refactor(test): colocate pure-domain tests and reduce test debt (#471)

* refactor(test): colocate pure-domain tests and reduce test debt

Move focused immutable domain/contracts/adapter tests from
tests/composition/** beside their production owners under src/** as
colocated *.test.ts/*.fixture.ts, and relocate persistence-shaped
composition tests under tests/boundary/filesystem/**. Update import
paths, the Vitest project topology (shared worker context for pure
domain/contracts and recording-port service projects), the test
migration ledger, testing docs, and AGENTS.md to match.

Generated with [Devin](https://devin.ai)

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>

* docs: remove test migration ledger

The cutover is complete and the ledger is no longer referenced anywhere
in source, scripts, or the docs gate. Drop the standalone artifact.

Generated with [Devin](https://devin.ai)

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>

* docs: clean up stale migration artifacts

Remove empty directories left by the test migration and replace the
"final cutover" language in docs/testing.md with standing PR guidance
that no longer references the completed migration.

Generated with [Devin](https://devin.ai)

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>

* fix: repair CI failures from schema, knip, and stale generated artifacts

Three root causes fixed:

1. catalog-schemas.mjs: valuesAt only traversed anyOf from Zod's
   toJSONSchema, not oneOf. The webScreenshotDiffSchema change to a
   discriminated union produces oneOf, so the product catalog generator
   could not derive the web_screenshot_diff schema version. Add oneOf
   traversal.

2. conformancePackage.ts: the test rewrite removed the only imports of
   ScenarioManifest, ReplayPlan, ShimPlan, and ExpectedEvidence, making
   them unused exports that knip flags. Remove the dead type aliases.

3. Regenerate stale artifacts (product catalog, MCP tool catalog, skill
   metadata, conformance manifest) that drifted from the source changes.

Generated with [Devin](https://devin.ai)

Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>

---------

Co-authored-by: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>

src/domain/javascriptSemanticGraphQuery.test.ts

@@ -0,0 +1,278 @@
+import { expect, it } from "vitest";
+
+import type { ApplicationGraphEvidence } from "./javascriptApplicationEvidenceSchemas.js";
+import {
+  JAVASCRIPT_SEMANTIC_NODE_KINDS,
+  JAVASCRIPT_SEMANTIC_RELATION_FAMILIES,
+  JAVASCRIPT_SEMANTIC_RELATIONS,
+} from "./javascriptSemanticGraphSchemas.js";
+import {
+  createJavaScriptSemanticFingerprint,
+  createJavaScriptSemanticGraph,
+  createJavaScriptSemanticGraphNode,
+  createJavaScriptSemanticGraphRelation,
+  createJavaScriptSemanticGraphUnknown,
+  type JavaScriptSemanticGraph,
+  type JavaScriptSemanticGraphNode,
+} from "./javascriptSemanticGraph.js";
+import {
+  parseJavaScriptSemanticGraph,
+  serializeJavaScriptSemanticGraph,
+} from "./javascriptSemanticGraphSerialization.js";
+
+const SHA = "a".repeat(64);
+const JAG_ID = `jag_${"b".repeat(64)}`;
+const completeCoverage = {
+  status: "complete",
+  truncated: false,
+  omitted_count: 0,
+  limits: [],
+} satisfies ApplicationGraphEvidence["coverage"];
+
+const evidence = (
+  state: "observed" | "inferred" = "observed",
+): ApplicationGraphEvidence => ({
+  authority:
+    state === "observed"
+      ? "ast-static-analysis"
+      : "static-relationship-inference",
+  state,
+  confidence: state === "observed" ? "exact" : "high",
+  artifact: { available: true, artifact_id: `art_${SHA}`, sha256: SHA },
+  location: {
+    available: true,
+    value: {
+      kind: "source-range",
+      source: "bundle.js",
+      start: { line: 1, column: 0 },
+      end: { line: 1, column: 10 },
+    },
+  },
+  extractor: {
+    name: "test",
+    version: "1",
+    operation: "recover-semantic-relation",
+    executable_sha256: null,
+  },
+  coverage: completeCoverage,
+  limitations:
+    state === "observed"
+      ? []
+      : ["Static reachability does not prove runtime execution."],
+  evidence_ids: [],
+});
+
+const unknownEvidence = (): ApplicationGraphEvidence => ({
+  authority: "unknown",
+  state: "unknown",
+  confidence: "unknown",
+  artifact: {
+    available: false,
+    reason: "unknown",
+    detail: "Unknown artifact.",
+  },
+  location: {
+    available: false,
+    reason: "unresolved",
+    detail: "Dynamic call target.",
+  },
+  extractor: {
+    name: "test",
+    version: "1",
+    operation: "retain-dynamic-call",
+    executable_sha256: null,
+  },
+  coverage: {
+    status: "unknown",
+    truncated: false,
+    omitted_count: null,
+    limits: [],
+  },
+  limitations: ["Dynamic call target remains unknown."],
+  evidence_ids: [],
+});
+
+const node = (
+  kind: (typeof JAVASCRIPT_SEMANTIC_NODE_KINDS)[number],
+  role: string,
+  properties: Record<string, string | number | boolean | null> = {},
+  functionNodeId: string | null = null,
+): JavaScriptSemanticGraphNode =>
+  createJavaScriptSemanticGraphNode({
+    kind,
+    identity: {
+      artifact_sha256: SHA,
+      module_path: "bundle.js",
+      source_range: {
+        start: { line: 1, column: role.length },
+        end: { line: 1, column: role.length + 1 },
+      },
+      role_key: role,
+    },
+    function_node_id: functionNodeId,
+    application_node_ids: [],
+    label: role,
+    properties,
+    evidence: evidence(),
+  });
+
+const fixtureGraph = (withUnknown = false): JavaScriptSemanticGraph => {
+  const module = node("module", "module");
+  const literal = node("literal", "literal", { value: "TOKEN" });
+  const binding = node("binding", "binding");
+  const callable = node("function", "function");
+  const request = node("request", "request", {
+    endpoint: "https://example.invalid/v1",
+  });
+  const relations = [
+    createJavaScriptSemanticGraphRelation({
+      source_node_id: literal.node_id,
+      target_node_id: binding.node_id,
+      relation: "defines",
+      resolution: "resolved",
+      properties: {},
+      evidence: evidence("inferred"),
+    }),
+    createJavaScriptSemanticGraphRelation({
+      source_node_id: binding.node_id,
+      target_node_id: callable.node_id,
+      relation: "captures",
+      resolution: "resolved",
+      properties: {},
+      evidence: evidence("inferred"),
+    }),
+    createJavaScriptSemanticGraphRelation({
+      source_node_id: callable.node_id,
+      target_node_id: request.node_id,
