From d2de2d698b3daf4128ba59992cd4b598bff69c32 Mon Sep 17 00:00:00 2001
From: Jay Yu <yibai14651@gmail.com>
Date: Sun, 25 Oct 2026 11:10:28 -0400
Subject: [PATCH 1/5] chore(packaging): resolve workspace-local distribution
 dependencies

---
 scripts/distribution-lock-resolution.mjs      | 125 +++++++++++++
 scripts/distribution-lock-resolution.test.mjs | 166 ++++++++++++++++++
 .../generate-coding-agent-install-lock.mjs    | 122 +++----------
 scripts/generate-coding-agent-shrinkwrap.mjs  | 150 +++-------------
 scripts/prepare-distribution.mjs              |   2 +-
 scripts/prepare-distribution.test.mjs         |   2 +-
 6 files changed, 343 insertions(+), 224 deletions(-)
 create mode 100644 scripts/distribution-lock-resolution.mjs
 create mode 100644 scripts/distribution-lock-resolution.test.mjs

diff --git a/scripts/distribution-lock-resolution.mjs b/scripts/distribution-lock-resolution.mjs
new file mode 100644
index 000000000..ff4de90be
--- /dev/null
+++ b/scripts/distribution-lock-resolution.mjs
@@ -0,0 +1,125 @@
+import { posix } from "node:path";
+
+export function packageDependencies(entry) {
+	return { ...(entry.dependencies ?? {}), ...(entry.optionalDependencies ?? {}) };
+}
+
+// Node's lookup walks ancestors, but never looks in node_modules/node_modules.
+export function resolveExternalDependency(packages, name, from) {
+	let directory = from;
+	while (true) {
+		if (posix.basename(directory) !== "node_modules") {
+			const candidate = `${directory ? `${directory}/` : ""}node_modules/${name}`;
+			if (packages[candidate] && !packages[candidate].link) return candidate;
+		}
+		if (!directory) break;
+		const parent = posix.dirname(directory);
+		directory = parent === "." ? "" : parent;
+	}
+	throw new Error(`Cannot resolve ${name} from ${from || "root"}`);
+}
+
+function assertExactVersion(name, spec, entry, from) {
+	if (/^\d+\.\d+\.\d+(?:-[0-9A-Za-z.-]+)?(?:\+[0-9A-Za-z.-]+)?$/.test(spec) && entry.version !== spec) {
+		throw new Error(`${from || "root"} dependency ${name}@${spec} resolves to ${entry.version}`);
+	}
+}
+
+// The published CLI flattens private workspaces. Resolve its dependencies in those
+// workspaces BEFORE relocating them; published paths are not source lookup paths.
+export function distributionExternalPackages({ lockPackages, manifest, workspaces, copyEntry }) {
+	const origins = new Map();
+	const visited = new Set();
+	function visit(name) {
+		if (visited.has(name)) return;
+		visited.add(name);
+		const workspace = workspaces.get(name);
+		if (!workspace) throw new Error(`Missing internal runtime workspace: ${name}`);
+		for (const [dependency, spec] of Object.entries(packageDependencies(workspace.packageJson))) {
+			if (workspaces.has(dependency)) visit(dependency);
+			else {
+				const list = origins.get(dependency) ?? [];
+				list.push({ from: workspace.lockPath, spec });
+				origins.set(dependency, list);
+			}
+		}
+	}
+	visit(manifest.name);
+	visit("@diffexai/diffex-evolution");
+	visit("@diffexai/diffex-harness-trace");
+
+	function equivalent(left, right, seen = new Set()) {
+		if (left === right) return true;
+		const pair = `${left}\n${right}`;
+		if (seen.has(pair)) return true;
+		seen.add(pair);
+		if (JSON.stringify(copyEntry(lockPackages[left])) !== JSON.stringify(copyEntry(lockPackages[right])))
+			return false;
+		return Object.keys(packageDependencies(lockPackages[left])).every((name) =>
+			equivalent(
+				resolveExternalDependency(lockPackages, name, left),
+				resolveExternalDependency(lockPackages, name, right),
+				seen,
+			),
+		);
+	}
+
+	const packages = {};
+	const sources = new Map();
+	const queue = [];
+	function add(source, target) {
+		packages[target] = copyEntry(lockPackages[source]);
+		sources.set(target, source);
+		queue.push({ source, target });
+	}
+
+	// Reserve all flattened direct dependencies first, independently of traversal order.
+	for (const [name, spec] of Object.entries(packageDependencies(manifest)).sort(([a], [b]) => a.localeCompare(b))) {
+		const candidates = origins.get(name);
+		if (!candidates?.length) throw new Error(`No originating workspace for ${name}`);
+		const resolved = candidates.map(({ from, spec: originalSpec }) => {
+			if (originalSpec !== spec) throw new Error(`Conflicting bundled runtime dependency: ${name}`);
+			const source = resolveExternalDependency(lockPackages, name, from);
+			assertExactVersion(name, spec, lockPackages[source], from);
+			return source;
+		});
+		const source = resolved[0];
+		for (const candidate of resolved) {
+			if (!equivalent(candidate, source)) {
+				throw new Error(`Conflicting workspace resolutions for flattened dependency ${name}`);
+			}
+		}
+		add(source, `node_modules/${name}`);
+	}
+
+	for (let index = 0; index < queue.length; index++) {
+		const { source, target } = queue[index];
+		for (const [name, spec] of Object.entries(packageDependencies(lockPackages[source])).sort(([a], [b]) =>
+			a.localeCompare(b),
+		)) {
+			const dependencySource = resolveExternalDependency(lockPackages, name, source);
+			assertExactVersion(name, spec, lockPackages[dependencySource], source);
+			let existing;
+			try {
+				existing = resolveExternalDependency(packages, name, target);
+			} catch {
+				// A new reachable installation location is needed.
+			}
+			if (existing && sources.get(existing) === dependencySource) continue;
+			const rootTarget = `node_modules/${name}`;
+			const dependencyTarget =
+				!packages[rootTarget] && dependencySource === rootTarget ? rootTarget : `${target}/node_modules/${name}`;
+			add(dependencySource, dependencyTarget);
+		}
+	}
+
+	// Check edges by identity, not just by the existence of a package with that name.
+	for (const { source, target } of queue) {
+		for (const name of Object.keys(packageDependencies(lockPackages[source]))) {
+			const expected = resolveExternalDependency(lockPackages, name, source);
+			const actual = resolveExternalDependency(packages, name, target);
+			if (sources.get(actual) !== expected) throw new Error(`Relocation changed ${target} dependency ${name}`);
+		}
+	}
+	return packages;
+}
diff --git a/scripts/distribution-lock-resolution.test.mjs b/scripts/distribution-lock-resolution.test.mjs
new file mode 100644
index 000000000..c5ff0c4ad
--- /dev/null
+++ b/scripts/distribution-lock-resolution.test.mjs
@@ -0,0 +1,166 @@
+import assert from "node:assert/strict";
+import { spawnSync } from "node:child_process";
+import { copyFileSync, mkdirSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import test from "node:test";
+import { distributionExternalPackages, resolveExternalDependency } from "./distribution-lock-resolution.mjs";
+
+function fixture() {
+	const manifest = { name: "@diffexai/diffex", dependencies: { sdk: "2.0.0", marked: "3.0.0" } };
+	const workspaces = new Map([
+		[
+			manifest.name,
+			{
+				lockPath: "packages/coding-agent",
+				packageJson: { dependencies: { "@diffexai/diffex-ai": "1.0.0", "@diffexai/diffex-tui": "1.0.0" } },
+			},
+		],
+		["@diffexai/diffex-ai", { lockPath: "packages/ai", packageJson: { dependencies: { sdk: "2.0.0" } } }],
+		["@diffexai/diffex-tui", { lockPath: "packages/tui", packageJson: { dependencies: { marked: "3.0.0" } } }],
+		["@diffexai/diffex-evolution", { lockPath: "packages/evolution", packageJson: {} }],
+		["@diffexai/diffex-harness-trace", { lockPath: "packages/harness-trace", packageJson: {} }],
+	]);
+	const lockPackages = {
+		"node_modules/sdk": { version: "1.0.0" },
+		"packages/ai/node_modules/sdk": {
+			version: "2.0.0",
+			dependencies: { shared: "2.0.0" },
+			optionalDependencies: { native: "1.0.0" },
+		},
+		"packages/ai/node_modules/shared": { version: "2.0.0", dependencies: { sdk: "2.0.0" } },
+		"packages/ai/node_modules/native": {
+			version: "1.0.0",
+			optional: true,
+			os: ["darwin"],
+			cpu: ["arm64"],
+			integrity: "native-integrity",
+		},
+		"packages/tui/node_modules/marked": { version: "3.0.0", dependencies: { shared: "1.0.0" } },
+		"node_modules/shared": { version: "1.0.0" },
+	};
+	return { manifest, workspaces, lockPackages, copyEntry: (entry) => ({ ...entry }) };
+}
+
+test("relocates workspace-local direct, transitive, optional and conflicting nested versions", () => {
+	const input = fixture();
+	const original = JSON.stringify(input.lockPackages);
+	const packages = distributionExternalPackages(input);
+	assert.equal(packages["node_modules/sdk"].version, "2.0.0");
+	assert.equal(packages["node_modules/marked"].version, "3.0.0");
+	const sdkShared = resolveExternalDependency(packages, "shared", "node_modules/sdk");
+	const markedShared = resolveExternalDependency(packages, "shared", "node_modules/marked");
+	assert.equal(packages[sdkShared].version, "2.0.0");
+	assert.equal(packages[markedShared].version, "1.0.0");
+	assert.equal(resolveExternalDependency(packages, "sdk", sdkShared), "node_modules/sdk");
+	const native = resolveExternalDependency(packages, "native", "node_modules/sdk");
+	assert.deepEqual(packages[native], input.lockPackages["packages/ai/node_modules/native"]);
+	assert.ok(Object.keys(packages).every((path) => path.startsWith("node_modules/")));
+	assert.equal(JSON.stringify(input.lockPackages), original);
+	assert.deepEqual(distributionExternalPackages(input), packages);
+});
+
+test("both generators emit deterministic deployable locks in an isolated fixture", () => {
+	const root = mkdtempSync(join(tmpdir(), "diffex-lock-resolution-"));
+	try {
+		const input = fixture();
+		input.manifest.version = "1.0.0";
+		for (const [name, version] of [
+			["@google/genai", "1.52.0"],
+			["protobufjs", "7.6.5"],
+		]) {
+			input.manifest.dependencies[name] = version;
+			input.workspaces.get(input.manifest.name).packageJson.dependencies[name] = version;
+			input.lockPackages[`node_modules/${name}`] = { version, hasInstallScript: true };
+		}
+		mkdirSync(join(root, "scripts"));
+		for (const file of [
+			"generate-coding-agent-shrinkwrap.mjs",
+			"generate-coding-agent-install-lock.mjs",
+			"distribution-lock-resolution.mjs",
+		]) {
+			copyFileSync(new URL(file, import.meta.url), join(root, "scripts", file));
+		}
+		writeFileSync(
+			join(root, "scripts/cli-distribution.mjs"),
+			`export function cliDistribution() { return { manifest: ${JSON.stringify(input.manifest)} }; }\n`,
+		);
+		for (const [name, workspace] of input.workspaces) {
+			const manifest = { name, version: "1.0.0", ...workspace.packageJson };
+			mkdirSync(join(root, workspace.lockPath), { recursive: true });
+			writeFileSync(join(root, workspace.lockPath, "package.json"), JSON.stringify(manifest));
+			input.lockPackages[workspace.lockPath] = manifest;
+		}
+		writeFileSync(
+			join(root, "package-lock.json"),
+			JSON.stringify({ lockfileVersion: 3, packages: input.lockPackages }),
+		);
+		for (const generator of ["generate-coding-agent-shrinkwrap.mjs", "generate-coding-agent-install-lock.mjs"]) {
+			for (const args of [[], ["--check"]]) {
+				const result = spawnSync(process.execPath, [join(root, "scripts", generator), ...args], {
+					encoding: "utf8",
+				});
+				assert.equal(result.status, 0, result.stderr);
+			}
+		}
+		const shrinkwrap = JSON.parse(readFileSync(join(root, "packages/coding-agent/npm-shrinkwrap.json"), "utf8"));
+		const install = JSON.parse(
+			readFileSync(join(root, "packages/coding-agent/install-lock/package-lock.json"), "utf8"),
+		);
+		for (const lock of [shrinkwrap, install]) {
+			assert.ok(Object.keys(lock.packages).every((path) => !path || path.startsWith("node_modules/")));
+			assert.equal(lock.packages["node_modules/sdk"].version, "2.0.0");
+			assert.equal(lock.packages["node_modules/marked"].version, "3.0.0");
+		}
+		for (const [path, entry] of Object.entries(shrinkwrap.packages)) {
+			if (path) assert.deepEqual(install.packages[path], entry);
+		}
+	} finally {
+		rmSync(root, { recursive: true, force: true });
+	}
+});
+
+test("lookup follows Node ancestors and never falls back to an unrelated unique entry", () => {
+	assert.throws(
+		() =>
+			resolveExternalDependency({ "packages/other/node_modules/only": { version: "1.0.0" } }, "only", "packages/ai"),
+		/Cannot resolve/,
+	);
+	const packages = {
+		"node_modules/@scope/pkg/node_modules/dep": { version: "2.0.0" },
+		"node_modules/@scope/pkg/node_modules/node_modules/dep": { version: "wrong" },
+	};
+	assert.equal(
+		resolveExternalDependency(packages, "dep", "node_modules/@scope/pkg/node_modules/child"),
+		"node_modules/@scope/pkg/node_modules/dep",
+	);
+});
+
+test("rejects an exact direct or transitive version mismatch", () => {
+	const direct = fixture();
+	direct.lockPackages["packages/ai/node_modules/sdk"].version = "1.0.0";
+	assert.throws(() => distributionExternalPackages(direct), /sdk@2.0.0 resolves to 1.0.0/);
+	const transitive = fixture();
+	transitive.lockPackages["packages/ai/node_modules/shared"].version = "9.0.0";
+	assert.throws(() => distributionExternalPackages(transitive), /shared@2.0.0 resolves to 9.0.0/);
+});
+
+test("rejects flattened workspace resolutions with different transitive graphs", () => {
+	const input = fixture();
+	input.workspaces.get("@diffexai/diffex-tui").packageJson.dependencies.sdk = "2.0.0";
+	input.lockPackages["packages/tui/node_modules/sdk"] = structuredClone(
+		input.lockPackages["packages/ai/node_modules/sdk"],
+	);
+	assert.throws(() => distributionExternalPackages(input), /Conflicting workspace resolutions/);
+});
+
+test("preserves deeper scoped overrides and optional dependency spec precedence", () => {
+	const input = fixture();
+	input.lockPackages["packages/ai/node_modules/sdk"].dependencies["@scope/leaf"] = "1.0.0";
+	input.lockPackages["packages/ai/node_modules/sdk"].optionalDependencies["@scope/leaf"] = "2.0.0";
+	input.lockPackages["packages/ai/node_modules/sdk/node_modules/@scope/leaf"] = { version: "2.0.0", optional: true };
+	const packages = distributionExternalPackages(input);
+	const leaf = resolveExternalDependency(packages, "@scope/leaf", "node_modules/sdk");
+	assert.equal(packages[leaf].version, "2.0.0");
+	assert.equal(packages[leaf].optional, true);
+});
diff --git a/scripts/generate-coding-agent-install-lock.mjs b/scripts/generate-coding-agent-install-lock.mjs
index a8a6e9818..4d6f05e3c 100644
--- a/scripts/generate-coding-agent-install-lock.mjs
+++ b/scripts/generate-coding-agent-install-lock.mjs
@@ -1,9 +1,10 @@
 #!/usr/bin/env node
 
