |
 | Interfaces | HTTP v2, Python SDK, CLI and generated safe MCP projection share the command boundary |
 | Execution | durable JobStore plus inline, thread, process, local GPU and Kubernetes/Kueue adapters |
 | Results | content-addressed artifacts, method-current caches, provenance and command observations |
@@ -66,7 +66,7 @@ those present files and contracts; they should not be interpreted as a release t
 ## Scope verdict
 
 The command/method/job/artifact substrate and the complete navigation shell exist. The
-product remains partial: 12/30 Views are connected, application-grade HCI action semantics
+product remains partial: 13/30 Views are connected, application-grade HCI action semantics
 are still being migrated, and individual scientific Methods need method-specific validation
 before prospective claims can be made. Workflow completeness and scientific validity are
 separate acceptance gates.

backend/db/migrations/048_object_kind_scientific_alignment.sql

@@ -0,0 +1,45 @@
+-- 048 · align the public ObjectKind vocabulary with scientific durable objects.
+--
+-- Scientific Motif objects were introduced behind a domain-specific enum in
+-- 037.  Public ObjectRef validation is governed by app.object_kind, so the two
+-- vocabularies must contain the same canonical values exposed by
+-- contracts/domain/object-kinds.json.
+BEGIN;
+
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'protein_structure_source';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'prepared_receptor_state';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'binding_site_hypothesis';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'complex_hypothesis';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'pose_hypothesis';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'pose_ensemble';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'conformer_ensemble';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'conformer_hypothesis';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'submitted_compound_record';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'chemical_entity';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'chemical_state_ensemble';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'chemical_microstate';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'parameterized_system';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'simulation_run';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'free_energy_transformation';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'evidence_item';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'evidence_snapshot';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'method_run';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'method_outcome';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'quality_assessment';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'routing_action';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'decision_snapshot';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'resource_lease';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'method_release';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'policy_release';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'condition';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'assumption';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'transformation';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'dataset_snapshot';
+ALTER TYPE app.object_kind ADD VALUE IF NOT EXISTS 'model_release';
+
+INSERT INTO meta.migration (filename,sha256,content_sha256,hash_source)
+VALUES ('048_object_kind_scientific_alignment.sql','\xeedc2d832ba50a8870535cb02b5e3c77588edff80fba28de21026a91228ab26f'::bytea,
+        '\xeedc2d832ba50a8870535cb02b5e3c77588edff80fba28de21026a91228ab26f'::bytea,'content')
+ON CONFLICT (filename) DO NOTHING;
+
+COMMIT;

backend/tests/test_execution_identity.py

@@ -210,7 +210,7 @@ def capture_invoke(_method_id, queued_payload, **kwargs):
 
     def test_stateful_route_hook_is_called_once_per_admission(self):
         from catalog import MethodCatalog
-        from invocation import InvocationService
+        from invocation import HandlerResult, InvocationService
 
         class StatefulExecutor:
             kind = "remote"
@@ -229,7 +229,16 @@ def execute(fn, *args):
 
         executor = StatefulExecutor()
         service = InvocationService(MethodCatalog.load(), executor=executor)
-        result = service.invoke("molecule.embed", {"smiles": "CCO"})
+        handler_result = HandlerResult(result={
+            "molecule": {
+                "kind": "molfile",
+                "content": "stateful route test molfile content" + " " * 16,
+                "dimensionality": 3,
+            }
+        }, artifacts=[("molecule.molfile", b"stateful route test molfile")])
+        with mock.patch("catalog.MethodSpec.handler",
+                        return_value=lambda _payload, _ctx: handler_result):
+            result = service.invoke("molecule.embed", {"smiles": "CCO"})
         self.assertTrue(result["ok"])
         self.assertEqual(executor.calls, 1)
         self.assertEqual(result["meta"]["execution_identity"]["executor_adapter"],

contracts/iface.d.ts

@@ -17,7 +17,7 @@ export type ErrorCode =
     | 'BAD_HOST' | 'CANCELLED' | 'INTERNAL' | 'NOT_FOUND'
     | 'DB_UNAVAILABLE' | 'AUTH_REQUIRED' | 'FORBIDDEN'
     | 'RATE_LIMITED' | 'QUOTA_EXCEEDED' | 'TLS_REQUIRED'
-    | 'INVALID_PARAMETERS';
+    | 'INVALID_PARAMETERS' | 'IDEMPOTENCY_CONFLICT';
 
 /** Discriminated union — a molfile alone is lossy (frontend review, blocker 3). */
 export type Ligand =

contracts/iface.pyi

@@ -16,7 +16,7 @@ ErrorCode = Literal['PARSE', 'UNCONVERGED', 'UNPARAMETERIZED', 'BUDGET',
                     'BAD_HOST', 'CANCELLED', 'INTERNAL', 'NOT_FOUND',
                     'DB_UNAVAILABLE', 'AUTH_REQUIRED', 'FORBIDDEN',
                     'RATE_LIMITED', 'QUOTA_EXCEEDED', 'TLS_REQUIRED',
-                    'INVALID_PARAMETERS']
+                    'INVALID_PARAMETERS', 'IDEMPOTENCY_CONFLICT']
 JobState = Literal['queued', 'running', 'done', 'failed', 'cancelled']  # seam: app.job (PLANNED)
 
 class EmbedMeta(TypedDict):