+      relation: "constructs-request",
+      resolution: "resolved",
+      properties: {},
+      evidence: evidence("inferred"),
+    }),
+  ];
+  const dynamic = createJavaScriptSemanticGraphUnknown({
+    node_id: callable.node_id,
+    family: "call-flow",
+    relation_kinds: ["calls"],
+    reason: "dynamic-call",
+    detail: "Computed callee is unresolved.",
+    candidate_node_ids: [],
+    evidence: unknownEvidence(),
+  });
+  const unknowns = withUnknown ? [dynamic] : [];
+  const coverageFamilies = JAVASCRIPT_SEMANTIC_RELATION_FAMILIES.map(
+    (family) => ({
+      family,
+      status:
+        withUnknown && family === "call-flow"
+          ? ("unknown" as const)
+          : ("complete" as const),
+      retained_relations: relations.filter(({ relation }) =>
+        relation === "defines"
+          ? family === "data-flow"
+          : relation === "captures"
+            ? family === "closure"
+            : family === "request",
+      ).length,
+      omitted_relations: withUnknown && family === "call-flow" ? null : 0,
+      unknown_ids:
+        withUnknown && family === "call-flow" ? [dynamic.unknown_id] : [],
+    }),
+  );
+  const fingerprint = createJavaScriptSemanticFingerprint({
+    function_node_id: callable.node_id,
+    algorithm: "rea.javascript-semantic-function/v1",
+    status: "complete",
+    components: {
+      parameter_arity: 0,
+      normalized_ast_sha256: "1".repeat(64),
+      control_flow_sha256: "2".repeat(64),
+      relation_shape_sha256: "3".repeat(64),
+      literal_set_sha256: "4".repeat(64),
+      effects: ["network"],
+    },
+    limitations: [],
+    evidence: evidence("inferred"),
+  });
+  return createJavaScriptSemanticGraph({
+    schema: "JavaScriptSemanticRelationGraph",
+    schema_version: 1,
+    root_artifact_sha256: SHA,
+    application_graph_id: JAG_ID,
+    root_node_ids: [module.node_id],
+    nodes: [request, callable, binding, literal, module],
+    relations,
+    fingerprints: [fingerprint],
+    unknowns,
+    coverage: {
+      status: withUnknown ? "partial" : "complete",
+      truncated: false,
+      omitted_nodes: withUnknown ? null : 0,
+      omitted_relations: withUnknown ? null : 0,
+      limits: [],
+      families: coverageFamilies,
+    },
+    limitations: withUnknown ? ["Dynamic call target remains unknown."] : [],
+  });
+};
+
+it("defines every required v1 relation family and canonicalizes records", () => {
+  expect(JAVASCRIPT_SEMANTIC_RELATIONS).toContain("argument-to-parameter");
+  expect(JAVASCRIPT_SEMANTIC_RELATIONS).toContain("detaches-task");
+  expect(JAVASCRIPT_SEMANTIC_RELATIONS).toContain("forwards-signal");
+  expect(JAVASCRIPT_SEMANTIC_RELATIONS).toContain("validates");
+  const graph = fixtureGraph();
+  expect(
+    parseJavaScriptSemanticGraph(
+      JSON.parse(serializeJavaScriptSemanticGraph(graph)),
+    ),
+  ).toEqual(graph);
+  expect(graph.nodes.map(({ node_id }) => node_id)).toEqual(
+    graph.nodes.map(({ node_id }) => node_id).toSorted(),
+  );
+});
+
+it("rejects stale identities, dangling endpoints, and incomplete coverage claims", () => {
+  const graph = fixtureGraph();
+  const { graph_id: _graphId, ...graphInput } = graph;
+  expect(() =>
+    parseJavaScriptSemanticGraph({
+      ...graph,
+      graph_id: `jsrg_${"0".repeat(64)}`,
+    }),
+  ).toThrow();
+  expect(() =>
+    createJavaScriptSemanticGraph({
+      ...graphInput,
+      relations: [
+        {
+          ...graph.relations[0],
+          target_node_id: `jsrg_node_${"f".repeat(64)}`,
+        },
+      ],
+    }),
+  ).toThrow();
+  expect(() =>
+    createJavaScriptSemanticGraph({
+      ...graphInput,
+      coverage: { ...graph.coverage, omitted_nodes: 1 },
+    }),
+  ).toThrow(/Complete graph coverage/u);
+  const graphWithUnknown = fixtureGraph(true);
+  const { graph_id: _unknownGraphId, ...unknownGraphInput } = graphWithUnknown;
+  const originalUnknown = graphWithUnknown.unknowns[0];
+  if (originalUnknown === undefined)
+    throw new Error("Expected unknown frontier");
+  const { unknown_id: _unknownId, ...unknownInput } = originalUnknown;
+  expect(() =>
+    createJavaScriptSemanticGraph({
+      ...unknownGraphInput,
+      unknowns: [
+        createJavaScriptSemanticGraphUnknown({
+          ...unknownInput,
+          candidate_node_ids: [`jsrg_node_${"f".repeat(64)}`],
+        }),
+      ],
+    }),
+  ).toThrow(/candidate node is absent/u);
+});