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
-import { dirname, join, posix, resolve } from "node:path";
+import { dirname, join, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
 import { cliDistribution } from "./cli-distribution.mjs";
+import { distributionExternalPackages, resolveExternalDependency } from "./distribution-lock-resolution.mjs";
 
 const scriptDir = dirname(fileURLToPath(import.meta.url));
 const repoRoot = resolve(scriptDir, "..");
@@ -150,88 +151,13 @@ function getInternalWorkspaces(lockPackages) {
 
 		workspaces.set(entry.name, {
 			lockPath,
-			packageJson:
-				entry.name === "@diffexai/diffex"
-					? cliDistribution(repoRoot).manifest
-					: readJson(join(repoRoot, lockPath, "package.json")),
+			packageJson: readJson(join(repoRoot, lockPath, "package.json")),
 		});
 	}
 
 	return workspaces;
 }
 
-function resolveExternalDependency(lockPackages, packageName, fromLockPath) {
-	const candidateDirs = [];
-	let current = fromLockPath;
-
-	while (current) {
-		candidateDirs.push(current);
-		const parent = posix.dirname(current);
-		if (parent === "." || parent === current) {
-			break;
-		}
-		current = parent;
-	}
-	candidateDirs.push("");
-
-	const tried = new Set();
-	for (const directory of candidateDirs) {
-		const candidate = directory ? `${directory}/node_modules/${packageName}` : `node_modules/${packageName}`;
-		if (tried.has(candidate)) {
-			continue;
-		}
-		tried.add(candidate);
-
-		const entry = lockPackages[candidate];
-		if (entry && !entry.link) {
-			return candidate;
-		}
-	}
-
-	const suffix = `node_modules/${packageName}`;
-	const matches = Object.entries(lockPackages)
-		.filter(([lockPath, entry]) => !entry.link && (lockPath === suffix || lockPath.endsWith(`/${suffix}`)))
-		.map(([lockPath]) => lockPath);
-
-	if (matches.length === 1) {
-		return matches[0];
-	}
-
-	throw new Error(
-		`Cannot resolve ${packageName} from ${fromLockPath || "root"}. ` +
-			(matches.length > 1 ? `Matches: ${matches.join(", ")}` : "No matching lockfile entry found."),
-	);
-}
-
-function addInternalWorkspace(installLockPackages, addedPaths, queue, name, workspace) {
-	const packageJson = workspace.packageJson;
-	const outputPath = `node_modules/${name}`;
-	const entry = copyPackageJsonEntry(packageJson, { includeName: false });
-	entry.resolved = registryTarballUrl(name, packageJson.version);
-
-	installLockPackages[outputPath] = sortedPackageEntry(entry);
-	addedPaths.add(outputPath);
-
-	for (const dependencyName of Object.keys(packageDependencies(packageJson))) {
-		queue.push({ name: dependencyName, from: outputPath });
-	}
-}
-
-function addExternalPackage(lockPackages, installLockPackages, addedPaths, queue, name, from) {
-	const lockPath = resolveExternalDependency(lockPackages, name, from);
-	if (addedPaths.has(lockPath)) {
-		return;
-	}
-
-	const entry = lockPackages[lockPath];
-	installLockPackages[lockPath] = copyLockEntry(entry);
-	addedPaths.add(lockPath);
-
-	for (const dependencyName of Object.keys(packageDependencies(entry))) {
-		queue.push({ name: dependencyName, from: lockPath });
-	}
-}
-
 function createInstallerPackageJson(codingAgentPackage) {
 	const packageJson = {
 		name: installPackageName,
@@ -289,6 +215,9 @@ function validateGeneratedFiles(installerPackageJson, installLock, internalNames
 		if (packageName) {
 			includedPackageNames.add(packageName);
 		}
+		if (lockPath && !lockPath.startsWith("node_modules/")) {
+			errors.push(`${lockPath} is not a published node_modules path`);
+		}
 		if (entry.link) {
 			errors.push(`${lockPath} is a link entry`);
 		}
@@ -361,7 +290,9 @@ function validateGeneratedFiles(installerPackageJson, installLock, internalNames
 	}
 
 	if (errors.length > 0) {
-		throw new Error(`Generated installer lock failed validation:\n${errors.map((error) => `  - ${error}`).join("\n")}`);
+		throw new Error(
+			`Generated installer lock failed validation:\n${errors.map((error) => `  - ${error}`).join("\n")}`,
+		);
 	}
 }
 
@@ -378,28 +309,19 @@ function generateInstallLock() {
 	const installLockPackages = {
 		"": createRootLockEntry(installerPackageJson),
 	};
-	const addedPaths = new Set([""]);
-	const internalNames = new Set();
-	const queue = Object.keys(packageDependencies(installerPackageJson)).map((name) => ({ name, from: "" }));
-
-	while (queue.length > 0) {
-		const item = queue.shift();
-		if (!item) {
-			break;
-		}
-
-		const workspace = internalWorkspaces.get(item.name);
-		if (workspace) {
-			const outputPath = `node_modules/${item.name}`;
-			internalNames.add(item.name);
-			if (!addedPaths.has(outputPath)) {
-				addInternalWorkspace(installLockPackages, addedPaths, queue, item.name, workspace);
-			}
-			continue;
-		}
-
-		addExternalPackage(lockPackages, installLockPackages, addedPaths, queue, item.name, item.from);
-	}
+	const internalNames = new Set([codingAgentPackage.name]);
+	const cliEntry = copyPackageJsonEntry(codingAgentPackage, { includeName: false });
+	cliEntry.resolved = registryTarballUrl(codingAgentPackage.name, codingAgentPackage.version);
+	installLockPackages[`node_modules/${codingAgentPackage.name}`] = sortedPackageEntry(cliEntry);
+	Object.assign(
+		installLockPackages,
+		distributionExternalPackages({
+			lockPackages,
+			manifest: codingAgentPackage,
+			workspaces: internalWorkspaces,
+			copyEntry: copyLockEntry,
+		}),
+	);
 
 	const installLock = {
 		name: installerPackageJson.name,
diff --git a/scripts/generate-coding-agent-shrinkwrap.mjs b/scripts/generate-coding-agent-shrinkwrap.mjs
index 4399b3bd9..12176fd63 100644
--- a/scripts/generate-coding-agent-shrinkwrap.mjs
+++ b/scripts/generate-coding-agent-shrinkwrap.mjs
@@ -1,9 +1,10 @@
 #!/usr/bin/env node
 
 import { existsSync, readFileSync, writeFileSync } from "node:fs";
-import { dirname, join, posix, resolve } from "node:path";
+import { dirname, join, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
 import { cliDistribution } from "./cli-distribution.mjs";
+import { distributionExternalPackages, resolveExternalDependency } from "./distribution-lock-resolution.mjs";
 
 const scriptDir = dirname(fileURLToPath(import.meta.url));
 const repoRoot = resolve(scriptDir, "..");
@@ -125,11 +126,6 @@ function packageNameFromLockPath(lockPath) {
 	return parts[0];
 }
 
-function registryTarballUrl(packageName, version) {
-	const tarballName = packageName.startsWith("@") ? packageName.split("/")[1] : packageName;
-	return `https://registry.npmjs.org/${packageName}/-/${tarballName}-${version}.tgz`;
-}
-
 function getInternalWorkspaces(lockPackages) {
 	const workspaces = new Map();
 
@@ -143,98 +139,21 @@ function getInternalWorkspaces(lockPackages) {
 
 		workspaces.set(entry.name, {
 			lockPath,
-			packageJson:
-				entry.name === "@diffexai/diffex"
-					? cliDistribution(repoRoot).manifest
-					: readJson(join(repoRoot, lockPath, "package.json")),
+			packageJson: readJson(join(repoRoot, lockPath, "package.json")),
 		});
 	}
 
 	return workspaces;
 }
 
-function resolveExternalDependency(lockPackages, packageName, fromLockPath) {
-	const candidateDirs = [];
-	let current = fromLockPath;
-
-	while (current) {
-		candidateDirs.push(current);
-		const parent = posix.dirname(current);
-		if (parent === "." || parent === current) {
-			break;
-		}
-		current = parent;
-	}
-	candidateDirs.push("");
-
-	const tried = new Set();
-	for (const directory of candidateDirs) {
-		const candidate = directory ? `${directory}/node_modules/${packageName}` : `node_modules/${packageName}`;
-		if (tried.has(candidate)) {
-			continue;
-		}
-		tried.add(candidate);
-
-		const entry = lockPackages[candidate];
-		if (entry && !entry.link) {
-			return candidate;
-		}
-	}
-
-	const suffix = `node_modules/${packageName}`;
-	const matches = Object.entries(lockPackages)
-		.filter(([lockPath, entry]) => !entry.link && (lockPath === suffix || lockPath.endsWith(`/${suffix}`)))
-		.map(([lockPath]) => lockPath);
-
-	if (matches.length === 1) {
-		return matches[0];
-	}
-
-	throw new Error(
-		`Cannot resolve ${packageName} from ${fromLockPath || "root"}. ` +
-			(matches.length > 1 ? `Matches: ${matches.join(", ")}` : "No matching lockfile entry found."),
-	);
-}
-
-function addInternalWorkspace(shrinkwrapPackages, addedPaths, queue, name, workspace) {
-	const packageJson = workspace.packageJson;
-	const outputPath = `node_modules/${name}`;
-	const entry = copyPackageJsonEntry(packageJson, { includeName: false });
-	entry.resolved = registryTarballUrl(name, packageJson.version);
-
-	shrinkwrapPackages[outputPath] = sortedPackageEntry(entry);
-	addedPaths.add(outputPath);
-
-	for (const dependencyName of Object.keys(packageDependencies(packageJson))) {
-		queue.push({ name: dependencyName, from: outputPath });
-	}
-}
-
-function addExternalPackage(lockPackages, shrinkwrapPackages, addedPaths, queue, name, from) {
-	const lockPath = resolveExternalDependency(lockPackages, name, from);
-	if (addedPaths.has(lockPath)) {
-		return;
-	}
-
-	const entry = lockPackages[lockPath];
-	shrinkwrapPackages[lockPath] = copyLockEntry(entry);
-	addedPaths.add(lockPath);
-
-	for (const dependencyName of Object.keys(packageDependencies(entry))) {
-		queue.push({ name: dependencyName, from: lockPath });
-	}
-}
-
-function validateShrinkwrap(shrinkwrap, internalNames) {
+function validateShrinkwrap(shrinkwrap) {
 	const errors = [];
-	const includedPaths = new Set(Object.keys(shrinkwrap.packages));
-	const includedPackageNames = new Set();
 	const seenAllowedInstallScriptPackages = new Set();
 
 	for (const [lockPath, entry] of Object.entries(shrinkwrap.packages)) {
 		const packageName = packageNameFromLockPath(lockPath);
-		if (packageName) {
-			includedPackageNames.add(packageName);
+		if (lockPath && !lockPath.startsWith("node_modules/")) {
+			errors.push(`${lockPath} is not a published node_modules path`);
 		}
 		if (entry.link) {
 			errors.push(`${lockPath} is a link entry`);
@@ -264,19 +183,19 @@ function validateShrinkwrap(shrinkwrap, internalNames) {
 		}
 	}
 
-	for (const name of internalNames) {
-		if (!includedPackageNames.has(name)) {
-			errors.push(`internal dependency ${name} is missing`);
-		}
-	}
-
 	for (const [lockPath, entry] of Object.entries(shrinkwrap.packages)) {
-		for (const dependencyName of Object.keys(packageDependencies(entry))) {
-			const dependencyIncluded = [...includedPaths].some(
-				(candidate) =>
-					candidate === `node_modules/${dependencyName}` || candidate.endsWith(`/node_modules/${dependencyName}`),
-			);
-			if (!dependencyIncluded) {
+		for (const [dependencyName, dependencySpec] of Object.entries(packageDependencies(entry))) {
+			try {
+				const resolved = resolveExternalDependency(shrinkwrap.packages, dependencyName, lockPath);
+				if (
+					/^\d+\.\d+\.\d+(?:-[0-9A-Za-z.-]+)?(?:\+[0-9A-Za-z.-]+)?$/.test(dependencySpec) &&
+					shrinkwrap.packages[resolved].version !== dependencySpec
+				) {
+					errors.push(
+						`${lockPath || "root"} dependency ${dependencyName}@${dependencySpec} resolves to ${shrinkwrap.packages[resolved].version}`,
+					);
+				}
+			} catch {
 				errors.push(`${lockPath || "root"} dependency ${dependencyName} is missing`);
 			}
 		}
@@ -306,28 +225,15 @@ function generateShrinkwrap() {
 	const shrinkwrapPackages = {
 		"": copyPackageJsonEntry(codingAgentPackage, { includeName: true }),
 	};
-	const addedPaths = new Set([""]);
-	const internalNames = new Set();
-	const queue = Object.keys(packageDependencies(codingAgentPackage)).map((name) => ({ name, from: "" }));
-
-	while (queue.length > 0) {
-		const item = queue.shift();
-		if (!item) {
-			break;
-		}
-
-		const workspace = internalWorkspaces.get(item.name);
-		if (workspace) {
-			const outputPath = `node_modules/${item.name}`;
-			internalNames.add(item.name);
-			if (!addedPaths.has(outputPath)) {
-				addInternalWorkspace(shrinkwrapPackages, addedPaths, queue, item.name, workspace);
-			}
-			continue;
-		}
-
-		addExternalPackage(lockPackages, shrinkwrapPackages, addedPaths, queue, item.name, item.from);
-	}
+	Object.assign(
+		shrinkwrapPackages,
+		distributionExternalPackages({
+			lockPackages,
+			manifest: codingAgentPackage,
+			workspaces: internalWorkspaces,
+			copyEntry: copyLockEntry,
+		}),
+	);
 
 	const shrinkwrap = {
 		name: codingAgentPackage.name,
@@ -337,7 +243,7 @@ function generateShrinkwrap() {
 		packages: sortedObject(shrinkwrapPackages),
 	};
 
