Atlas seed-harvest pipeline (Tier 1-3, approval artifact, sync)

fixtures/atlas/aggregate/adk-occ-saga.json

@@ -0,0 +1,124 @@
+{
+  "_comment": "ADK-OCC saga (spec §6.3): ag-ui issue #1732 -> PR #1746 -> issue #1753 -> issue #1754, all about the agui-adk subsystem. These four pre-fusion CandidateFragments must aggregate into ONE higher-order fragment carrying all four sources as fused_from evidence, with the most-restrictive sensitivity (internal, because #1732 is public but the rest are internal). This is the pre-fusion form of worked row §12.1 (derived:agui-adk:occ-concurrency-handling).",
+  "fragments": [
+    {
+      "sourcetype": "github-issue",
+      "subsystem": "agui-adk",
+      "claimSlugHint": "occ-concurrency-handling",
+      "source_name": "github-issue",
+      "repo_url": "https://github.com/ag-ui-protocol/ag-ui",
+      "ref": "1732",
+      "title": "ADK agent-run state suffers lost-update bugs under concurrent writes",
+      "content": "Concurrent mutations of ADK agent-run state clobber each other, producing lost updates. The root cause is an unguarded read-modify-write on shared run state. This issue is the origin of the optimistic-concurrency-control decision for ADK run-state.",
+      "provenance": {
+        "source": "github-issue",
+        "url": "https://github.com/ag-ui-protocol/ag-ui/issues/1732",
+        "date": "2026-05-12",
+        "classification": {
+          "sensitivity": "public",
+          "knowledge_type": "root-cause",
+          "audience": "all-staff",
+          "validation_status": "unverified",
+          "confidence": "high",
+          "provenance_class": "primary",
+          "freshness": { "as_of": "2026-05-12", "re_verify_by": "2026-09-12" }
+        }
+      },
+      "evidence": [
+        { "kind": "linked_issue", "url": "issues/1732" },
+        { "kind": "thread", "body": "root-cause narrative in #1732" }
+      ],
+      "needsReview": false,
+      "validationTargets": []
+    },
+    {
+      "sourcetype": "github-pr",
+      "subsystem": "agui-adk",
+      "claimSlugHint": "occ-concurrency-handling",
+      "source_name": "github-pr",
+      "repo_url": "https://github.com/ag-ui-protocol/ag-ui",
+      "ref": "1746",
+      "title": "Adopt optimistic concurrency control for ADK agent-run state writes",
+      "content": "ADK run-state writes are now version-checked: a concurrent mutation detects a version conflict and retries rather than holding a lock, trading a small retry cost for deadlock-freedom. Callers must tolerate a retried apply because writes are idempotent.",
+      "provenance": {
+        "source": "github-pr",
+        "url": "https://github.com/ag-ui-protocol/ag-ui/pull/1746",
+        "date": "2026-05-14",
+        "classification": {
+          "sensitivity": "internal",
+          "knowledge_type": "architecture",
+          "audience": "engineering",
+          "validation_status": "source-verified",
+          "confidence": "high",
+          "provenance_class": "primary",
+          "freshness": { "as_of": "2026-05-14", "re_verify_by": "2026-09-14" }
+        }
+      },
+      "evidence": [
+        { "kind": "changed_file", "path": "integrations/google-adk/src/run-state.ts" },
+        { "kind": "linked_issue", "url": "issues/1732" }
+      ],
+      "needsReview": false,
+      "validationTargets": ["integrations/google-adk/src/run-state.ts"]
+    },
+    {
+      "sourcetype": "github-issue",
+      "subsystem": "agui-adk",
+      "claimSlugHint": "occ-concurrency-handling",
+      "source_name": "github-issue",
+      "repo_url": "https://github.com/ag-ui-protocol/ag-ui",
+      "ref": "1753",
+      "title": "Document that ADK run-state writes are version-checked and idempotent",
+      "content": "Follow-up to the OCC adoption: the public-facing behavior is that ADK run-state writes are version-checked and idempotent, so integrators should expect a retried apply under contention rather than an error.",
+      "provenance": {
+        "source": "github-issue",
+        "url": "https://github.com/ag-ui-protocol/ag-ui/issues/1753",
+        "date": "2026-05-18",
+        "classification": {
+          "sensitivity": "internal",
+          "knowledge_type": "architecture",
+          "audience": "all-staff",
+          "validation_status": "unverified",
+          "confidence": "medium",
+          "provenance_class": "derived",
+          "freshness": { "as_of": "2026-05-18", "re_verify_by": "2026-09-18" }
+        }
+      },
+      "evidence": [
+        { "kind": "linked_issue", "url": "issues/1753" }
+      ],
+      "needsReview": false,
+      "validationTargets": []
+    },
+    {
+      "sourcetype": "github-issue",
+      "subsystem": "agui-adk",
+      "claimSlugHint": "occ-concurrency-handling",
+      "source_name": "github-issue",
+      "repo_url": "https://github.com/ag-ui-protocol/ag-ui",
+      "ref": "1754",
+      "title": "Reuse the OCC retry shape for ADK tool-call state",
+      "content": "A second site (tool-call state) hits the same lost-update class; #1754 notes it is the 'same OCC shape' as run-state and should reuse the version-check-and-retry approach rather than inventing a new locking scheme.",
+      "provenance": {
+        "source": "github-issue",
+        "url": "https://github.com/ag-ui-protocol/ag-ui/issues/1754",
+        "date": "2026-05-20",
+        "classification": {
+          "sensitivity": "internal",
+          "knowledge_type": "architecture",
+          "audience": "engineering",
+          "validation_status": "unverified",
+          "confidence": "medium",
+          "provenance_class": "derived",
+          "freshness": { "as_of": "2026-05-20", "re_verify_by": "2026-09-20" }
+        }
+      },
+      "evidence": [
+        { "kind": "linked_issue", "url": "issues/1754" },
+        { "kind": "thread", "body": "#1754 notes 'same OCC shape'" }
+      ],
+      "needsReview": false,
+      "validationTargets": []
+    }
+  ]
+}

