Close superseded Morphogenesis transitions and publish v0.5 evidence

.github/workflows/ci.yml

@@ -52,6 +52,17 @@ jobs:
       - run: pnpm install --frozen-lockfile
       - run: pnpm run audit:dependencies:production
       - run: pnpm run check
+      - name: Verify persistent Morphogenesis and paper evidence
+        run: |
+          node examples/agent-morphogenesis/persistent.mjs /tmp/morphogenesis-persistent-ci
+          node experiments/morphogenesis-paper/governance/verify-persistent.mjs /tmp/morphogenesis-persistent-ci
+          node experiments/morphogenesis-paper/governance/verify.mjs docs/research/morphogenesis-paper-v0.5/governance
+          MORPHOGENESIS_GOVERNANCE_EVIDENCE=docs/research/morphogenesis-paper-v0.5/governance node --test experiments/morphogenesis-paper/governance/verify.test.mjs
+        env:
+          MORPHOGENESIS_PG_PORT: "5432"
+          PGUSER: agentplat_test
+          PGDATABASE: agentplat_test
+          PGPASSWORD: agentplat_test
       - run: pnpm --filter @agentplat/sessions-redis test
       - run: pnpm --filter @agentplat/audit-postgres test
         env:

CHANGELOG.md

@@ -2,6 +2,18 @@
 
 ## Unreleased
 
+## 0.3.0-beta.9 — prepared, not yet published
+
+- Add opt-in Morphogenesis supersession admission and terminal cleanup receipts,
+  retaining stable owner operation identities and the accepted morphology head.
+- Add a workflow compensation adapter and authority-neutral Room projection.
+- Preserve original fence timestamps during delayed owner reconciliation.
+- Add a runnable PostgreSQL Room/Team/Work example, contract tests and bounded
+  TLA+ model. Publish paper v0.5 with separate adversarial admission evidence.
+- All 65 packages move together; npm `next` distribution requires the existing
+  protected release workflow and human staged-package approval. No `latest`
+  promotion or production-reliability claim is part of this change.
+
 ## 0.3.0-beta.8 — published 2026-09-14 (UTC)
 
 All 65 public packages are available under `next`; `latest` was not promoted.

docs/adr/0054-morphogenesis-superseded-resolution.md

@@ -0,0 +1,57 @@
+# ADR 0054: explicit resolution of a superseded Morphogenesis execution
+
+Status: implemented, opt-in preview. Historical evidence remains versioned.
+
+## Problem
+
+Morphology-head CAS selects one successor but does not roll back Team or Work
+effects of another admitted proposal. The v0.3 paper integration demonstrated
+owner cleanup while the losing V1 execution remained `committing_morphology`.
+A timeout or a later head alone cannot establish that a proposal never committed.
+
+## Decision
+
+`beginSupersededResolution` reads the authoritative head through the optional
+`inspectHead` activation port. It admits only `team_active` or
+`committing_morphology`, with no retained activation receipt, and a different
+proposal at exactly expected epoch + 1 in the same scope. The observed head is
+persisted in an immutable supersession binding by execution CAS. Legacy ports
+without inspection fail closed. Later epochs require historical proof outside
+this API; the coordinator does not guess.
+
+`advanceSupersededResolution` reuses the existing owner pipeline: checkpoint,
+fence authority, drain/detach or retire, release budget, then `superseded`.
+Uncertain effects keep their prepared operation identity and reconcile through
+the original owner. Missing evidence blocks progress. Cleanup never modifies the
+accepted head. The terminal supersession receipt is distinct from a normal
+activation/completion receipt, and `complete` refuses supersession executions.
+
+The workflow compensation adapter opts into this exact loser-specific path.
+It is not a generic pre-Team cancellation or post-commit rollback facility.
+Room projection is optional, tenant-scoped and grants no authority.
+
+## Compatibility and obligations
+
+The execution schema version remains 1; supersession fields are absent from
+legacy records so their canonical digests do not change. New phases are emitted
+only by the opt-in API. Exhaustive TypeScript consumers must accommodate
+`superseding` and `superseded`; use `isMorphogenesisExecutionTerminalV1` when both
+successful completion and compensated loss are terminal for the application.
+This addition requires a new coordinated preview package release.
+
+Owners still authenticate, deduplicate stable operation IDs, prevent new work
+once fenced, and wait for admitted work to drain. The optional original
+`fencedAtLogicalMs` result preserves receipt identity across delayed reconciliation;
+omission retains legacy behavior. A receipt is evidence, not an authority grant.
+
+## Validation
+
+`tests/morphogenesis-supersession.test.mjs` covers recruitment and creation,
+lost acknowledgements, concurrent resolution, ambiguous histories, unavailable
+owners, forged receipts, legacy record digests and authority-neutral projection.
+`examples/agent-morphogenesis/persistent-local.mjs` exercises real PostgreSQL,
+Room approval, Team and Work reducers, head contention and pending work.
+Its catalog/membership and reviewers are fixtures; its rollback witness is
+process-local. These results are not independent-host recovery evidence.
+The bounded TLA+ abstraction under `experiments/morphogenesis-paper/model` is
+separate evidence, not a refinement proof of this implementation.