-	validateShrinkwrap(shrinkwrap, internalNames);
+	validateShrinkwrap(shrinkwrap);
 	return shrinkwrap;
 }
 
diff --git a/scripts/prepare-distribution.mjs b/scripts/prepare-distribution.mjs
index d983efbd0..a2a3d9dfe 100644
--- a/scripts/prepare-distribution.mjs
+++ b/scripts/prepare-distribution.mjs
@@ -74,7 +74,7 @@ export function preparePackageDistribution(directory) {
 		}
 		for (const [name, version, license, file] of [
 			["highlight.js", "11.9.0", "BSD-3-Clause", "legal/upstream/highlight-11.9.0.LICENSE"],
-			["marked", "18.0.5", "MIT", "node_modules/marked/LICENSE"],
+			["marked", "18.0.5", "MIT", "legal/upstream/marked-18.0.5.LICENSE"],
 		]) {
 			const text = readFileSync(join(root, file), "utf8");
 			notices += `\n===== ${name}@${version} (${license}) =====\n${text}\n`;
diff --git a/scripts/prepare-distribution.test.mjs b/scripts/prepare-distribution.test.mjs
index 9f6bbe633..2533d9ca9 100644
--- a/scripts/prepare-distribution.test.mjs
+++ b/scripts/prepare-distribution.test.mjs
@@ -40,7 +40,7 @@ test("packed CLI links to online documentation and excludes the docs directory",
 			"AGENTS_release.md",
 			"docs/release/distribution-policy.json",
 			"legal/upstream/highlight-11.9.0.LICENSE",
-			"node_modules/marked/LICENSE",
+			"legal/upstream/marked-18.0.5.LICENSE",
 			"packages/coding-agent/npm-shrinkwrap.json",
 			"packages/coding-agent/install-lock/package.json",
 			"packages/coding-agent/install-lock/package-lock.json",

From f1b67deec972f4f2b75d0970c5f49c62f325da12 Mon Sep 17 00:00:00 2001
From: Jay Yu <yibai14651@gmail.com>
Date: Sun, 25 Oct 2026 11:10:32 -0400
Subject: [PATCH 2/5] chore(deps): update compatible stable dependencies and
 security fixes

---
 docs/dependency-maintenance.md                |   38 +
 package-lock.json                             | 1626 +++++++----------
 package.json                                  |    1 +
 packages/agent/package.json                   |   10 +-
 packages/ai/package.json                      |   10 +-
 packages/client/package.json                  |    2 +-
 packages/coding-agent-server/package.json     |    5 +-
 packages/coding-agent/docs/development.md     |   13 +-
 .../install-lock/package-lock.json            |  721 +++-----
 packages/coding-agent/npm-shrinkwrap.json     |  721 +++-----
 packages/coding-agent/package.json            |   18 +-
 packages/coding-agent/test/mermaid.test.ts    |   18 +-
 packages/evals/package.json                   |    4 +-
 packages/evolution/package.json               |    4 +-
 packages/harness-state/package.json           |    6 +-
 packages/harness-trace/package.json           |    2 +-
 packages/protocol/package.json                |    4 +-
 packages/server/package.json                  |    6 +-
 .../session-backends/sqlite-node/package.json |    4 +-
 packages/telemetry/package.json               |    2 +-
 packages/tui/package.json                     |    4 +-
 21 files changed, 1325 insertions(+), 1894 deletions(-)
 create mode 100644 docs/dependency-maintenance.md