fixtures/atlas/aggregate/cross-source-subsystem.json

@@ -0,0 +1,151 @@
+{
+  "_comment": "Cross-source fusion (spec §4.4): a PR fragment + an issue fragment + a memory fragment + a Notion ADR fragment ALL about the same subsystem (agui-protocol interrupt-resume keying) must fuse into ONE higher-order fragment carrying all four sources as fused_from evidence. Sensitivities span public/internal/proprietary so the reconciled sensitivity must be the most restrictive (proprietary). A trailing UNRELATED fragment (railway-deploy) must NOT be fused into this group.",
+  "fragments": [
+    {
+      "sourcetype": "notion-doc",
+      "subsystem": "agui-protocol",
+      "claimSlugHint": "interrupt-resume-keying",
+      "source_name": "notion-doc",
+      "repo_url": "https://github.com/ag-ui-protocol/ag-ui",
+      "ref": "interrupts-adr",
+      "title": "Interrupt resume links via interruptId, NOT parentRunId",
+      "content": "The Interrupts design decided a resume is linked to its interrupt via interruptId rather than parentRunId, because parentRunId is a branching primitive and reusing it would conflate resume with branch.",
+      "provenance": {
+        "source": "notion-doc",
+        "url": "https://www.notion.so/copilotkit/Interrupts-Proposal-Design-Decisions-Reasoning",
+        "date": "2026-04-18",
+        "classification": {
+          "sensitivity": "internal",
+          "knowledge_type": "design-rationale",
+          "audience": "engineering",
+          "validation_status": "source-verified",
+          "confidence": "high",
+          "provenance_class": "primary",
+          "freshness": { "as_of": "2026-04-18", "re_verify_by": "2026-09-18" }
+        }
+      },
+      "evidence": [
+        { "kind": "thread", "body": "Interrupts Proposal — Design Decisions & Reasoning (decision: resume keying)" }
+      ],
+      "needsReview": false,
+      "validationTargets": []
+    },
+    {
+      "sourcetype": "github-pr",
+      "subsystem": "agui-protocol",
+      "claimSlugHint": "interrupt-resume-keying",
+      "source_name": "github-pr",
+      "repo_url": "https://github.com/ag-ui-protocol/ag-ui",
+      "ref": "1801",
+      "title": "Wire interruptId as the resume handle in the verify state machine",
+      "content": "Implements the ADR: the verify state machine now keys a resume off interruptId. parentRunId is left to express run lineage only.",
+      "provenance": {
+        "source": "github-pr",
+        "url": "https://github.com/ag-ui-protocol/ag-ui/pull/1801",
+        "date": "2026-04-25",
+        "classification": {
+          "sensitivity": "public",
+          "knowledge_type": "architecture",
+          "audience": "all-staff",
+          "validation_status": "source-verified",
+          "confidence": "high",
+          "provenance_class": "primary",
+          "freshness": { "as_of": "2026-04-25", "re_verify_by": "2026-09-25" }
+        }
+      },
+      "evidence": [
+        { "kind": "changed_file", "path": "client/verify/verify.ts" },
+        { "kind": "linked_issue", "url": "issues/1799" }
+      ],
+      "needsReview": false,
+      "validationTargets": ["client/verify/verify.ts"]
+    },
+    {
+      "sourcetype": "github-issue",
+      "subsystem": "agui-protocol",
+      "claimSlugHint": "interrupt-resume-keying",
+      "source_name": "github-issue",
+      "repo_url": "https://github.com/ag-ui-protocol/ag-ui",
+      "ref": "1799",
+      "title": "Resume incorrectly reuses parentRunId, conflating resume with branch",