docs/research/morphogenesis-paper-v0.5/README.md

@@ -0,0 +1,80 @@
+# Agent Morphogenesis paper v0.5
+
+The manuscript separates historical v0.4 results from the new opt-in runtime and
+its evidence. PDF: `output/pdf/agent-morphogenesis-paper-v0.5.pdf`.
+
+## Evidence index
+
+- `manuscript.md`, `references.bib`: editable paper and citation metadata.
+- `historical-cells.md`: all 48 historical condition/shape/fault cells, computed
+  from the unchanged v0.4 oracle scores. Seeds are not independent reliability trials.
+- `governance/`: 36 prescribed authority/recovery cells with four real controllers,
+  PostgreSQL and a common experimental signed admission envelope. The registration
+  retains the issuer trust anchor, code hashes and the explicitly bounded design.
+- `persistent/`: PostgreSQL Room/Team/Work integration, competing successors,
+  terminal supersession, lost fence acknowledgement, pending work and real mandate
+  expiry. The environment records compiled module hashes and fixture limitations.
+- `model/`: TLC logs for the two-proposal finite model and three failing mutations.
+- `verifier-tests.txt`: independent verifier's positive and negative controls.
+- `development-attempts/`: engineering pilots and failed integration attempts,
+  excluded from the final observations.
+- `review-response.md`: addressed feedback and remaining research limitations.
+
+The v0.4 frozen artifact is available at the
+[paper publication revision](https://github.com/Agentplat/agentplat/tree/22b60bdae0411496a5295021d8a3988118721a82/docs/research/morphogenesis-paper-v0.4).
+Its experiment source baseline remains
+[the original source revision](https://github.com/Agentplat/agentplat/tree/e978544915a329387e13883fa352191f6993dcc7).
+Do not run that frozen registration against the new runtime and relabel the result
+as the historical execution. New runtime evidence has its own source manifests.
+
+The new runtime, paper and evidence are pinned together by the
+[paper-v0.5 source tag](https://github.com/Agentplat/agentplat/tree/paper-v0.5).
+Use that tag for reproduction; the separate environment manifests retain the
+pre-commit working-tree and compiled-module hashes recorded during execution.
+
+## Reproduce the new extension
+
+From the `paper-v0.5` checkout, Node.js 22.13+, pnpm 11.25 and Docker:
+
+```sh
+pnpm install --frozen-lockfile
+pnpm --filter @agentplat/workflows-postgres... --filter @agentplat/collective-host-postgres... --filter @agentplat/collective-control-postgres... --filter @agentplat/rooms-mesh... --filter @agentplat/workflows-rooms... --filter @agentplat/runtime-mock... build
+node experiments/morphogenesis-paper/governance/run-local.mjs /tmp/governance-new
+node experiments/morphogenesis-paper/governance/verify.mjs /tmp/governance-new
+MORPHOGENESIS_GOVERNANCE_EVIDENCE=/tmp/governance-new node --test experiments/morphogenesis-paper/governance/verify.test.mjs
+node examples/agent-morphogenesis/persistent-local.mjs /tmp/persistent-new
+node experiments/morphogenesis-paper/governance/verify-persistent.mjs /tmp/persistent-new
+node --test tests/morphogenesis-supersession.test.mjs tests/morphogenesis.test.mjs
+```
+
+Output directories must be new. Both wrappers create and remove dedicated
+loopback PostgreSQL containers. No model keys or external inference are needed.
+Signatures, UUIDs, timings and the identity of the race winner can differ between
+runs; compare validated invariants and per-cell outcomes, not random bytes.
+
+For retained evidence, use the same verifiers with this directory's `governance`
+and `persistent` subdirectories. `model/` corresponds to
+`experiments/morphogenesis-paper/model/Supersession.tla`; follow that folder's
+README to repeat TLC with Java and the upstream TLC 1.7.4 jar. The tool and Java
+runtime are development dependencies, not vendored binaries or npm dependencies.
+
+Render with ReportLab and Times New Roman/Arial/Arial Unicode fonts:
+
+```sh
+python3 -B experiments/morphogenesis-paper/render-v05.py
+```
+
+## Evidence limits
+
+The new authority matrix measures the common owner's admission contract, not a
+security feature unique to the Morphogenesis core. The strongest workflow
+baseline ties on admission safety and terminal controller-chain reconstruction.
+The fixed controller has no organizational transition denominator. The minimal
+controller's retained admission chains do not imply successful cleanup.
+
+The persistent contention test is Morphogenesis-specific; comparative full P5
+coverage across contending workflows is not established. Identity/catalog inputs
+and scripted reviewers are fixtures; the rollback witness is process-local.
+TLC explores a bounded abstraction under stated fairness and owner assumptions,
+not the full TypeScript implementation. No LLM-quality or production-reliability
+claim is made. This preprint has not been submitted to a venue by this task.