diff --git a/docs/dependency-maintenance.md b/docs/dependency-maintenance.md
new file mode 100644
index 000000000..854541974
--- /dev/null
+++ b/docs/dependency-maintenance.md
@@ -0,0 +1,38 @@
+# Dependency maintenance
+
+Direct external dependencies are pinned to exact versions. Refresh the root lockfile with `npm install --package-lock-only --ignore-scripts`, hydrate with `npm install --ignore-scripts`, then regenerate the CLI distribution locks:
+
+```bash
+node scripts/generate-coding-agent-shrinkwrap.mjs
+node scripts/generate-coding-agent-install-lock.mjs
+npm run check
+./test.sh
+```
+
+Keep each dependency's pins synchronized across consuming workspaces and examples. Update live documentation examples when their dependency versions change; do not rewrite historical release records or notices for unchanged vendored files. The HTML exporter still vendors marked 18.0.5 and highlight.js 11.9.0; packaging reads their tracked licenses under `legal/upstream/`, independently of installed runtime versions.
+
+## Compatibility exceptions
+
+- Vitest and `@vitest/coverage-v8` use **4.1.12**, the patched 4.x release. The latest `vitest-evals` (**0.17.0**) requires `vitest >=4 <5`, so Vitest 5 is not compatible with the evaluation workspace.
+- `hosted-git-info` remains **9.0.3**. Version 10.1.1 requires Node `^22.22.2 || ^24.15.0 || >=26.0.0`, above the project's Node 22.19.0 minimum.
+- `@typescript/native-preview` has no stable release under that package name; do not replace its existing pin with another prerelease as part of a stable-only update.
+
+## Install tooling
+
+npm 10.9.3 can crash while resolving optional Vitest peers (`Cannot read properties of null (reading 'edgesOut')`). npm **11.21.1** supports the project's minimum Node version and can be invoked temporarily without changing the global installation:
+
+```bash
+npm exec --yes --ignore-scripts --package=npm@11.21.1 -- npm install --package-lock-only --ignore-scripts
+```
+
+If changed dependencies remain duplicated under workspaces, run `npm dedupe --package-lock-only --ignore-scripts` before regenerating distribution locks. The generators resolve dependencies from their originating workspace and relocate them to published `node_modules/` paths, preserving nested version differences and platform-specific optional dependencies. They reject unresolved or conflicting flattened dependencies. The root OpenTelemetry API pin also makes SDK optional peers available to the browser smoke check.
+
+The repository normally enforces a two-day minimum release age. Do not disable it without explicit approval. This update batch received approval to use `npm_config_min_release_age=0` on install commands only; `.npmrc` remains unchanged.
+
+## Networking review
+
+[Undici 8.12.3](https://github.com/nodejs/undici/releases/tag/v8.12.3) fixes HTTP/2 connection replacement following stream timeouts and preserves caller async context for queued pool requests. These can affect timeout recovery and request attribution; review networking tests when updating. It retains the Node 22.19.0 minimum.
+
+## Security review
+
+The initial audit reported seven affected packages, all present in the baseline lockfile. Updating Vitest/coverage to 4.1.12 and refreshing compatible Vite and source-map-js transitives removes five findings. The remaining sandbox-runtime/Zod dependency chain requires further review; do not force a Zod major-version override across consumers without checking their APIs.
diff --git a/package-lock.json b/package-lock.json
index 7a64ff3a2..21323f821 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -18,6 +18,7 @@
 			"devDependencies": {
 				"@anthropic-ai/sandbox-runtime": "0.0.26",
 				"@biomejs/biome": "2.3.5",
+				"@opentelemetry/api": "1.10.0",
 				"@types/node": "22.19.19",
 				"@typescript/native-preview": "7.0.0-dev.20260120.1",
 				"esbuild": "0.28.1",
@@ -71,106 +72,18 @@
 				}
 			}
 		},
-		"node_modules/@aws-crypto/crc32": {
-			"version": "5.2.0",
-			"resolved": "https://registry.npmjs.org/@aws-crypto/crc32/-/crc32-5.2.0.tgz",
-			"integrity": "sha512-nLbCWqQNgUiwwtFsen1AdzAtvuLRsQS8rYgMuxCrdKf9kOssamGLuPwyTY9wyYblNr9+1XM8v6zoDTPPSIeANg==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-crypto/util": "^5.2.0",
-				"@aws-sdk/types": "^3.222.0",
-				"tslib": "^2.6.2"
-			},
-			"engines": {
-				"node": ">=16.0.0"
-			}
-		},
-		"node_modules/@aws-crypto/sha256-browser": {
-			"version": "5.2.0",
-			"resolved": "https://registry.npmjs.org/@aws-crypto/sha256-browser/-/sha256-browser-5.2.0.tgz",
-			"integrity": "sha512-AXfN/lGotSQwu6HNcEsIASo7kWXZ5HYWvfOmSNKDsEqC4OashTp8alTmaz+F7TC2L083SFv5RdB+qU3Vs1kZqw==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-crypto/sha256-js": "^5.2.0",
-				"@aws-crypto/supports-web-crypto": "^5.2.0",
-				"@aws-crypto/util": "^5.2.0",
-				"@aws-sdk/types": "^3.222.0",
-				"@aws-sdk/util-locate-window": "^3.0.0",
-				"@smithy/util-utf8": "^2.0.0",
-				"tslib": "^2.6.2"
-			}
-		},
-		"node_modules/@aws-crypto/sha256-js": {
-			"version": "5.2.0",
-			"resolved": "https://registry.npmjs.org/@aws-crypto/sha256-js/-/sha256-js-5.2.0.tgz",
-			"integrity": "sha512-FFQQyu7edu4ufvIZ+OadFpHHOt+eSTBaYaki44c+akjg7qZg9oOQeLlk77F6tSYqjDAFClrHJk9tMf0HdVyOvA==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-crypto/util": "^5.2.0",
-				"@aws-sdk/types": "^3.222.0",
-				"tslib": "^2.6.2"
-			},
-			"engines": {
-				"node": ">=16.0.0"
-			}
-		},
-		"node_modules/@aws-crypto/supports-web-crypto": {
-			"version": "5.2.0",
-			"resolved": "https://registry.npmjs.org/@aws-crypto/supports-web-crypto/-/supports-web-crypto-5.2.0.tgz",
-			"integrity": "sha512-iAvUotm021kM33eCdNfwIN//F77/IADDSs58i+MDaOqFrVjZo9bAal0NK7HurRuWLLpF1iLX7gbWrjHjeo+YFg==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"tslib": "^2.6.2"
-			}
-		},
-		"node_modules/@aws-crypto/util": {
-			"version": "5.2.0",
-			"resolved": "https://registry.npmjs.org/@aws-crypto/util/-/util-5.2.0.tgz",
-			"integrity": "sha512-4RkU9EsI6ZpBve5fseQlGNUWKMa1RLPQ1dnjnQoe07ldfIzcsGb5hC5W0Dm7u423KWzawlrpbjXBrXCEv9zazQ==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-sdk/types": "^3.222.0",
-				"@smithy/util-utf8": "^2.0.0",
-				"tslib": "^2.6.2"
-			}
-		},
-		"node_modules/@aws-sdk/client-bedrock-runtime": {
-			"version": "3.1048.0",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/client-bedrock-runtime/-/client-bedrock-runtime-3.1048.0.tgz",
-			"integrity": "sha512-u+NT61JZEkRFtpL0CAw1N1dwxnaLgwVXQl/zjJxTGgLyS/jTIdg2SdoEoCTHxgDyCnqa1HEi9QOoE9/pYRNpOQ==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-crypto/sha256-browser": "5.2.0",
-				"@aws-crypto/sha256-js": "5.2.0",
-				"@aws-sdk/core": "^3.974.11",
-				"@aws-sdk/credential-provider-node": "^3.972.42",
-				"@aws-sdk/eventstream-handler-node": "^3.972.16",
-				"@aws-sdk/middleware-eventstream": "^3.972.12",
-				"@aws-sdk/middleware-websocket": "^3.972.19",
-				"@aws-sdk/token-providers": "3.1048.0",
-				"@aws-sdk/types": "^3.973.8",
-				"@smithy/core": "^3.24.2",
-				"@smithy/fetch-http-handler": "^5.4.2",
-				"@smithy/node-http-handler": "^4.7.2",
-				"@smithy/types": "^4.14.1",
-				"tslib": "^2.6.2"
-			},
-			"engines": {
-				"node": ">=20.0.0"
-			}
-		},
 		"node_modules/@aws-sdk/core": {
-			"version": "3.974.11",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/core/-/core-3.974.11.tgz",
-			"integrity": "sha512-QpnINq5FZH6EOaDEkmHdT7eUunbvD27pDNQypaWjFyYz7Zl1q3UCMQErBZxpmfGfI7MvI2TlK8KTkgNpv8b1ug==",
+			"version": "3.978.5",
+			"resolved": "https://registry.npmjs.org/@aws-sdk/core/-/core-3.978.5.tgz",
+			"integrity": "sha512-ruI0AWqcrfL20XDS6SwZIJFPOBZ6N0ADa9nLzWlBhxk1aoUjbUX3JkTR9vEmk7o35XpAHi68ahZ4T6RE2U9XyA==",
 			"license": "Apache-2.0",
 			"dependencies": {
-				"@aws-sdk/types": "^3.973.8",
-				"@aws-sdk/xml-builder": "^3.972.24",
-				"@aws/lambda-invoke-store": "^0.2.2",
-				"@smithy/core": "^3.24.2",
-				"@smithy/signature-v4": "^5.4.2",
-				"@smithy/types": "^4.14.1",
+				"@aws-sdk/types": "^3.975.0",
+				"@aws-sdk/xml-builder": "^3.972.41",
+				"@aws/lambda-invoke-store": "^0.3.0",
+				"@smithy/core": "^3.36.1",
+				"@smithy/signature-v4": "^5.7.4",
+				"@smithy/types": "^4.19.0",
 				"bowser": "^2.11.0",
 				"tslib": "^2.6.2"
 			},
@@ -178,217 +91,19 @@
 				"node": ">=20.0.0"
 			}
 		},
-		"node_modules/@aws-sdk/credential-provider-env": {
-			"version": "3.972.37",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-env/-/credential-provider-env-3.972.37.tgz",
-			"integrity": "sha512-/jpPvEh6f7ntmIzf7dNxoNX6Q8vt8UpesCjbW6mFfk4V1NW6bIy9qxcQ6WbA8As5yQhsZOe+xeNd4xHX8kdY2Q==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-sdk/core": "^3.974.11",
-				"@aws-sdk/types": "^3.973.8",
-				"@smithy/core": "^3.24.2",
-				"@smithy/types": "^4.14.1",
-				"tslib": "^2.6.2"
-			},
-			"engines": {
-				"node": ">=20.0.0"
-			}
-		},
-		"node_modules/@aws-sdk/credential-provider-http": {
-			"version": "3.972.39",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-http/-/credential-provider-http-3.972.39.tgz",
-			"integrity": "sha512-pIgTpisWyWg7X1bUbzSjuUYosYTD0Ghz2M0hkSTmb3a6i3qV3uU+NYJPI/E2XSC0HcsZh5rsLPzeXrkb2DS0Cg==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-sdk/core": "^3.974.11",
-				"@aws-sdk/types": "^3.973.8",
-				"@smithy/core": "^3.24.2",
-				"@smithy/fetch-http-handler": "^5.4.2",
-				"@smithy/node-http-handler": "^4.7.2",
-				"@smithy/types": "^4.14.1",
-				"tslib": "^2.6.2"
-			},
-			"engines": {
-				"node": ">=20.0.0"
-			}
-		},
-		"node_modules/@aws-sdk/credential-provider-ini": {
-			"version": "3.972.41",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-ini/-/credential-provider-ini-3.972.41.tgz",
-			"integrity": "sha512-u2tyjaxJJzW8UtW4SM1ZcPMDwO6y+kV+llvou+Adts0FAKyzes5jG4izQN+KX3yE8ZROpS5y1LJ//xL2iSf76w==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-sdk/core": "^3.974.11",
-				"@aws-sdk/credential-provider-env": "^3.972.37",
-				"@aws-sdk/credential-provider-http": "^3.972.39",
-				"@aws-sdk/credential-provider-login": "^3.972.41",
-				"@aws-sdk/credential-provider-process": "^3.972.37",
-				"@aws-sdk/credential-provider-sso": "^3.972.41",
-				"@aws-sdk/credential-provider-web-identity": "^3.972.41",
-				"@aws-sdk/nested-clients": "^3.997.9",
-				"@aws-sdk/types": "^3.973.8",
-				"@smithy/core": "^3.24.2",
-				"@smithy/credential-provider-imds": "^4.3.2",
-				"@smithy/types": "^4.14.1",
-				"tslib": "^2.6.2"
-			},
-			"engines": {
-				"node": ">=20.0.0"
-			}
-		},
-		"node_modules/@aws-sdk/credential-provider-login": {
-			"version": "3.972.41",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-login/-/credential-provider-login-3.972.41.tgz",
-			"integrity": "sha512-0LBitxXiAiaE5nlFPfpNIww/8FRY/I7WIndWsc9GmNFOM7cE1wNpVNQEGEk9Outg5l8xl+3vybxFyUy4l9q/LQ==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-sdk/core": "^3.974.11",
-				"@aws-sdk/nested-clients": "^3.997.9",
-				"@aws-sdk/types": "^3.973.8",
-				"@smithy/core": "^3.24.2",
-				"@smithy/types": "^4.14.1",
-				"tslib": "^2.6.2"
-			},
-			"engines": {
-				"node": ">=20.0.0"
-			}
-		},
-		"node_modules/@aws-sdk/credential-provider-node": {
-			"version": "3.972.42",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-node/-/credential-provider-node-3.972.42.tgz",
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+			}
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+			"resolved": "https://registry.npmjs.org/@aws-sdk/middleware-eventstream/-/middleware-eventstream-3.972.33.tgz",
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+			"license": "Apache-2.0",
+			"dependencies": {
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+				"@smithy/types": "^4.19.0",
+				"tslib": "^2.6.2"
+			},
+			"engines": {
+				"node": ">=20.0.0"
+			}
+		},
+		"packages/ai/node_modules/@aws-sdk/middleware-websocket": {
+			"version": "3.972.58",
+			"resolved": "https://registry.npmjs.org/@aws-sdk/middleware-websocket/-/middleware-websocket-3.972.58.tgz",
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+			"license": "Apache-2.0",
+			"dependencies": {
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+				"@aws-sdk/types": "^3.975.0",
