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/application/JavaScriptSemanticGraphResources.test.ts

@@ -0,0 +1,318 @@
+import { expect, it } from "vitest";
+
+import { buildJavaScriptSemanticGraph } from "./JavaScriptSemanticGraphBuilder.js";
+import type { JavaScriptArtifactAnalysis } from "./JavaScriptArtifactAnalysisTypes.js";
+import type { JavaScriptArtifactFile } from "./JavaScriptArtifactFiles.js";
+import { queryJavaScriptSemanticGraph } from "../domain/javascriptSemanticQuery.js";
+import { analyzeJavaScriptSemantics } from "../domain/javascriptSemanticAnalysis.js";
+import {
+  DEFAULT_JAVASCRIPT_SEMANTIC_LIMITS,
+  type JavaScriptSemanticLimits,
+} from "../domain/javascriptSemanticIr.js";
+
+const SHA256 = "a".repeat(64);
+const GRAPH_ID = `jag_${"b".repeat(64)}`;
+
+it("projects literal events and exact timer cancellation", () => {
+  const graph = graphFor(`
+      function run(bus, dynamicName) {
+        const handle = setInterval(tick, 10);
+        bus.on("ready", handler);
+        bus.once(dynamicName, handler);
+        bus.emit("ready");
+        bus.removeListener("ready", handler);
+        clearInterval(handle);
+      }
+    `);
+
+  const relations = new Set(graph.relations.map(({ relation }) => relation));
+  for (const expected of [
+    "cancels-timer",
+    "dispatches-candidate",
+    "registers-listener",
+    "removes-listener",
+    "schedules-timer",
+  ] as const)
+    expect(relations.has(expected)).toBe(true);
+  expect(
+    graph.nodes.find(
+      ({ kind, properties }) =>
+        kind === "event" && properties.event_name === "ready",
+    ),
+  ).toBeDefined();
+  expect(
+    graph.unknowns.some(
+      ({ family, detail }) =>
+        family === "event" && detail.includes("Dynamic once event name"),
+    ),
+  ).toBe(true);
+  expect(
+    graph.coverage.families.find(({ family }) => family === "event"),
+  ).toMatchObject({ status: "partial" });
+  expect(
+    graph.coverage.families.find(({ family }) => family === "timer"),
+  ).toMatchObject({ status: "partial" });
+});
+
+it("projects child-process creation, I/O, listeners, and signals", () => {
+  const graph = graphFor(`
+      import { spawn } from "node:child_process";
+      function run(command) {
+        const child = spawn(
+          command,
+          ["--mode", "fast"],
+          { env: process.env, stdio: "pipe" },
+        );
+        child.on("exit", onExit);
+        child.once("error", onError);
+        child.kill("SIGTERM");
+      }
+    `);
+
+  const relations = new Set(graph.relations.map(({ relation }) => relation));
+  for (const expected of [
+    "connects-stdio",
+    "forwards-signal",
+    "listens-error",
+    "listens-exit",
+    "spawns",
+    "supplies-argv",
+    "supplies-env",
+  ] as const)
+    expect(relations.has(expected)).toBe(true);
+  expect(
+    graph.nodes.find(
+      ({ kind, properties }) =>
+        kind === "child-process" &&
+        properties.method === "spawn" &&
+        properties.command === null,
+    ),
+  ).toBeDefined();
+  expect(
+    graph.unknowns.some(
+      ({ family, detail }) =>
+        family === "child-process" &&
+        detail.includes("command remains unresolved"),
+    ),
+  ).toBe(true);
+  expect(
+    graph.coverage.families.find(({ family }) => family === "child-process"),
+  ).toMatchObject({ status: "partial" });
+});
+
+it("projects config precedence, request fields, and boundaries", () => {
+  const graph = graphFor(`
+      import { readFileSync } from "node:fs";
+      async function run(schema) {
+        const endpoint = process.env.API_URL ?? "https://fallback.test";
+        const raw = readFileSync("./config.json", "utf8");
+        const parsed = JSON.parse(raw);
+        const port = Number(process.argv[2]);
+        const validated = schema.parse(parsed);
+        const response = await fetch(endpoint, {
+          method: "POST",
+          body: validated,
+        });
+        return response.json();
+      }
+    `);
+
+  const relations = new Set(graph.relations.map(({ relation }) => relation));
+  for (const expected of [
+    "coerces",
+    "constructs-request",
+    "consumed-by",
+    "defaults",
+    "overrides",
+    "parses",
+    "reads-argv",
+    "reads-config",
+    "reads-environment",
+    "supplies-request-field",
+  ] as const)
+    expect(relations.has(expected)).toBe(true);
+  expect(
+    graph.nodes.find(
+      ({ kind, properties }) =>
+        kind === "request" && properties.method === "fetch",
+    ),
+  ).toBeDefined();
+  expect(
+    graph.nodes.filter(({ kind }) => kind === "boundary"),
+  ).not.toHaveLength(0);
+  expect(
+    graph.coverage.families.find(({ family }) => family === "configuration"),
+  ).toMatchObject({ status: "partial" });
+  expect(
+    graph.coverage.families.find(({ family }) => family === "request"),
+  ).toMatchObject({ status: "partial" });
+  expect(
+    graph.coverage.families.find(({ family }) => family === "boundary"),
+  ).toMatchObject({ status: "partial" });
+});
+
+it("projects built-in resource acquisition and release", () => {