docs/research/morphogenesis-paper-v0.5/development-attempts/governance-before-module-manifest/cases/decision_expired-durable.json

@@ -0,0 +1,163 @@
+{
+  "schemaVersion": 1,
+  "id": "authority-decision_expired-durable",
+  "condition": "durable",
+  "cell": "decision_expired",
+  "clock": {
+    "origin": "2026-09-20T00:00:00.000Z",
+    "admissionMs": 300,
+    "scope": "prescribed owner clock; no skew tested"
+  },
+  "trustedPublicKey": "-----BEGIN PUBLIC KEY-----\nMCowBQYDK2VwAyEAMfu0J4jWbQ7FuHnbOqp128BwAlAo8k8ivcux4jb667w=\n-----END PUBLIC KEY-----\n",
+  "proposal": {
+    "schemaVersion": 1,
+    "proposalId": "proposal:authority-decision_expired-durable",
+    "scopeDigest": "sha256:3e47e49a21d3ba805b0aa16ee286b87d518e8dee9f871d1c02cd64cbf0283c99",
+    "currentSnapshotDigest": "sha256:2e5b56c49070db022d69eef49227459bc87e493e29901418375c896f49f41029",
+    "expectedCurrentEpoch": 1,
+    "needDigest": "sha256:1de032b0dcf9d83f7bbcf9b8cd06071b0a0f78acfab6b9154138b3259c864be4",
+    "targetDigest": "sha256:173669cf05c79d692da68da68bab25861f00d465c280b712e600999737b079ae",
+    "operations": [
+      {
+        "schemaVersion": 1,
+        "operationId": "operation:recruit:authority-decision_expired-durable",
+        "operator": "recruit_existing",
+        "effectClass": "protected_external",
+        "dependsOnOperationIds": [],
+        "targetReferenceDigest": "sha256:52ef937a941e557ed5d14ed62a7d5bcf462d2523d814860c058a7688bed1a3d1",
+        "compensation": "none",
+        "operationDigest": "sha256:53df618d24d99619e81374ef2c6abed6b9061bc07b5b7d4826238747b7bce94f"
+      }
+    ],
+    "processDefinitionDigest": "sha256:62c37a60ab175f36e6ba0ff4025a9bb1f77a3c402075fa7e82515e3bda12d017",
+    "budget": {
+      "maximumActiveAgents": 3,
+      "maximumNewAgents": 0,
+      "maximumConcurrentProvisioning": 0,
+      "maximumResourceUnits": 10,
+      "maximumInteractionUnits": 100,
+      "maximumActionUnits": 10,
+      "maximumInputTokens": 100,
+      "maximumOutputTokens": 100,
+      "maximumTotalTokens": 200,
+      "maximumDurationMs": 1000,
+      "maximumCosts": [
+        {
+          "currency": "USD",
+          "micros": 1000000
+        }
+      ],
+      "budgetDigest": "sha256:e55a2b7cc011fcd30dc92e5988ac8184bc8c11b28db1eae81308b8165fb20afe"
+    },
+    "decisionRoute": "authorized_agent",
+    "proposerId": "agent:planner",
+    "proposerVersion": 1,
+    "proposerImplementationDigest": "sha256:eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee",
+    "proposedAtLogicalMs": 220,
+    "expiresAtLogicalMs": 500,
+    "advisoryOnly": true,
+    "proposalDigest": "sha256:8f625e04f3eea08b2db5c9c8ac150a4e3de3a7b2c7be4ba5079d0fb1ed2f2648"
+  },
+  "admissions": [
+    {
+      "request": {
+        "operationId": "authority-decision_expired-durable:durable-activate",
+        "proposalDigest": "sha256:8f625e04f3eea08b2db5c9c8ac150a4e3de3a7b2c7be4ba5079d0fb1ed2f2648",
+        "scopeDigest": "sha256:3e47e49a21d3ba805b0aa16ee286b87d518e8dee9f871d1c02cd64cbf0283c99",
+        "subject": "agent:statistics"
+      },