+				"@smithy/core": "^3.36.1",
+				"@smithy/fetch-http-handler": "^5.8.0",
+				"@smithy/signature-v4": "^5.7.4",
+				"@smithy/types": "^4.19.0",
+				"tslib": "^2.6.2"
+			},
+			"engines": {
+				"node": ">= 14.0.0"
+			}
+		},
+		"packages/ai/node_modules/@smithy/credential-provider-imds": {
+			"version": "4.5.2",
+			"resolved": "https://registry.npmjs.org/@smithy/credential-provider-imds/-/credential-provider-imds-4.5.2.tgz",
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+			"license": "Apache-2.0",
+			"dependencies": {
+				"@smithy/core": "^3.33.2",
+				"@smithy/types": "^4.17.2",
+				"tslib": "^2.6.2"
+			},
+			"engines": {
+				"node": ">=18.0.0"
+			}
+		},
 		"packages/ai/node_modules/@types/node": {
 			"version": "24.12.4",
 			"resolved": "https://registry.npmjs.org/@types/node/-/node-24.12.4.tgz",
@@ -5592,7 +5262,7 @@
 			},
 			"devDependencies": {
 				"shx": "0.4.0",
-				"vitest": "4.1.9"
+				"vitest": "4.1.12"
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@@ -5615,17 +5285,17 @@
 				"cross-spawn": "7.0.6",
 				"diff": "8.0.4",
 				"glob": "13.0.6",
-				"grok-mermaid": "0.2.2",
+				"grok-mermaid": "0.2.3",
 				"highlight.js": "10.7.3",
 				"hosted-git-info": "9.0.3",
-				"ignore": "7.0.5",
+				"ignore": "7.0.14",
 				"jiti": "2.7.0",
-				"minimatch": "10.2.5",
+				"minimatch": "10.2.6",
 				"proper-lockfile": "4.1.2",
-				"semver": "7.8.0",
-				"typebox": "1.3.7",
-				"undici": "8.12.2",
-				"yaml": "2.9.0"
+				"semver": "7.8.5",
+				"typebox": "1.4.3",
+				"undici": "8.12.3",
+				"yaml": "2.9.1"
 			},
 			"bin": {
 				"diffex": "dist/cli.js"
@@ -5637,10 +5307,10 @@
 				"@types/ms": "2.1.0",
 				"@types/node": "24.12.4",
 				"@types/proper-lockfile": "4.1.4",
-				"@types/semver": "7.7.1",
+				"@types/semver": "7.8.0",
 				"shx": "0.4.0",
 				"typescript": "5.9.3",
-				"vitest": "4.1.9"
+				"vitest": "4.1.12"
 			},
 			"engines": {
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@@ -5663,9 +5333,10 @@
 			},
 			"devDependencies": {
 				"@diffexai/diffex-client": "^0.3.2",
+				"@types/ws": "8.18.2",
 				"shx": "0.4.0",
-				"vitest": "4.1.9",
-				"ws": "8.21.0"
+				"vitest": "4.1.12",
+				"ws": "8.22.0"
 			},
 			"engines": {
 				"node": ">=22.19.0"
@@ -5718,6 +5389,31 @@
 				"undici-types": "~7.16.0"
 			}
 		},
+		"packages/coding-agent/node_modules/@types/semver": {
+			"version": "7.8.0",
+			"resolved": "https://registry.npmjs.org/@types/semver/-/semver-7.8.0.tgz",
+			"integrity": "sha512-1mAINjtQCXXeLkJ9ehXkwOcBpqtLxiVtKhpUf83DdRNdQKV0iXZpaHYqRr7nj+wvxuJzoAmAwXI+sCNMv1CzLQ==",
+			"dev": true,
+			"license": "MIT"
+		},
+		"packages/coding-agent/node_modules/grok-mermaid": {
+			"version": "0.2.3",
+			"resolved": "https://registry.npmjs.org/grok-mermaid/-/grok-mermaid-0.2.3.tgz",
+			"integrity": "sha512-/4KopAbsjvuRP9MdPtlDjOHUmUVEohOX73JNcsWpzAtFxh+bq5+Dhb6gzvRieLDwIPQIR3/vy8V1NNTuz4Zsmg==",
+			"license": "Apache-2.0",
+			"engines": {
+				"node": ">=18"
+			}
+		},
+		"packages/coding-agent/node_modules/undici": {
+			"version": "8.12.3",
+			"resolved": "https://registry.npmjs.org/undici/-/undici-8.12.3.tgz",
+			"integrity": "sha512-+fdndUTwBP86cVjihTp21hZHo7d6oj1c/47XPA3lL8mM0XHs+C4EkcjmgRsFnFk2f/UONGDy9ItBItmXsLOQHw==",
+			"license": "MIT",
+			"engines": {
+				"node": ">=22.19.0"
+			}
+		},
 		"packages/coding-agent/node_modules/undici-types": {
 			"version": "7.16.0",
 			"resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.16.0.tgz",
@@ -5734,8 +5430,8 @@
 				"@types/node": "24.12.4",
 				"shx": "0.4.0",
 				"typescript": "5.9.3",
-				"vitest": "4.1.9",
-				"vitest-evals": "0.15.0"
+				"vitest": "4.1.12",
+				"vitest-evals": "0.17.0"
 			}
 		},
 		"packages/evals/node_modules/@types/node": {
@@ -5748,6 +5444,26 @@
 				"undici-types": "~7.16.0"
 			}
 		},
+		"packages/evals/node_modules/@vitest-evals/core": {
+			"version": "0.17.0",
+			"resolved": "https://registry.npmjs.org/@vitest-evals/core/-/core-0.17.0.tgz",
+			"integrity": "sha512-X1OBxLYWQnB+siIhI/BcDySMfpZ3AfeLiPRoZUi0iWMXeELwxxzOuzfsd2UZbJjeqyDbixRspdCfIzXYqzGxAw==",
+			"dev": true,
+			"license": "Apache-2.0",
+			"dependencies": {
+				"zod": ">=3 <5"
+			}
+		},
+		"packages/evals/node_modules/@vitest-evals/report-ui": {
+			"version": "0.17.0",
+			"resolved": "https://registry.npmjs.org/@vitest-evals/report-ui/-/report-ui-0.17.0.tgz",
+			"integrity": "sha512-7IWu7QoJpAomDsKO/RTKl8eichmJ9qQEmbQTJU5tao2gwQVzGvHx9bt79dB3b1MWuG7ZKMohv1h4FLGkZHUMqQ==",
+			"dev": true,
+			"license": "Apache-2.0",
+			"dependencies": {
+				"@vitest-evals/core": "0.17.0"
+			}
+		},
 		"packages/evals/node_modules/undici-types": {
 			"version": "7.16.0",
 			"resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.16.0.tgz",
@@ -5755,6 +5471,34 @@
 			"dev": true,
 			"license": "MIT"
 		},
+		"packages/evals/node_modules/vitest-evals": {
+			"version": "0.17.0",
+			"resolved": "https://registry.npmjs.org/vitest-evals/-/vitest-evals-0.17.0.tgz",
+			"integrity": "sha512-GCQEveS5tVhCNBjAW77usjeWxPi+TqI+wJEfF0BqpD6bq5Qw/9JhAmnbrnzbOvIn8MWzUA0Wc1aonCgWxRKawg==",
+			"dev": true,
+			"license": "Apache-2.0",
+			"dependencies": {
+				"@vitest-evals/core": "0.17.0",
+				"@vitest-evals/report-ui": "0.17.0"
+			},
+			"bin": {
+				"vitest-evals": "bin/vitest-evals.js"
+			},
+			"peerDependencies": {
+				"ai": ">=4 <7",
+				"tinyrainbow": ">=2 <4",
+				"vitest": ">=4 <5",
+				"zod": ">=3 <5"
+			},
+			"peerDependenciesMeta": {
+				"ai": {
+					"optional": true
+				},
+				"zod": {
+					"optional": true
+				}
+			}
+		},
 		"packages/evolution": {
 			"name": "@diffexai/diffex-evolution",
 			"version": "0.3.2",
@@ -5768,8 +5512,8 @@
 				"@types/node": "24.12.4",
 				"@types/proper-lockfile": "4.1.4",
 				"shx": "0.4.0",
-				"typebox": "1.3.7",
-				"vitest": "4.1.9"
+				"typebox": "1.4.3",
+				"vitest": "4.1.12"
 			},
 			"engines": {
 				"node": ">=22.19.0"
@@ -5798,13 +5542,13 @@
 			"license": "Apache-2.0",
 			"dependencies": {
 				"proper-lockfile": "4.1.2",
-				"typebox": "1.3.7",
-				"yaml": "2.9.0"
+				"typebox": "1.4.3",
+				"yaml": "2.9.1"
 			},
 			"devDependencies": {
 				"@types/proper-lockfile": "4.1.4",
 				"shx": "0.4.0",
-				"vitest": "4.1.9"
+				"vitest": "4.1.12"
 			},
 			"engines": {
 				"node": ">=22.19.0"
@@ -5820,7 +5564,7 @@
 			"devDependencies": {
 				"@types/node": "24.12.4",
 				"shx": "0.4.0",
-				"vitest": "4.1.9"
+				"vitest": "4.1.12"
 			},
 			"engines": {
 				"node": ">=22.19.0"
@@ -5848,11 +5592,11 @@
 			"version": "0.3.2",
 			"license": "Apache-2.0",
 			"dependencies": {
-				"typebox": "1.3.7"
+				"typebox": "1.4.3"
 			},
 			"devDependencies": {
 				"shx": "0.4.0",
-				"vitest": "4.1.9"
+				"vitest": "4.1.12"
 			},
 			"engines": {
 				"node": ">=22.19.0"
@@ -5865,12 +5609,12 @@
 			"dependencies": {
 				"@diffexai/diffex-ai": "^0.3.2",
 				"@diffexai/diffex-protocol": "^0.3.2",
-				"ws": "8.21.0"
+				"ws": "8.22.0"
 			},
 			"devDependencies": {
-				"@types/ws": "8.18.1",
+				"@types/ws": "8.18.2",
 				"shx": "0.4.0",
-				"vitest": "4.1.9"
+				"vitest": "4.1.12"
 			},
 			"engines": {
 				"node": ">=22.19.0"
@@ -5885,8 +5629,8 @@
 				"@diffexai/diffex-ai": "^0.3.2"
 			},
 			"devDependencies": {
-				"@vitest/coverage-v8": "4.1.9",
-				"vitest": "4.1.9"
+				"@vitest/coverage-v8": "4.1.12",
+				"vitest": "4.1.12"
 			},
 			"engines": {
 				"node": ">=22.19.0"
@@ -5898,7 +5642,7 @@
 			"license": "Apache-2.0",
 			"devDependencies": {
 				"@types/node": "24.12.4",
-				"vitest": "4.1.9"
+				"vitest": "4.1.12"
 			},
 			"engines": {
 				"node": ">=22.19.0"
@@ -5926,8 +5670,8 @@
 			"version": "0.3.2",
 			"license": "Apache-2.0",
 			"dependencies": {
-				"get-east-asian-width": "1.6.0",
-				"marked": "18.0.5"
+				"get-east-asian-width": "1.7.0",
+				"marked": "18.1.1"
 			},
 			"devDependencies": {
 				"@xterm/headless": "5.5.0",
@@ -5936,6 +5680,30 @@
 			"engines": {
 				"node": ">=22.19.0"
 			}
+		},
+		"packages/tui/node_modules/get-east-asian-width": {
+			"version": "1.7.0",
+			"resolved": "https://registry.npmjs.org/get-east-asian-width/-/get-east-asian-width-1.7.0.tgz",
+			"integrity": "sha512-XjH1AECxf0giL2V1aU8vKyRR2ppRUb5c0EvT7zuJTokQ74bNo52zOtghqdWIqrhUD79fo3x0WfKZdOqxF6LG1Q==",
+			"license": "MIT",
+			"engines": {
+				"node": ">=18"
+			},
+			"funding": {
+				"url": "https://github.com/sponsors/sindresorhus"
+			}
+		},
+		"packages/tui/node_modules/marked": {
+			"version": "18.1.1",
+			"resolved": "https://registry.npmjs.org/marked/-/marked-18.1.1.tgz",
+			"integrity": "sha512-zEGgrtUG8crk+TrMacJSVABU4DYDDkS8uqgU3ohrn/2fW9C2AEfUrO3m6IhpIpQpl7YcVpiXXC9cSMWDANT3dg==",
+			"license": "MIT",
+			"bin": {
+				"marked": "bin/marked.js"
+			},
+			"engines": {
+				"node": ">= 20"
+			}
 		}
 	}
 }
diff --git a/package.json b/package.json
index 70956bcd2..effa86ead 100644
--- a/package.json
+++ b/package.json
@@ -53,6 +53,7 @@
 	"devDependencies": {
 		"@anthropic-ai/sandbox-runtime": "0.0.26",
 		"@biomejs/biome": "2.3.5",
+		"@opentelemetry/api": "1.10.0",
 		"@types/node": "22.19.19",
 		"@typescript/native-preview": "7.0.0-dev.20260120.1",
 		"esbuild": "0.28.1",
diff --git a/packages/agent/package.json b/packages/agent/package.json
index b01023c35..0e0c41da3 100644
--- a/packages/agent/package.json
+++ b/packages/agent/package.json
@@ -44,9 +44,9 @@
 		"@diffexai/diffex-ai": "^0.3.2",
 		"@diffexai/diffex-telemetry": "^0.3.2",
 		"diff": "8.0.4",
-		"ignore": "7.0.5",
-		"typebox": "1.3.7",
-		"yaml": "2.9.0"
+		"ignore": "7.0.14",
+		"typebox": "1.4.3",
+		"yaml": "2.9.1"
 	},
 	"keywords": [
 		"ai",
@@ -67,9 +67,9 @@
 	},
 	"devDependencies": {
 		"@types/node": "24.12.4",
-		"@vitest/coverage-v8": "4.1.9",
+		"@vitest/coverage-v8": "4.1.12",
 		"typescript": "5.9.3",
-		"vitest": "4.1.9"
+		"vitest": "4.1.12"
 	},
 	"private": true
 }
diff --git a/packages/ai/package.json b/packages/ai/package.json
index 824b02078..f7712e217 100644
--- a/packages/ai/package.json
+++ b/packages/ai/package.json
@@ -67,17 +67,17 @@
 	},
 	"dependencies": {
 		"@anthropic-ai/sdk": "0.91.1",
-		"@aws-sdk/client-bedrock-runtime": "3.1048.0",
+		"@aws-sdk/client-bedrock-runtime": "3.1156.0",
 		"@diffexai/diffex-telemetry": "^0.3.2",
 		"@google/genai": "1.52.0",
 		"@mistralai/mistralai": "2.2.6",
-		"@opentelemetry/api": "1.9.0",
-		"@smithy/node-http-handler": "4.7.3",
+		"@opentelemetry/api": "1.10.0",
+		"@smithy/node-http-handler": "4.12.1",
 		"http-proxy-agent": "7.0.2",
 		"https-proxy-agent": "7.0.6",
 		"openai": "6.26.0",
 		"partial-json": "0.1.7",
-		"typebox": "1.3.7"
+		"typebox": "1.4.3"
 	},
 	"keywords": [
 		"ai",
@@ -102,7 +102,7 @@
 	"devDependencies": {
 		"@types/node": "24.12.4",
 		"canvas": "3.2.3",
-		"vitest": "4.1.9"
+		"vitest": "4.1.12"
 	},
 	"private": true
 }
diff --git a/packages/client/package.json b/packages/client/package.json
index 204ff74e5..ef75f0ad7 100644
--- a/packages/client/package.json
+++ b/packages/client/package.json
@@ -65,7 +65,7 @@
 	},
 	"devDependencies": {
 		"shx": "0.4.0",
-		"vitest": "4.1.9"
+		"vitest": "4.1.12"
 	},
 	"private": true
 }
diff --git a/packages/coding-agent-server/package.json b/packages/coding-agent-server/package.json
index bcb880ea7..336a54dc8 100644
--- a/packages/coding-agent-server/package.json
+++ b/packages/coding-agent-server/package.json
@@ -47,9 +47,10 @@
 	},
 	"devDependencies": {
 		"@diffexai/diffex-client": "^0.3.2",
+		"@types/ws": "8.18.2",
 		"shx": "0.4.0",
-		"vitest": "4.1.9",
-		"ws": "8.21.0"
+		"vitest": "4.1.12",
+		"ws": "8.22.0"
 	},
 	"private": true
 }
diff --git a/packages/coding-agent/docs/development.md b/packages/coding-agent/docs/development.md
index 233d3dddf..c37db56a6 100644
--- a/packages/coding-agent/docs/development.md
+++ b/packages/coding-agent/docs/development.md
@@ -7,7 +7,7 @@ See [AGENTS.md](https://github.com/diffexai/diffex/blob/main/AGENTS.md) for addi
 ```bash
 git clone https://github.com/diffexai/diffex
 cd diffex
-npm install
+npm install --ignore-scripts
 npm run build
 ```
 