+  const graph = graphFor(`
+      import { open } from "node:fs/promises";
+      import { connect } from "node:net";
+      async function run(path) {
+        const file = await open(path);
+        const socket = connect({ port: 9000 });
+        await file.close();
+        socket.end();
+      }
+    `);
+
+  const relations = new Set(graph.relations.map(({ relation }) => relation));
+  expect(relations.has("acquires")).toBe(true);
+  expect(relations.has("releases")).toBe(true);
+  expect(graph.nodes.filter(({ kind }) => kind === "resource")).toHaveLength(2);
+  expect(
+    graph.coverage.families.find(
+      ({ family }) => family === "resource-lifecycle",
+    ),
+  ).toMatchObject({ status: "partial" });
+});
+
+it("projects literal seeds and static object flow", () => {
+  const graph = graphFor(`
+      const source = { token: "TOKEN", count: 1 };
+      const { token } = source;
+      const copy = { ...source };
+      source.count = 2;
+      const read = source.token;
+    `);
+
+  const relations = new Set(graph.relations.map(({ relation }) => relation));
+  for (const expected of [
+    "destructures",
+    "reads-property",
+    "spreads",
+    "writes-property",
+  ] as const)
+    expect(relations.has(expected)).toBe(true);
+  expect(
+    graph.nodes.find(
+      ({ kind, properties }) =>
+        kind === "property-slot" && properties.name === "token",
+    ),
+  ).toBeDefined();
+  const literal = queryJavaScriptSemanticGraph(graph, {
+    seed: { kind: "literal", value: "TOKEN" },
+    direction: "forward-influence",
+  });
+  expect(literal.status).toBe("ambiguous");
+  expect(literal.summary.total_seed_matches).toBe(3);
+  const property = queryJavaScriptSemanticGraph(graph, {
+    seed: { kind: "property", name: "token" },
+    direction: "forward-influence",
+  });
+  expect(property.status).toBe("found");
+});
+
+it("does not promote transformed return expressions to resolved aliases", () => {
+  const graph = graphFor(`
+      function increment(value) { return value + 1; }
+      const input = 1;
+      const output = increment(input);
+    `);
+  const returnNode = graph.nodes.find(({ kind }) => kind === "return-site");
+  if (returnNode === undefined) throw new Error("Expected return site");
+  expect(
+    graph.relations.filter(
+      ({ relation, target_node_id }) =>
+        relation === "aliases" && target_node_id === returnNode.node_id,
+    ),
+  ).toEqual([expect.objectContaining({ resolution: "candidate" })]);
+  const output = graph.nodes.find(
+    ({ kind, label }) => kind === "binding" && label === "output",
+  );
+  const input = graph.nodes.find(
+    ({ kind, label }) => kind === "binding" && label === "input",
+  );
+  if (output === undefined || input === undefined)
+    throw new Error("Expected caller bindings");
+  const strict = queryJavaScriptSemanticGraph(graph, {
+    seed: { kind: "semantic-node", node_id: output.node_id },
+    direction: "backward-provenance",
+  });
+  expect(strict.nodes.map(({ node_id }) => node_id)).not.toContain(
+    input.node_id,
+  );
+  expect(strict.status).toBe("ambiguous");
+});
+
+it("uses unavailable evidence when no source produced semantic IR", () => {
+  const graph = buildJavaScriptSemanticGraph({
+    rootArtifactSha256: SHA256,
+    applicationGraph: { graph_id: GRAPH_ID, nodes: [] },
+    analysis: emptyAnalysis(),
+  });
+  expect(graph.nodes).toHaveLength(1);
+  expect(graph.nodes[0]?.evidence).toMatchObject({
+    authority: "unknown",
+    state: "unavailable",
+    location: { available: false, reason: "not-observed" },
+  });
+});
+
+const emptyAnalysis = (): JavaScriptArtifactAnalysis => ({
+  files: [],
+  packages: [],
+  json_modules: [],
+  html_scripts: [],
+  source_maps: [],
+  visited_ast_nodes: 0,
+  findings: 0,
+  modules: 0,
+  parse_failures: 0,
+  truncated_scopes: 0,
+  limitations: [],
+});
+
+const graphFor = (
+  source: string,
+  inputLimits: Partial<JavaScriptSemanticLimits> = {},
+) => {
+  const file: JavaScriptArtifactFile = {
+    path: "app.js",
+    container_sha256: SHA256,
+    sha256: SHA256,
+    bytes: Buffer.byteLength(source),
+    inventory_artifact_id: `art_${SHA256}`,
+    kind: "javascript",
+    unpacked: false,
+    text: { included: true, value: source },
+  };
+  const semanticLimits = {
+    ...DEFAULT_JAVASCRIPT_SEMANTIC_LIMITS,
+    ...inputLimits,
+  };
+  const analysis: JavaScriptArtifactAnalysis = {
+    files: [
+      {
+        file,
+        javascript: null,
+        semantic: {
+          ir: analyzeJavaScriptSemantics(source, inputLimits),
+          limits: semanticLimits,
+        },
+      },
+    ],
+    packages: [],
+    json_modules: [],
+    html_scripts: [],
+    source_maps: [],
+    visited_ast_nodes: 0,
+    findings: 0,
+    modules: 0,
+    parse_failures: 0,
+    truncated_scopes: 0,
+    limitations: [],
+  };
+  return buildJavaScriptSemanticGraph({
+    rootArtifactSha256: SHA256,
+    applicationGraph: { graph_id: GRAPH_ID, nodes: [] },
+    analysis,
+  });
+};