+      "content": "Bug report: resuming an interrupted run reuses parentRunId, which the branching code also reads, so a resume is indistinguishable from a branch. This motivated the interruptId resume handle.",
+      "provenance": {
+        "source": "github-issue",
+        "url": "https://github.com/ag-ui-protocol/ag-ui/issues/1799",
+        "date": "2026-04-15",
+        "classification": {
+          "sensitivity": "internal",
+          "knowledge_type": "root-cause",
+          "audience": "engineering",
+          "validation_status": "unverified",
+          "confidence": "medium",
+          "provenance_class": "primary",
+          "freshness": { "as_of": "2026-04-15", "re_verify_by": "2026-09-15" }
+        }
+      },
+      "evidence": [
+        { "kind": "linked_issue", "url": "issues/1799" }
+      ],
+      "needsReview": false,
+      "validationTargets": []
+    },
+    {
+      "sourcetype": "memory",
+      "subsystem": "agui-protocol",
+      "claimSlugHint": "interrupt-resume-keying",
+      "source_name": "memory-store",
+      "repo_url": "https://github.com/ag-ui-protocol/ag-ui",
+      "ref": "feedback_interrupt_resume_keying",
+      "title": "Resume keys off interruptId; do not thread parentRunId for resume",
+      "content": "Durable note: when implementing resume in any integration, key off interruptId. parentRunId is for branching only. This is proprietary integration guidance derived from internal escalations.",
+      "provenance": {
+        "source": "memory-store",
+        "url": "file:///Users/jpr5/.local/share/copilotkit/memory/store/feedback_interrupt_resume_keying.md",
+        "date": "2026-05-02",
+        "classification": {
+          "sensitivity": "proprietary",
+          "knowledge_type": "design-rationale",
+          "audience": "engineering",
+          "validation_status": "unverified",
+          "confidence": "high",
+          "provenance_class": "primary",
+          "freshness": { "as_of": "2026-05-02", "re_verify_by": "2026-11-02" }
+        }
+      },
+      "evidence": [
+        { "kind": "thread", "body": "feedback_interrupt_resume_keying" }
+      ],
+      "needsReview": false,
+      "validationTargets": []
+    },
+    {
+      "sourcetype": "memory",
+      "subsystem": "railway-deploy",
+      "claimSlugHint": "image-entrypoint-shell-escape",
+      "source_name": "memory-store",
+      "repo_url": "https://github.com/CopilotKit/pathfinder",
+      "ref": "feedback_railway_image_shell_escape",
+      "title": "Railway image entrypoints must escape shell metacharacters",
+      "content": "An unescaped shell metacharacter in a Railway start command silently breaks the container boot. This is an UNRELATED subsystem and must not fuse into the interrupt-resume group.",
+      "provenance": {
+        "source": "memory-store",
+        "url": "file:///Users/jpr5/.local/share/copilotkit/memory/store/feedback_railway_image_shell_escape.md",
+        "date": "2026-05-15",
+        "classification": {
+          "sensitivity": "internal",
+          "knowledge_type": "operational",
+          "audience": "engineering",
+          "validation_status": "source-verified",
+          "confidence": "high",
+          "provenance_class": "primary",
+          "freshness": { "as_of": "2026-05-15", "re_verify_by": "2026-11-15" }
+        }
+      },
+      "evidence": [
+        { "kind": "thread", "body": "feedback_railway_image_shell_escape" }
+      ],
+      "needsReview": false,
+      "validationTargets": []
+    }
+  ]
+}