@@ -55,11 +55,16 @@ Never use `__dirname` directly for package assets.
 ## Testing
 
 ```bash
-./test.sh                         # Run non-LLM tests (no API keys needed)
-npm test                          # Run all tests
-npm test -- test/specific.test.ts # Run specific test
+./test.sh # Run non-E2E tests with credentials isolated
+
+# From the relevant package directory:
+node ../../node_modules/vitest/dist/cli.js --run test/specific.test.ts
 ```
 
+Do not run the full Vitest suite directly: endpoint or authentication environment variables can activate provider E2E tests.
+
+See [dependency maintenance](../../../docs/dependency-maintenance.md) for dependency update constraints and validation.
+
 ## Project Structure
 
 ```
diff --git a/packages/coding-agent/install-lock/package-lock.json b/packages/coding-agent/install-lock/package-lock.json
index 01f3eec84..5dace40c9 100644
--- a/packages/coding-agent/install-lock/package-lock.json
+++ b/packages/coding-agent/install-lock/package-lock.json
@@ -34,324 +34,288 @@
 				"anthropic-ai-sdk": "bin/cli"
 			}
 		},
-		"node_modules/@aws-crypto/crc32": {
-			"version": "5.2.0",
-			"resolved": "https://registry.npmjs.org/@aws-crypto/crc32/-/crc32-5.2.0.tgz",
-			"integrity": "sha512-nLbCWqQNgUiwwtFsen1AdzAtvuLRsQS8rYgMuxCrdKf9kOssamGLuPwyTY9wyYblNr9+1XM8v6zoDTPPSIeANg==",
+		"node_modules/@aws-sdk/client-bedrock-runtime": {
+			"version": "3.1156.0",
+			"resolved": "https://registry.npmjs.org/@aws-sdk/client-bedrock-runtime/-/client-bedrock-runtime-3.1156.0.tgz",
+			"integrity": "sha512-YtYsel8aoGP0K//ZO4qqgab6W/wYKHL+8MiWE4Z2SKKWz7MbVWMfUKKySdAle5RcE1yTviRF2RMlXE5MVPW/mA==",
 			"license": "Apache-2.0",
 			"dependencies": {
-				"@aws-crypto/util": "^5.2.0",
-				"@aws-sdk/types": "^3.222.0",
+				"@aws-sdk/core": "^3.978.5",
+				"@aws-sdk/credential-provider-node": "^3.972.88",
+				"@aws-sdk/eventstream-handler-node": "^3.972.38",
+				"@aws-sdk/middleware-eventstream": "^3.972.33",
+				"@aws-sdk/middleware-websocket": "^3.972.58",
+				"@aws-sdk/token-providers": "3.1156.0",
+				"@aws-sdk/types": "^3.975.0",
+				"@smithy/core": "^3.36.1",
+				"@smithy/fetch-http-handler": "^5.8.0",
+				"@smithy/node-http-handler": "^4.12.1",
+				"@smithy/types": "^4.19.0",
 				"tslib": "^2.6.2"
 			},
 			"engines": {
-				"node": ">=16.0.0"
-			}
-		},
-		"node_modules/@aws-crypto/sha256-browser": {
-			"version": "5.2.0",
-			"resolved": "https://registry.npmjs.org/@aws-crypto/sha256-browser/-/sha256-browser-5.2.0.tgz",
-			"integrity": "sha512-AXfN/lGotSQwu6HNcEsIASo7kWXZ5HYWvfOmSNKDsEqC4OashTp8alTmaz+F7TC2L083SFv5RdB+qU3Vs1kZqw==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-crypto/sha256-js": "^5.2.0",
-				"@aws-crypto/supports-web-crypto": "^5.2.0",
-				"@aws-crypto/util": "^5.2.0",
-				"@aws-sdk/types": "^3.222.0",
-				"@aws-sdk/util-locate-window": "^3.0.0",
-				"@smithy/util-utf8": "^2.0.0",
-				"tslib": "^2.6.2"
+				"node": ">=20.0.0"
 			}
 		},
-		"node_modules/@aws-crypto/sha256-js": {
-			"version": "5.2.0",
-			"resolved": "https://registry.npmjs.org/@aws-crypto/sha256-js/-/sha256-js-5.2.0.tgz",
-			"integrity": "sha512-FFQQyu7edu4ufvIZ+OadFpHHOt+eSTBaYaki44c+akjg7qZg9oOQeLlk77F6tSYqjDAFClrHJk9tMf0HdVyOvA==",
+		"node_modules/@aws-sdk/client-bedrock-runtime/node_modules/@aws-sdk/credential-provider-node": {
+			"version": "3.972.88",
+			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-node/-/credential-provider-node-3.972.88.tgz",
+			"integrity": "sha512-AG0KID5qhQPzrFkh5b0Cws1Amytvzo0L0Xj6hMgJXEwD6ZXAqninDhSNAWJiN5zU4YVVZnuidnqwPwYJ04IamA==",
 			"license": "Apache-2.0",
 			"dependencies": {
-				"@aws-crypto/util": "^5.2.0",
-				"@aws-sdk/types": "^3.222.0",
+				"@aws-sdk/credential-provider-env": "^3.972.76",
+				"@aws-sdk/credential-provider-http": "^3.972.78",
+				"@aws-sdk/credential-provider-ini": "^3.973.21",
+				"@aws-sdk/credential-provider-process": "^3.972.76",
+				"@aws-sdk/credential-provider-sso": "^3.973.20",
+				"@aws-sdk/credential-provider-web-identity": "^3.972.82",
+				"@aws-sdk/types": "^3.975.0",
+				"@smithy/core": "^3.36.1",
+				"@smithy/credential-provider-imds": "^4.5.2",
+				"@smithy/types": "^4.19.0",
 				"tslib": "^2.6.2"
 			},
 			"engines": {
-				"node": ">=16.0.0"
-			}
-		},
-		"node_modules/@aws-crypto/supports-web-crypto": {
-			"version": "5.2.0",
-			"resolved": "https://registry.npmjs.org/@aws-crypto/supports-web-crypto/-/supports-web-crypto-5.2.0.tgz",
-			"integrity": "sha512-iAvUotm021kM33eCdNfwIN//F77/IADDSs58i+MDaOqFrVjZo9bAal0NK7HurRuWLLpF1iLX7gbWrjHjeo+YFg==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"tslib": "^2.6.2"
-			}
-		},
-		"node_modules/@aws-crypto/util": {
-			"version": "5.2.0",
-			"resolved": "https://registry.npmjs.org/@aws-crypto/util/-/util-5.2.0.tgz",
-			"integrity": "sha512-4RkU9EsI6ZpBve5fseQlGNUWKMa1RLPQ1dnjnQoe07ldfIzcsGb5hC5W0Dm7u423KWzawlrpbjXBrXCEv9zazQ==",
-			"license": "Apache-2.0",
-			"dependencies": {
-				"@aws-sdk/types": "^3.222.0",
-				"@smithy/util-utf8": "^2.0.0",
-				"tslib": "^2.6.2"
+				"node": ">=20.0.0"
 			}
 		},
-		"node_modules/@aws-sdk/client-bedrock-runtime": {
-			"version": "3.1048.0",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/client-bedrock-runtime/-/client-bedrock-runtime-3.1048.0.tgz",
-			"integrity": "sha512-u+NT61JZEkRFtpL0CAw1N1dwxnaLgwVXQl/zjJxTGgLyS/jTIdg2SdoEoCTHxgDyCnqa1HEi9QOoE9/pYRNpOQ==",
+		"node_modules/@aws-sdk/client-bedrock-runtime/node_modules/@aws-sdk/credential-provider-node/node_modules/@aws-sdk/credential-provider-env": {
+			"version": "3.972.76",
+			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-env/-/credential-provider-env-3.972.76.tgz",
+			"integrity": "sha512-YxmL1Ar7bV9ZkJvtv+lj+MF6le76NnZnbmgySyZuxpZaCv0/1lZ3KxKy6RIj1h9ui2hWnVjZxbmTMeO0y/NrQA==",
 			"license": "Apache-2.0",
 			"dependencies": {
-				"@aws-crypto/sha256-browser": "5.2.0",
-				"@aws-crypto/sha256-js": "5.2.0",
-				"@aws-sdk/core": "^3.974.11",
-				"@aws-sdk/credential-provider-node": "^3.972.42",
-				"@aws-sdk/eventstream-handler-node": "^3.972.16",
-				"@aws-sdk/middleware-eventstream": "^3.972.12",
-				"@aws-sdk/middleware-websocket": "^3.972.19",
-				"@aws-sdk/token-providers": "3.1048.0",
-				"@aws-sdk/types": "^3.973.8",
-				"@smithy/core": "^3.24.2",
-				"@smithy/fetch-http-handler": "^5.4.2",
-				"@smithy/node-http-handler": "^4.7.2",
-				"@smithy/types": "^4.14.1",
+				"@aws-sdk/core": "^3.978.5",
+				"@aws-sdk/types": "^3.975.0",
+				"@smithy/core": "^3.36.1",
+				"@smithy/types": "^4.19.0",
 				"tslib": "^2.6.2"
 			},
 			"engines": {
 				"node": ">=20.0.0"
 			}
 		},
-		"node_modules/@aws-sdk/core": {
-			"version": "3.974.11",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/core/-/core-3.974.11.tgz",
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+		"node_modules/@aws-sdk/client-bedrock-runtime/node_modules/@aws-sdk/credential-provider-node/node_modules/@aws-sdk/credential-provider-http": {
+			"version": "3.972.78",
+			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-http/-/credential-provider-http-3.972.78.tgz",
+			"integrity": "sha512-3VHknDRngoebsaqyT1iR75b5cBT2zfEtODK6yYmYltljkK1HEAQLs2FEd1IpWqAeOYdMGaG9wikngWLTufY7RA==",
 			"license": "Apache-2.0",
 			"dependencies": {
-				"@aws-sdk/types": "^3.973.8",
-				"@aws-sdk/xml-builder": "^3.972.24",
-				"@aws/lambda-invoke-store": "^0.2.2",
-				"@smithy/core": "^3.24.2",
-				"@smithy/signature-v4": "^5.4.2",
-				"@smithy/types": "^4.14.1",
-				"bowser": "^2.11.0",
+				"@aws-sdk/core": "^3.978.5",
+				"@aws-sdk/types": "^3.975.0",
+				"@smithy/core": "^3.36.1",
+				"@smithy/fetch-http-handler": "^5.8.0",
+				"@smithy/node-http-handler": "^4.12.1",
+				"@smithy/types": "^4.19.0",
 				"tslib": "^2.6.2"
 			},
 			"engines": {
 				"node": ">=20.0.0"
 			}
 		},
-		"node_modules/@aws-sdk/credential-provider-env": {
-			"version": "3.972.37",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-env/-/credential-provider-env-3.972.37.tgz",
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+		"node_modules/@aws-sdk/client-bedrock-runtime/node_modules/@aws-sdk/credential-provider-node/node_modules/@aws-sdk/credential-provider-ini": {
+			"version": "3.973.21",
+			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-ini/-/credential-provider-ini-3.973.21.tgz",
+			"integrity": "sha512-aLx9hbCX6mGAyv4ZZd8UagJ4RASHVJw6BFDSIyuKmLkqNL6H47EjBPK6qaJ4B5TDV6mc+vMa0SJFYyo4mkvVQg==",
 			"license": "Apache-2.0",
 			"dependencies": {
-				"@aws-sdk/core": "^3.974.11",
-				"@aws-sdk/types": "^3.973.8",
-				"@smithy/core": "^3.24.2",
-				"@smithy/types": "^4.14.1",
+				"@aws-sdk/core": "^3.978.5",
+				"@aws-sdk/credential-provider-env": "^3.972.76",
+				"@aws-sdk/credential-provider-http": "^3.972.78",
+				"@aws-sdk/credential-provider-login": "^3.972.83",
+				"@aws-sdk/credential-provider-process": "^3.972.76",
+				"@aws-sdk/credential-provider-sso": "^3.973.20",
+				"@aws-sdk/credential-provider-web-identity": "^3.972.82",
+				"@aws-sdk/nested-clients": "^3.997.50",
+				"@aws-sdk/types": "^3.975.0",
+				"@smithy/core": "^3.36.1",
+				"@smithy/credential-provider-imds": "^4.5.2",
+				"@smithy/types": "^4.19.0",
 				"tslib": "^2.6.2"
 			},
 			"engines": {
 				"node": ">=20.0.0"
 			}
 		},
-		"node_modules/@aws-sdk/credential-provider-http": {
-			"version": "3.972.39",
-			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-http/-/credential-provider-http-3.972.39.tgz",
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+		"node_modules/@aws-sdk/client-bedrock-runtime/node_modules/@aws-sdk/credential-provider-node/node_modules/@aws-sdk/credential-provider-ini/node_modules/@aws-sdk/credential-provider-login": {
+			"version": "3.972.83",
+			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-login/-/credential-provider-login-3.972.83.tgz",
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-				"@smithy/fetch-http-handler": "^5.4.2",
-				"@smithy/node-http-handler": "^4.7.2",
-				"@smithy/types": "^4.14.1",
+				"@aws-sdk/core": "^3.978.5",
+				"@aws-sdk/nested-clients": "^3.997.50",
+				"@aws-sdk/types": "^3.975.0",
+				"@smithy/core": "^3.36.1",
+				"@smithy/types": "^4.19.0",
 				"tslib": "^2.6.2"
 			},
 			"engines": {
 				"node": ">=20.0.0"
 			}
 		},
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+		"node_modules/@aws-sdk/client-bedrock-runtime/node_modules/@aws-sdk/credential-provider-node/node_modules/@aws-sdk/credential-provider-process": {
+			"version": "3.972.76",
+			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-process/-/credential-provider-process-3.972.76.tgz",
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 			"license": "Apache-2.0",
 			"dependencies": {
-				"@aws-sdk/core": "^3.974.11",
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-				"@aws-sdk/credential-provider-http": "^3.972.39",
-				"@aws-sdk/credential-provider-login": "^3.972.41",
-				"@aws-sdk/credential-provider-process": "^3.972.37",
-				"@aws-sdk/credential-provider-sso": "^3.972.41",
-				"@aws-sdk/credential-provider-web-identity": "^3.972.41",
-				"@aws-sdk/nested-clients": "^3.997.9",
-				"@aws-sdk/types": "^3.973.8",
-				"@smithy/core": "^3.24.2",
-				"@smithy/credential-provider-imds": "^4.3.2",
-				"@smithy/types": "^4.14.1",
+				"@aws-sdk/core": "^3.978.5",
+				"@aws-sdk/types": "^3.975.0",
+				"@smithy/core": "^3.36.1",
+				"@smithy/types": "^4.19.0",
 				"tslib": "^2.6.2"
 			},
 			"engines": {
 				"node": ">=20.0.0"
 			}
 		},
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-			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-login/-/credential-provider-login-3.972.41.tgz",
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+		"node_modules/@aws-sdk/client-bedrock-runtime/node_modules/@aws-sdk/credential-provider-node/node_modules/@aws-sdk/credential-provider-sso": {
+			"version": "3.973.20",
+			"resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-sso/-/credential-provider-sso-3.973.20.tgz",
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 			"license": "Apache-2.0",
 			"dependencies": {
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-				"@aws-sdk/types": "^3.973.8",
-				"@smithy/core": "^3.24.2",
-				"@smithy/types": "^4.14.1",
+				"@aws-sdk/core": "^3.978.5",
+				"@aws-sdk/nested-clients": "^3.997.50",
+				"@aws-sdk/token-providers": "3.1155.0",
+				"@aws-sdk/types": "^3.975.0",
+				"@smithy/core": "^3.36.1",
+				"@smithy/types": "^4.19.0",
 				"tslib": "^2.6.2"
 			},
 			"engines": {
 				"node": ">=20.0.0"
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-					"type": "github",
-					"url": "https://github.com/sponsors/NaturalIntelligence"
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-		},
 		"node_modules/ts-algebra": {
 			"version": "2.0.0",
 			"resolved": "https://registry.npmjs.org/ts-algebra/-/ts-algebra-2.0.0.tgz",
@@ -1906,15 +1726,15 @@
 			"license": "0BSD"
 		},
 		"node_modules/typebox": {
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+			"version": "1.4.3",
+			"resolved": "https://registry.npmjs.org/typebox/-/typebox-1.4.3.tgz",
+			"integrity": "sha512-u3nyf7ZciAv1GOijVpI0TDt9At5wmEi7lSHSlRrnjuThv1DcB7fgGBqqrz+fGZ54jAfTpOOX0JXwxSIg3pnxQA==",
 			"license": "MIT"
 		},
 		"node_modules/undici": {
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-			"resolved": "https://registry.npmjs.org/undici/-/undici-8.12.2.tgz",
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+			"version": "8.12.3",
+			"resolved": "https://registry.npmjs.org/undici/-/undici-8.12.3.tgz",
+			"integrity": "sha512-+fdndUTwBP86cVjihTp21hZHo7d6oj1c/47XPA3lL8mM0XHs+C4EkcjmgRsFnFk2f/UONGDy9ItBItmXsLOQHw==",
 			"license": "MIT",
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@@ -1951,9 +1771,9 @@
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+			"version": "8.22.0",
+			"resolved": "https://registry.npmjs.org/ws/-/ws-8.22.0.tgz",
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@@ -1971,25 +1791,10 @@
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-			"license": "MIT",
-			"engines": {
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-			"funding": [
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-					"type": "github",
-					"url": "https://github.com/sponsors/NaturalIntelligence"
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 		"node_modules/yaml": {