+      "payload": "{\"proposalDigest\":\"sha256:8f625e04f3eea08b2db5c9c8ac150a4e3de3a7b2c7be4ba5079d0fb1ed2f2648\",\"scopeDigest\":\"sha256:3e47e49a21d3ba805b0aa16ee286b87d518e8dee9f871d1c02cd64cbf0283c99\",\"subject\":\"agent:statistics\",\"issuer\":\"authority:reference\",\"validFrom\":200,\"decisionUntil\":290,\"mandateUntil\":400}",
+      "signature": "RYIKkhp4kuElnkct40IZzxfZ+RNiHtie8WjuQnP1xRc4EM+qwcXAWBdzy1gGVm+Omn0pXIqK/fFZJO98JdgcCA==",
+      "at": 300,
+      "ownerAllows": true,
+      "allowed": false
+    }
+  ],
+  "roles": [],
+  "chains": [],
+  "events": [
+    {
+      "sequence": 1,
+      "phase": 0,
+      "kind": "artifact-accepted",
+      "artifactDigest": "sha256:31c0a2313fa7c248fc8f01ec72696691f9d280dda42134bb84a72ccd0c2598f6"
+    },
+    {
+      "sequence": 2,
+      "phase": 1,
+      "kind": "artifact-accepted",
+      "artifactDigest": "sha256:372966a351b3dd6c84060035b4b4990f5a964edf6567c5bb2385a47364c6ed64"
+    },
+    {
+      "sequence": 3,
+      "phase": 2,
+      "kind": "artifact-accepted",
+      "artifactDigest": "sha256:90ecde2f899e0d1d036fa4cc30be3328c7c59c424d89f093f085e503e3bc4c6d"
+    },
+    {
+      "sequence": 4,
+      "phase": 3,
+      "kind": "owner-authorization"
+    },
+    {
+      "sequence": 5,
+      "phase": 3,
+      "kind": "owner-reconciliation",
+      "operationId": "authority-decision_expired-durable:durable-activate"
+    }
+  ],
+  "controller": {
+    "condition": "durable",
+    "done": false,
+    "role": null,
+    "workflowStates": [
+      {
+        "schemaVersion": 1,
+        "tenantId": "missions",
+        "runId": "authority-decision_expired-durable:activate",
+        "processId": "mission-role",
+        "processVersion": "1",
+        "definitionDigest": "sha256:997b2b32d3bb926054e301bb701115f94dde9c409f64249be306e78a80cb990b",
+        "revision": 1,
+        "status": "failed",
+        "stageStates": [
+          {
+            "stageId": "authorize",
+            "status": "terminal",
+            "attempt": 1,
+            "startedAt": "2026-09-19T12:00:30.000Z",
+            "taskRunId": "authority-decision_expired-durable:activate:authorize:1",
+            "outcome": "succeeded",
+            "finishedAt": "2026-09-19T12:00:30.000Z"
+          },
+          {
+            "stageId": "apply",
+            "status": "terminal",
+            "attempt": 1,
+            "startedAt": "2026-09-19T12:00:30.000Z",
+            "taskRunId": "authority-decision_expired-durable:activate:apply:1",
+            "outcome": "failed",
+            "finishedAt": "2026-09-19T12:00:30.000Z",
+            "reasonCode": "task_executor_error"
+          },
+          {
+            "stageId": "finalize",
+            "status": "terminal",
+            "attempt": 0,
+            "outcome": "skipped",
+            "finishedAt": "2026-09-19T12:00:30.000Z"
+          }
+        ],
+        "input": {
+          "caseId": "authority-decision_expired-durable",
+          "action": "activate"
+        },
+        "createdAt": "2026-09-19T12:00:30.000Z",
+        "updatedAt": "2026-09-19T12:00:30.000Z",
+        "stateDigest": "sha256:bb14e0ed3c6704a0a3c16a3d3ce856c5fe70660ab962749485291f163c07960c"
+      }
+    ]
+  },
+  "denied": true,
+  "limits": "Synthetic signed admission envelope around real controllers and PostgreSQL; not a production identity provider or policy benchmark"
+}