fixtures/atlas/aggregate/dedup-and-unrelated.json

@@ -0,0 +1,92 @@
+{
+  "_comment": "Dedup + no-spurious-fusion: two byte-identical fragments (same subsystem + same source + same content + same ref) must collapse so their identity is not double-counted in fused_from; and two fragments in DIFFERENT subsystems must remain two separate output fragments (no cross-subsystem fusion).",
+  "fragments": [
+    {
+      "sourcetype": "github-pr",
+      "subsystem": "cpk-runtime",
+      "claimSlugHint": "two-layer-shim",
+      "source_name": "github-pr",
+      "repo_url": "https://github.com/CopilotKit/CopilotKit",
+      "ref": "2001",
+      "title": "CopilotRuntime is a two-layer compat shim",
+      "content": "The public CopilotRuntime delegates to the v2 CopilotRuntime, which is itself a shim selecting CopilotSseRuntime / CopilotIntelligenceRuntime.",
+      "provenance": {
+        "source": "github-pr",
+        "url": "https://github.com/CopilotKit/CopilotKit/pull/2001",
+        "date": "2026-06-08",
+        "classification": {
+          "sensitivity": "internal",
+          "knowledge_type": "architecture",
+          "audience": "engineering",
+          "validation_status": "source-verified",
+          "confidence": "high",
+          "provenance_class": "primary",
+          "freshness": { "as_of": "2026-06-08", "re_verify_by": "2026-09-08" }
+        }
+      },
+      "evidence": [
+        { "kind": "changed_file", "path": "packages/runtime/src/v2/runtime/core/runtime.ts:348" }
+      ],
+      "needsReview": false,
+      "validationTargets": []
+    },
+    {
+      "sourcetype": "github-pr",
+      "subsystem": "cpk-runtime",
+      "claimSlugHint": "two-layer-shim",
+      "source_name": "github-pr",
+      "repo_url": "https://github.com/CopilotKit/CopilotKit",
+      "ref": "2001",
+      "title": "CopilotRuntime is a two-layer compat shim",
+      "content": "The public CopilotRuntime delegates to the v2 CopilotRuntime, which is itself a shim selecting CopilotSseRuntime / CopilotIntelligenceRuntime.",
+      "provenance": {
+        "source": "github-pr",
+        "url": "https://github.com/CopilotKit/CopilotKit/pull/2001",
+        "date": "2026-06-08",
+        "classification": {
+          "sensitivity": "internal",
+          "knowledge_type": "architecture",
+          "audience": "engineering",
+          "validation_status": "source-verified",
+          "confidence": "high",
+          "provenance_class": "primary",
+          "freshness": { "as_of": "2026-06-08", "re_verify_by": "2026-09-08" }
+        }
+      },
+      "evidence": [
+        { "kind": "changed_file", "path": "packages/runtime/src/v2/runtime/core/runtime.ts:348" }
+      ],
+      "needsReview": false,
+      "validationTargets": []
+    },
+    {
+      "sourcetype": "memory",
+      "subsystem": "testing-sse",
+      "claimSlugHint": "buffer-replay-timing-invariant",
+      "source_name": "memory-store",
+      "repo_url": "https://github.com/ag-ui-protocol/ag-ui",
+      "ref": "feedback_streaming_tests_assert_timing",
+      "title": "Assert wall-clock spread, not payload, to prove SSE streaming",
+      "content": "A buffered-then-dumped SSE stream is byte-identical to a truly streamed one; assert the wall-clock spread between chunk arrivals to prove streaming.",
+      "provenance": {
+        "source": "memory-store",
+        "url": "file:///Users/jpr5/.local/share/copilotkit/memory/store/feedback_streaming_tests_assert_timing.md",
+        "date": "2026-05-30",
+        "classification": {
+          "sensitivity": "internal",
+          "knowledge_type": "operational",
+          "audience": "engineering",
+          "validation_status": "source-verified",
+          "confidence": "high",
+          "provenance_class": "primary",
+          "freshness": { "as_of": "2026-05-30", "re_verify_by": "2026-11-30" }
+        }
+      },
+      "evidence": [
+        { "kind": "thread", "body": "feedback_streaming_tests_assert_timing" }
+      ],
+      "needsReview": false,
+      "validationTargets": []
+    }
+  ]
+}

fixtures/atlas/checkout/README.md

@@ -0,0 +1,21 @@
+# Fixture checkout (fake `origin/main` tree) — S14 validation gate
+
+A deliberately tiny, hermetic stand-in for a read-only checkout of
+`origin/main`, grepped by `src/atlas/validate.ts` (`promoteValidation`) to
+source-verify a candidate's `validationTargets`.
+
+What it asserts (see `src/__tests__/atlas-validate.test.ts`):
+
+- `src/db/atlas.ts` contains the symbol `upsertAtlasSeedCandidate`.
+- `src/runtime/shim.ts` contains the symbol `TwoLayerShim`.
+- The §7 worked-proof negative symbol appears NOWHERE in this tree (a candidate
+  whose validationTarget is that absent symbol yields 0 grep hits, stays
+  `unverified`, and — being an architecture fact — is marked `approvable=false`).
+
+IMPORTANT: because the gate does a REAL recursive text grep over this whole
+tree, the negative-case symbol must not appear in ANY file here — not even in a
+comment or this README. Do not write that token anywhere under
+`fixtures/atlas/checkout/`, or the source-verify grep will spuriously match it.
+
+This tree is intentionally outside the TypeScript build (`tsconfig.json`
+excludes `fixtures/`); the `.ts` files here are grep targets, not compiled code.