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+			"version": "2.9.1",
+			"resolved": "https://registry.npmjs.org/yaml/-/yaml-2.9.1.tgz",
+			"integrity": "sha512-3NxN8+78OdzbT7C/WjGsyfPAtJaN3FNDsWxv7Y7mcDsT/oOmgW8BpyQQFFBnvZE3j9Y2Sdz1ULFLezL7Eb2yFw==",
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diff --git a/packages/coding-agent/npm-shrinkwrap.json b/packages/coding-agent/npm-shrinkwrap.json
index 5385929c0..038405a6a 100644
--- a/packages/coding-agent/npm-shrinkwrap.json
+++ b/packages/coding-agent/npm-shrinkwrap.json
@@ -10,34 +10,34 @@
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 			"dependencies": {
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-				"@aws-sdk/client-bedrock-runtime": "3.1048.0",
+				"@aws-sdk/client-bedrock-runtime": "3.1156.0",
 				"@google/genai": "1.52.0",
 				"@mistralai/mistralai": "2.2.6",
 				"@napi-rs/keyring": "1.3.0",
-				"@opentelemetry/api": "1.9.0",
+				"@opentelemetry/api": "1.10.0",
 				"@silvia-odwyer/photon-node": "0.3.4",
-				"@smithy/node-http-handler": "4.7.3",
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 				"chalk": "5.6.2",
 				"cross-spawn": "7.0.6",
 				"diff": "8.0.4",
-				"get-east-asian-width": "1.6.0",
+				"get-east-asian-width": "1.7.0",
 				"glob": "13.0.6",
-				"grok-mermaid": "0.2.2",
+				"grok-mermaid": "0.2.3",
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 				"hosted-git-info": "9.0.3",
 				"http-proxy-agent": "7.0.2",
 				"https-proxy-agent": "7.0.6",
-				"ignore": "7.0.5",
+				"ignore": "7.0.14",
 				"jiti": "2.7.0",
-				"marked": "18.0.5",
-				"minimatch": "10.2.5",
+				"marked": "18.1.1",
+				"minimatch": "10.2.6",
 				"openai": "6.26.0",
 				"partial-json": "0.1.7",
 				"proper-lockfile": "4.1.2",
-				"semver": "7.8.0",
-				"typebox": "1.3.7",
-				"undici": "8.12.2",
-				"yaml": "2.9.0"
+				"semver": "7.8.5",
+				"typebox": "1.4.3",
+				"undici": "8.12.3",
+				"yaml": "2.9.1"
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@@ -69,324 +69,288 @@
 				"anthropic-ai-sdk": "bin/cli"
 			}
 		},
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 			"license": "Apache-2.0",
 			"dependencies": {
-				"@aws-crypto/util": "^5.2.0",
-				"@aws-sdk/types": "^3.222.0",
+				"@aws-sdk/core": "^3.978.5",
+				"@aws-sdk/credential-provider-node": "^3.972.88",
+				"@aws-sdk/eventstream-handler-node": "^3.972.38",
+				"@aws-sdk/middleware-eventstream": "^3.972.33",
+				"@aws-sdk/middleware-websocket": "^3.972.58",
+				"@aws-sdk/token-providers": "3.1156.0",
+				"@aws-sdk/types": "^3.975.0",
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+		"node_modules/@aws-sdk/client-bedrock-runtime/node_modules/@aws-sdk/credential-provider-node/node_modules/@aws-sdk/credential-provider-env": {
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+		"node_modules/@aws-sdk/client-bedrock-runtime/node_modules/@aws-sdk/credential-provider-node/node_modules/@aws-sdk/credential-provider-http": {
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-			"resolved": "https://registry.npmjs.org/semver/-/semver-7.8.0.tgz",
-			"integrity": "sha512-AcM7dV/5ul4EekoQ29Agm5vri8JNqRyj39o0qpX6vDF2GZrtutZl5RwgD1XnZjiTAfncsJhMI48QQH3sN87YNA==",
+			"version": "7.8.5",
+			"resolved": "https://registry.npmjs.org/semver/-/semver-7.8.5.tgz",
+			"integrity": "sha512-Y7/KDsb8LjooZpwaqGyulO6DQlksgCncchHGk+sZIY4SBvUocMBEFH5Ur1fI4dV+Jvl0w6cjvucaIi40puRioA==",
 			"license": "ISC",
 			"bin": {
 				"semver": "bin/semver.js"
@@ -1871,18 +1703,6 @@
 			"integrity": "sha512-wnD2ZE+l+SPC/uoS0vXeE9L1+0wuaMqKlfz9AMUo38JsyLSBWSFcHR1Rri62LZc12vLr1gb3jl7iwQhgwpAbGQ==",
 			"license": "ISC"
 		},
-		"node_modules/strnum": {
-			"version": "2.3.0",
-			"resolved": "https://registry.npmjs.org/strnum/-/strnum-2.3.0.tgz",
-			"integrity": "sha512-ums3KNd42PGyx5xaoVTO1mjU1bH3NpY4vsrVlnv9PNGqQj8wd7rJ6nEypLrJ7z5vxK5RP0yMLo6J/Gsm62DI5Q==",
-			"license": "MIT",
-			"funding": [
-				{
-					"type": "github",
-					"url": "https://github.com/sponsors/NaturalIntelligence"
-				}
-			]
-		},
 		"node_modules/ts-algebra": {
 			"version": "2.0.0",
 			"resolved": "https://registry.npmjs.org/ts-algebra/-/ts-algebra-2.0.0.tgz",
@@ -1896,15 +1716,15 @@
 			"license": "0BSD"
 		},
 		"node_modules/typebox": {
-			"version": "1.3.7",
-			"resolved": "https://registry.npmjs.org/typebox/-/typebox-1.3.7.tgz",
-			"integrity": "sha512-meKuifc33Pccx0O6PdIzYMq3Og8zvP4TIi/a+Bw3AEMZMxOD0+RHGQvpglEe6Zdy3wZ8nqn/j95h8LUZLk/6Hg==",
+			"version": "1.4.3",
+			"resolved": "https://registry.npmjs.org/typebox/-/typebox-1.4.3.tgz",
+			"integrity": "sha512-u3nyf7ZciAv1GOijVpI0TDt9At5wmEi7lSHSlRrnjuThv1DcB7fgGBqqrz+fGZ54jAfTpOOX0JXwxSIg3pnxQA==",
 			"license": "MIT"
 		},
 		"node_modules/undici": {
-			"version": "8.12.2",
-			"resolved": "https://registry.npmjs.org/undici/-/undici-8.12.2.tgz",
-			"integrity": "sha512-XtuDWVdqTLr3NAxm2ly9/hU6kUsJOgGh1RASzMBbsw6aWCOaQzHdW+QQDfdERjfJ2V5vL5pRPa4RetO9UfivDg==",
+			"version": "8.12.3",
+			"resolved": "https://registry.npmjs.org/undici/-/undici-8.12.3.tgz",
+			"integrity": "sha512-+fdndUTwBP86cVjihTp21hZHo7d6oj1c/47XPA3lL8mM0XHs+C4EkcjmgRsFnFk2f/UONGDy9ItBItmXsLOQHw==",
 			"license": "MIT",
 			"engines": {
 				"node": ">=22.19.0"
@@ -1941,9 +1761,9 @@
 			}
 		},
 		"node_modules/ws": {
-			"version": "8.21.0",
-			"resolved": "https://registry.npmjs.org/ws/-/ws-8.21.0.tgz",
-			"integrity": "sha512-Vsp28b7DRcimFQvrqu2Wek3z1iYxDCWqHYB8Qsnk/S4RfaCQzPGPyBNuVjJV3cd6UiKtUtp6sNM77gWvzcCH+g==",
+			"version": "8.22.0",
+			"resolved": "https://registry.npmjs.org/ws/-/ws-8.22.0.tgz",
+			"integrity": "sha512-Ydggc987+RO0AnWtZ/7Wq9FtNvcrL1b/RO0ud9mWjUPgDrsAAwQSF51sm2hm1XofbU/4jkpGEsLFsZZxU+1DOg==",
 			"license": "MIT",
 			"peerDependencies": {
 				"bufferutil": "^4.0.1",
@@ -1961,25 +1781,10 @@
 				"node": ">=10.0.0"
 			}
 		},
-		"node_modules/xml-naming": {
-			"version": "0.1.0",
-			"resolved": "https://registry.npmjs.org/xml-naming/-/xml-naming-0.1.0.tgz",
-			"integrity": "sha512-k8KO9hrMyNk6tUWqUfkTEZbezRRpONVOzUTnc97VnCvyj6Tf9lyUR9EDAIeiVLv56jsMcoXEwjW8Kv5yPY52lw==",
-			"license": "MIT",
-			"engines": {
-				"node": ">=16.0.0"
-			},
-			"funding": [
-				{
-					"type": "github",
-					"url": "https://github.com/sponsors/NaturalIntelligence"
-				}
-			]
-		},
 		"node_modules/yaml": {
-			"version": "2.9.0",
-			"resolved": "https://registry.npmjs.org/yaml/-/yaml-2.9.0.tgz",
-			"integrity": "sha512-2AvhNX3mb8zd6Zy7INTtSpl1F15HW6Wnqj0srWlkKLcpYl/gMIMJiyuGq2KeI2YFxUPjdlB+3Lc10seMLtL4cA==",
+			"version": "2.9.1",
+			"resolved": "https://registry.npmjs.org/yaml/-/yaml-2.9.1.tgz",
+			"integrity": "sha512-3NxN8+78OdzbT7C/WjGsyfPAtJaN3FNDsWxv7Y7mcDsT/oOmgW8BpyQQFFBnvZE3j9Y2Sdz1ULFLezL7Eb2yFw==",
 			"license": "ISC",
 			"bin": {
 				"yaml": "bin.mjs"
diff --git a/packages/coding-agent/package.json b/packages/coding-agent/package.json
index ce49744b2..e086174ce 100644
--- a/packages/coding-agent/package.json
+++ b/packages/coding-agent/package.json
@@ -62,17 +62,17 @@
 		"cross-spawn": "7.0.6",
 		"diff": "8.0.4",
 		"glob": "13.0.6",
-		"grok-mermaid": "0.2.2",
+		"grok-mermaid": "0.2.3",
 		"highlight.js": "10.7.3",
 		"hosted-git-info": "9.0.3",
-		"ignore": "7.0.5",
+		"ignore": "7.0.14",
 		"jiti": "2.7.0",
-		"minimatch": "10.2.5",
+		"minimatch": "10.2.6",
 		"proper-lockfile": "4.1.2",
-		"semver": "7.8.0",
-		"typebox": "1.3.7",
-		"undici": "8.12.2",
-		"yaml": "2.9.0"
+		"semver": "7.8.5",
+		"typebox": "1.4.3",
+		"undici": "8.12.3",
+		"yaml": "2.9.1"
 	},
 	"overrides": {
 		"protobufjs": "7.6.5",
@@ -91,10 +91,10 @@
 		"@types/ms": "2.1.0",
 		"@types/node": "24.12.4",
 		"@types/proper-lockfile": "4.1.4",
-		"@types/semver": "7.7.1",
+		"@types/semver": "7.8.0",
 		"shx": "0.4.0",
 		"typescript": "5.9.3",
-		"vitest": "4.1.9"
+		"vitest": "4.1.12"
 	},
 	"keywords": [
 		"coding-agent",
diff --git a/packages/coding-agent/test/mermaid.test.ts b/packages/coding-agent/test/mermaid.test.ts
index 13fa524ac..fb95a873c 100644
--- a/packages/coding-agent/test/mermaid.test.ts
+++ b/packages/coding-agent/test/mermaid.test.ts
@@ -63,14 +63,14 @@ describe("Mermaid rendering", () => {
 	});
 
 	it("falls back to the code block with a warning after streaming", () => {
-		const markdown = "```mermaid\nflowchart LR\n  A[Foo]:::highlight --> B[Bar]\n```";
+		const markdown = "```mermaid\nflowchart LR\n  A[Foo] ??? B[Bar]\n```";
 		const final = transformMermaid(markdown);
 		const followedByText = transformMermaid(`${markdown}\nFollowing text`);
 		const streaming = transformMermaid(markdown, { isStreaming: true });
 
 		expect(final).toContain(markdown);
 		expect(final).toContain("```\n`Mermaid diagram not rendered");
-		expect(final).toContain('dropped, expected a link: ":::highlight --> B[Bar]"');
+		expect(final).toContain('dropped, expected a link: "??? B[Bar]"');
 		expect(final).not.toContain("more)");
 		expect(followedByText).toContain("  \nFollowing text");
 		expect(streaming).not.toContain("Mermaid diagram not rendered");
@@ -79,13 +79,21 @@ describe("Mermaid rendering", () => {
 	});
 
 	it("summarizes additional partial-render warnings", () => {
-		const markdown = "```mermaid\nflowchart LR\n  A[Foo]:::highlight --> B[Bar]\n  C[Baz]:::other --> D[Qux]\n```";
+		const markdown = "```mermaid\nflowchart LR\n  A[Foo] ??? B[Bar]\n  C[Baz] ??? D[Qux]\n```";
 		const rendered = transformMermaid(markdown);
 
 		expect(rendered).toContain(markdown);
-		expect(rendered).toContain('dropped, expected a link: ":::highlight --> B[Bar]"');
+		expect(rendered).toContain('dropped, expected a link: "??? B[Bar]"');
 		expect(rendered).toContain("(+1 more)");
-		expect(rendered).not.toContain('dropped, expected a link: ":::other --> D[Qux]"');
+		expect(rendered).not.toContain('dropped, expected a link: "??? D[Qux]"');
+	});
+
+	it("renders flowchart class annotations without a fallback warning", () => {
+		const rendered = transformMermaid("```mermaid\nflowchart LR\n  A[Foo]:::highlight --> B[Bar]\n```");
+
+		expect(rendered).toContain("│ Foo ├───▶│ Bar │");
+		expect(rendered).not.toContain("```mermaid");
+		expect(rendered).not.toContain("Mermaid diagram not rendered");
 	});
 
 	it("respects rendering modes and skips thinking blocks", () => {
diff --git a/packages/evals/package.json b/packages/evals/package.json
index 4bd297b17..df15cf198 100644
--- a/packages/evals/package.json
+++ b/packages/evals/package.json
@@ -14,7 +14,7 @@
 		"@types/node": "24.12.4",
 		"shx": "0.4.0",
 		"typescript": "5.9.3",
-		"vitest-evals": "0.15.0",
-		"vitest": "4.1.9"
+		"vitest-evals": "0.17.0",
+		"vitest": "4.1.12"
 	}
 }
diff --git a/packages/evolution/package.json b/packages/evolution/package.json
index ef94a9f80..e490875d7 100644
--- a/packages/evolution/package.json
+++ b/packages/evolution/package.json
@@ -44,7 +44,7 @@
 		"@types/node": "24.12.4",
 		"@types/proper-lockfile": "4.1.4",
 		"shx": "0.4.0",
-		"typebox": "1.3.7",
-		"vitest": "4.1.9"
+		"typebox": "1.4.3",
+		"vitest": "4.1.12"
 	}
 }
diff --git a/packages/harness-state/package.json b/packages/harness-state/package.json
index 7b43b476e..1914fb672 100644
--- a/packages/harness-state/package.json
+++ b/packages/harness-state/package.json
@@ -44,13 +44,13 @@
 	},
 	"dependencies": {
 		"proper-lockfile": "4.1.2",
-		"typebox": "1.3.7",
-		"yaml": "2.9.0"
+		"typebox": "1.4.3",
+		"yaml": "2.9.1"
 	},
 	"devDependencies": {
 		"@types/proper-lockfile": "4.1.4",
 		"shx": "0.4.0",
-		"vitest": "4.1.9"
+		"vitest": "4.1.12"
 	},
 	"private": true
 }
diff --git a/packages/harness-trace/package.json b/packages/harness-trace/package.json
index e1c7998ab..9ec2dfad8 100644
--- a/packages/harness-trace/package.json
+++ b/packages/harness-trace/package.json
@@ -41,6 +41,6 @@
 	"devDependencies": {
 		"@types/node": "24.12.4",
 		"shx": "0.4.0",
-		"vitest": "4.1.9"
+		"vitest": "4.1.12"
 	}
 }
diff --git a/packages/protocol/package.json b/packages/protocol/package.json
index d5e3937a5..77d9f3bbd 100644
--- a/packages/protocol/package.json
+++ b/packages/protocol/package.json
@@ -45,11 +45,11 @@
 		"node": ">=22.19.0"
 	},
 	"dependencies": {
-		"typebox": "1.3.7"
+		"typebox": "1.4.3"
 	},
 	"devDependencies": {
 		"shx": "0.4.0",
-		"vitest": "4.1.9"
+		"vitest": "4.1.12"
 	},
 	"private": true
 }
diff --git a/packages/server/package.json b/packages/server/package.json
index 78ac968a1..24bfffb2e 100644
--- a/packages/server/package.json
+++ b/packages/server/package.json
@@ -59,12 +59,12 @@
 	"dependencies": {
 		"@diffexai/diffex-ai": "^0.3.2",
 		"@diffexai/diffex-protocol": "^0.3.2",
-		"ws": "8.21.0"
+		"ws": "8.22.0"
 	},
 	"devDependencies": {
-		"@types/ws": "8.18.1",
+		"@types/ws": "8.18.2",
 		"shx": "0.4.0",
-		"vitest": "4.1.9"
+		"vitest": "4.1.12"
 	},
 	"private": true
 }
diff --git a/packages/session-backends/sqlite-node/package.json b/packages/session-backends/sqlite-node/package.json
index 7e9e41261..31a1217d7 100644
--- a/packages/session-backends/sqlite-node/package.json
+++ b/packages/session-backends/sqlite-node/package.json
@@ -44,8 +44,8 @@
 		"@diffexai/diffex-agent-core": "^0.3.2"
 	},
 	"devDependencies": {
-		"@vitest/coverage-v8": "4.1.9",
-		"vitest": "4.1.9"
+		"@vitest/coverage-v8": "4.1.12",
+		"vitest": "4.1.12"
 	},
 	"private": true
 }
diff --git a/packages/telemetry/package.json b/packages/telemetry/package.json
index dfa16b497..84e6fcf28 100644
--- a/packages/telemetry/package.json
+++ b/packages/telemetry/package.json
@@ -48,7 +48,7 @@
 	},
 	"devDependencies": {
 		"@types/node": "24.12.4",
-		"vitest": "4.1.9"
+		"vitest": "4.1.12"
 	},
 	"private": true
 }
diff --git a/packages/tui/package.json b/packages/tui/package.json
index dabff1e17..a80527ebb 100644
--- a/packages/tui/package.json
+++ b/packages/tui/package.json
@@ -47,8 +47,8 @@
 	},
 	"types": "./dist/index.d.ts",
 	"dependencies": {
-		"get-east-asian-width": "1.6.0",
-		"marked": "18.0.5"
+		"get-east-asian-width": "1.7.0",
+		"marked": "18.1.1"
 	},
 	"devDependencies": {
 		"@xterm/headless": "5.5.0",

From afbe0f87409729ed01bd0403bc95853e270df395 Mon Sep 17 00:00:00 2001
From: Jay Yu <yibai14651@gmail.com>
Date: Sun, 25 Oct 2026 14:40:14 -0400
Subject: [PATCH 3/5] chore(ci): run standard checks for stacked pull requests

---
 .github/workflows/ci.yml     |  1 -
 scripts/ci-workflow.test.mjs | 26 ++++++++++++++++++++++++++
 2 files changed, 26 insertions(+), 1 deletion(-)
 create mode 100644 scripts/ci-workflow.test.mjs

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 40f43665f..bb7f6ceed 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -4,7 +4,6 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main]
 
 concurrency:
   group: ci-${{ github.ref }}
diff --git a/scripts/ci-workflow.test.mjs b/scripts/ci-workflow.test.mjs
new file mode 100644
index 000000000..52f1944b8
--- /dev/null
+++ b/scripts/ci-workflow.test.mjs
@@ -0,0 +1,26 @@
+import assert from "node:assert/strict";
+import { readFileSync } from "node:fs";
+import test from "node:test";
+import { parse } from "yaml";
+
+const workflow = parse(readFileSync(new URL("../.github/workflows/ci.yml", import.meta.url), "utf8"));
+
+test("standard CI runs for pull requests targeting main or a stacked branch", () => {
+	assert.ok(Object.hasOwn(workflow.on, "pull_request"));
+	for (const filter of ["branches", "branches-ignore", "paths", "paths-ignore"]) {
+		assert.equal(workflow.on.pull_request?.[filter], undefined, `${filter} must not exclude stacked PRs`);
+	}
+	assert.deepEqual(workflow.on.push.branches, ["main"]);
+});
+
+test("the CI aggregate requires build checks and every isolated test shard", () => {
+	const jobs = workflow.jobs;
+	assert.deepEqual(jobs["build-check-test"].needs, ["build-check", "workspace-tests", "coding-agent"]);
+	assert.equal(jobs["build-check-test"].if, "always()");
+	assert.ok(jobs["build-check"].steps.some((step) => step.run === "npm run check"));
+	assert.deepEqual(jobs["workspace-tests"].strategy.matrix.shard, [1, 2]);
+	assert.deepEqual(jobs["coding-agent"].strategy.matrix.shard, [1, 2, 3, 4]);
+	for (const job of ["workspace-tests", "coding-agent"]) {
+		assert.ok(jobs[job].steps.some((step) => step.run?.startsWith("./test.sh ")));
+	}
+});

From 6e7d839b574b91cffe9050378f96f7b8ad7eb7a3 Mon Sep 17 00:00:00 2001
From: Jay Yu <yibai14651@gmail.com>
Date: Sun, 25 Oct 2026 15:01:31 -0400
Subject: [PATCH 4/5] chore(ci): keep distribution test fixtures out of
 generated code

---
 scripts/distribution-lock-resolution.test.mjs | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/distribution-lock-resolution.test.mjs b/scripts/distribution-lock-resolution.test.mjs
index c5ff0c4ad..478f1c9ff 100644
--- a/scripts/distribution-lock-resolution.test.mjs
+++ b/scripts/distribution-lock-resolution.test.mjs
@@ -81,9 +81,11 @@ test("both generators emit deterministic deployable locks in an isolated fixture
 		]) {
 			copyFileSync(new URL(file, import.meta.url), join(root, "scripts", file));
 		}
+		writeFileSync(join(root, "manifest.json"), JSON.stringify(input.manifest));
 		writeFileSync(
 			join(root, "scripts/cli-distribution.mjs"),
-			`export function cliDistribution() { return { manifest: ${JSON.stringify(input.manifest)} }; }\n`,
+			'import { readFileSync } from "node:fs";\n' +
+				'export function cliDistribution() { return { manifest: JSON.parse(readFileSync(new URL("../manifest.json", import.meta.url), "utf8")) }; }\n',
 		);
 		for (const [name, workspace] of input.workspaces) {
 			const manifest = { name, version: "1.0.0", ...workspace.packageJson };

From e2b95528cffe9c6f6d19b04784d060ff5e5b1274 Mon Sep 17 00:00:00 2001
From: Jay Yu <yibai14651@gmail.com>
Date: Sun, 25 Oct 2026 15:20:57 -0400
Subject: [PATCH 5/5] chore(ci): make lifecycle registry fault checks
 connection-safe

---
 scripts/npm-lifecycle-registry.mjs      |  39 ++++++++
 scripts/npm-lifecycle-registry.test.mjs | 121 ++++++++++++++++++++++++
 scripts/npm-lifecycle.mjs               |  68 ++++++-------
 3 files changed, 191 insertions(+), 37 deletions(-)
 create mode 100644 scripts/npm-lifecycle-registry.mjs
 create mode 100644 scripts/npm-lifecycle-registry.test.mjs

diff --git a/scripts/npm-lifecycle-registry.mjs b/scripts/npm-lifecycle-registry.mjs
new file mode 100644
index 000000000..2c9057244
--- /dev/null
+++ b/scripts/npm-lifecycle-registry.mjs
@@ -0,0 +1,39 @@
+import { createHash } from "node:crypto";
+import { createServer } from "node:http";
+
+export function createLifecycleRegistry({ metadata, bytes, getMode, onArchive }) {
+	const server = createServer((request, reply) => {
+		// npm can do synchronous dependency graph work between metadata and archive requests.
+		// Do not leave an idle socket available for reuse after the server's keep-alive deadline.
+		reply.setHeader("connection", "close");
+		const path = decodeURIComponent(request.url);
+		const mode = getMode();
+		if (path === `/${metadata.name}`) {
+			const pkg = {
+				...metadata,
+				dist: {
+					tarball: `http://127.0.0.1:${server.address().port}/diffex.tgz`,
+					integrity: `sha512-${createHash("sha512")
+						.update(mode === "corrupt" ? "wrong bytes" : bytes)
+						.digest("base64")}`,
+				},
+			};
+			reply.setHeader("content-type", "application/json");
+			reply.end(
+				JSON.stringify({
+					name: metadata.name,
+					"dist-tags": { latest: metadata.version },
+					versions: { [metadata.version]: pkg },
+				}),
+			);
+		} else if (path === "/diffex.tgz") {
+			onArchive(mode, reply);
+			// Interrupt at the request boundary, without sending headers or archive bytes.
+			if (mode === "interrupt") return;
+			reply.end(bytes);
+		} else {
+			reply.writeHead(404).end();
+		}
+	});
+	return server;
+}
diff --git a/scripts/npm-lifecycle-registry.test.mjs b/scripts/npm-lifecycle-registry.test.mjs
new file mode 100644
index 000000000..6577a2e6f
--- /dev/null
+++ b/scripts/npm-lifecycle-registry.test.mjs
@@ -0,0 +1,121 @@
+import assert from "node:assert/strict";
+import { createHash } from "node:crypto";
+import { once } from "node:events";
+import { Agent, get } from "node:http";
+import test from "node:test";
+import { createLifecycleRegistry } from "./npm-lifecycle-registry.mjs";
+
+const metadata = { name: "@diffexai/diffex", version: "1.2.3", description: "local fixture" };
+const bytes = Buffer.from([0x1f, 0x8b, 0, 0xff, 0x0a, 0x80, 0x42]);
+const integrity = `sha512-${createHash("sha512").update(bytes).digest("base64")}`;
+
+async function fixture(t, getMode = () => "valid", onArchive = () => {}) {
+	const server = createLifecycleRegistry({ metadata, bytes, getMode, onArchive });
+	const agent = new Agent({ keepAlive: true, maxSockets: 1 });
+	t.after(async () => {
+		agent.destroy();
+		server.closeAllConnections();
+		await new Promise((done) => server.close(done));
+	});
+	server.listen(0, "127.0.0.1");
+	await once(server, "listening");
+	return { server, agent, url: `http://127.0.0.1:${server.address().port}` };
+}
+
+async function request(url, agent) {
+	let socket;
+	let closed;
+	const response = await new Promise((done, reject) => {
+		const req = get(url, { agent }, (reply) => {
+			const chunks = [];
+			reply.on("data", (chunk) => chunks.push(chunk));
+			reply.on("end", () => done({ status: reply.statusCode, headers: reply.headers, body: Buffer.concat(chunks) }));
+			reply.on("error", reject);
+		});
+		req.on("socket", (value) => {
+			socket = value;
+			closed = once(socket, "close");
+		});
+		req.on("error", reject);
+	});
+	await closed;
+	assert(socket.destroyed, "The server must close the socket, even with a keep-alive client");
+	return { ...response, socket };
+}
+
+test("metadata and exact archive bytes use closed, distinct sockets", { timeout: 5000 }, async (t) => {
+	let archiveRequests = 0;
+	const { url, agent } = await fixture(t, undefined, (mode) => {
+		assert.equal(mode, "valid");
+		archiveRequests++;
+	});
+	const manifest = await request(`${url}/@diffexai%2fdiffex`, agent);
+	assert.equal(manifest.status, 200);
+	assert.equal(manifest.headers.connection, "close");
+	assert.equal(manifest.headers["content-type"], "application/json");
+	const parsed = JSON.parse(manifest.body);
+	assert.deepEqual(parsed["dist-tags"], { latest: metadata.version });
+	assert.equal(parsed.name, metadata.name);
+	const pkg = parsed.versions[metadata.version];
+	assert.deepEqual(pkg, { ...metadata, dist: { tarball: `${url}/diffex.tgz`, integrity } });
+	assert.equal(archiveRequests, 0);
+	const archive = await request(pkg.dist.tarball, agent);
+	assert.equal(archive.status, 200);
+	assert.equal(archive.headers.connection, "close");
+	assert.deepEqual(archive.body, bytes);
+	assert.notEqual(archive.socket, manifest.socket);
+	assert.equal(archiveRequests, 1);
+	const missing = await request(`${url}/missing`, agent);
+	assert.equal(missing.status, 404);
+	assert.equal(missing.headers.connection, "close");
+});
+
+test("corrupt mode changes only metadata integrity, never archive bytes", { timeout: 5000 }, async (t) => {
+	let mode = "corrupt";
+	const { url, agent } = await fixture(t, () => mode);
+	const manifest = await request(`${url}/@diffexai/diffex`, agent);
+	assert.equal(manifest.headers.connection, "close");
+	const pkg = JSON.parse(manifest.body).versions[metadata.version];
+	assert.equal(pkg.dist.integrity, `sha512-${createHash("sha512").update("wrong bytes").digest("base64")}`);
+	assert.notEqual(pkg.dist.integrity, integrity);
+	const archive = await request(pkg.dist.tarball, agent);
+	assert.equal(archive.headers.connection, "close");
+	assert.deepEqual(archive.body, bytes);
+	mode = "valid";
+	const repaired = await request(`${url}/@diffexai/diffex`, agent);
+	assert.equal(JSON.parse(repaired.body).versions[metadata.version].dist.integrity, integrity);
+});
+
+test("interrupt callback runs before headers or body; cleanup closes the held request", { timeout: 5000 }, async (t) => {
+	let reachBoundary;
+	const boundary = new Promise((done) => {
+		reachBoundary = done;
+	});
+	let callbacks = 0;
+	const { server, url, agent } = await fixture(t, () => "interrupt", (mode, reply) => {
+		assert.equal(mode, "interrupt");
+		assert.equal(reply.getHeader("connection"), "close");
+		assert.equal(reply.headersSent, false);
+		assert.equal(reply.writableLength, 0);
+		assert.equal(reply.writableEnded, false);
+		callbacks++;
+		reachBoundary(reply);
+	});
+	let receivedResponse = false;
+	const req = get(`${url}/diffex.tgz`, { agent }, () => {
+		receivedResponse = true;
+	});
+	const failed = once(req, "error");
+	const closed = new Promise((done) => req.once("close", done));
+	const reply = await boundary;
+	assert.equal(callbacks, 1);
+	assert.equal(reply.headersSent, false);
+	assert.equal(reply.writableEnded, false);
+	server.closeAllConnections();
+	await new Promise((done) => server.close(done));
+	const [error] = await failed;
+	assert.equal(error.code, "ECONNRESET");
+	await closed;
+	assert.equal(receivedResponse, false);
+	assert.equal(server.listening, false);
+});
diff --git a/scripts/npm-lifecycle.mjs b/scripts/npm-lifecycle.mjs
index 589f005dd..0be2511bf 100644
--- a/scripts/npm-lifecycle.mjs
+++ b/scripts/npm-lifecycle.mjs
@@ -13,12 +13,12 @@ import {
 	rmSync,
 	writeFileSync,
 } from "node:fs";
-import { createServer } from "node:http";
 import { tmpdir } from "node:os";
 import { dirname, join, resolve } from "node:path";
 import { fileURLToPath, pathToFileURL } from "node:url";
 import { promisify } from "node:util";
 import { isolatedEnvironment } from "./artifact-acceptance.mjs";
+import { createLifecycleRegistry } from "./npm-lifecycle-registry.mjs";
 import { findNpmRecoveryDirectory } from "./npm-recovery.mjs";
 
 const run = promisify(execFile);
@@ -90,36 +90,14 @@ const evidence = {
 let mode = "valid";
 let interrupt;
 let tarballRequests = 0;
-const server = createServer((request, reply) => {
-	const path = decodeURIComponent(request.url);
-	if (path === "/@diffexai/diffex") {
-		const pkg = {
-			...metadata,
-			dist: {
-				tarball: `http://127.0.0.1:${server.address().port}/diffex.tgz`,
-				integrity: `sha512-${createHash("sha512")
-					.update(mode === "corrupt" ? "wrong bytes" : bytes)
-					.digest("base64")}`,
-			},
-		};
-		reply.setHeader("content-type", "application/json");
-		reply.end(
-			JSON.stringify({
-				name: metadata.name,
-				"dist-tags": { latest: metadata.version },
-				versions: { [metadata.version]: pkg },
-			}),
-		);
-	} else if (path === "/diffex.tgz") {
+const server = createLifecycleRegistry({
+	metadata,
+	bytes,
+	getMode: () => mode,
+	onArchive: (archiveMode) => {
 		tarballRequests++;
-		if (mode === "interrupt") {
-			interrupt?.();
-			return;
-		}
-		reply.end(bytes);
-	} else {
-		reply.writeHead(404).end();
-	}
+		if (archiveMode === "interrupt") interrupt?.();
+	},
 });
 await new Promise((done) => server.listen(0, "127.0.0.1", done));
 
@@ -216,28 +194,44 @@ try {
 			const child = spawn(process.execPath, ["--import", guard, executable, "update", "--self", "--force"], {
 				...options,
 				detached: true,
-				stdio: "ignore",
+				stdio: ["ignore", "pipe", "pipe"],
 			});
+			// Keep draining both pipes, retaining only the last 64 KiB per stream.
+			const captured = { stdout: Buffer.alloc(0), stderr: Buffer.alloc(0) };
+			for (const name of ["stdout", "stderr"]) {
+				child[name].on("data", (chunk) => {
+					captured[name] = Buffer.concat([captured[name], chunk]).subarray(-64 * 1024);
+				});
+			}
 			let interrupted = false;
 			interrupt = () => {
 				interrupted = true;
 				process.kill(-child.pid, "SIGTERM");
 			};
 			const deadline = setTimeout(() => process.kill(-child.pid, "SIGKILL"), 30000);
+			let result;
 			try {
-				await new Promise((done, reject) => {
-					child.on("close", done);
+				result = await new Promise((done, reject) => {
+					child.on("close", (exitCode, signal) => done({ exitCode, signal }));
 					child.on("error", reject);
 				});
 			} finally {
 				clearTimeout(deadline);
+				interrupt = undefined;
 			}
-			assert(interrupted, "Interrupted update must reach the real npm archive download");
-			evidence.commands.push({
+			const diagnostic = {
 				command: "diffex update --self --force",
-				signal: "SIGTERM",
+				...result,
 				boundary: "npm archive download",
-			});
+				interrupted,
+				stdout: captured.stdout.toString("utf8"),
+				stderr: captured.stderr.toString("utf8"),
+			};
+			evidence.commands.push(diagnostic);
+			assert(
+				interrupted,
+				`Interrupted update must reach the real npm archive download; child exited before boundary: ${JSON.stringify(diagnostic)}`,
+			);
 		}
 		const installationUnchanged = snapshot(prefix) === stable;
 		if (fault === "corrupt") assert(installationUnchanged, "Integrity failure mutated the prefix");