@schlenkr/ragents 0.1.5 → 0.1.6

package/packages/agent/src/core/package-manager.ts

@@ -1,2441 +0,0 @@
-import type { ChildProcess, ChildProcessByStdio } from "node:child_process";
-import { createHash } from "node:crypto";
-import { chmodSync, existsSync, mkdirSync, readdirSync, readFileSync, rmSync, statSync, writeFileSync } from "node:fs";
-import { homedir } from "node:os";
-
-function getEnv(): NodeJS.ProcessEnv {
-	if (process.platform !== "linux" || Object.keys(process.env).length > 0) {
-		return process.env;
-	}
-	try {
-		const data = readFileSync("/proc/self/environ", "utf-8");
-		const env: NodeJS.ProcessEnv = {};
-		for (const entry of data.split("\0")) {
-			const idx = entry.indexOf("=");
-			if (idx > 0) {
-				env[entry.slice(0, idx)] = entry.slice(idx + 1);
-			}
-		}
-		return env;
-	} catch {
-		return process.env;
-	}
-}
-
-import { basename, dirname, join, relative, resolve, sep } from "node:path";
-import type { Readable } from "node:stream";
-import { globSync } from "glob";
-import ignore from "ignore";
-import { minimatch } from "minimatch";
-import { satisfies, valid, validRange } from "semver";
-import { CONFIG_DIR_NAME } from "../config.ts";
-import { spawnProcess, spawnProcessSync } from "../utils/child-process.ts";
-import { type GitSource, parseGitUrl } from "../utils/git.ts";
-import { canonicalizePath, isLocalPath, markPathIgnoredByCloudSync, resolvePath } from "../utils/paths.ts";
-import { isStdoutTakenOver } from "./output-guard.ts";
-import type { PackageSource, SettingsManager } from "./settings-manager.ts";
-
-const NETWORK_TIMEOUT_MS = 10000;
-const GIT_UPDATE_CONCURRENCY = 4;
-
-function isExactNpmVersion(version: string | undefined): boolean {
-	return valid(version ?? "") !== null;
-}
-
-function getNpmVersionRange(version: string | undefined): string | undefined {
-	return version ? (validRange(version) ?? undefined) : undefined;
-}
-
-export interface PathMetadata {
-	source: string;
-	scope: SourceScope;
-	origin: "package" | "top-level";
-	baseDir?: string;
-}
-
-export interface ResolvedResource {
-	path: string;
-	enabled: boolean;
-	metadata: PathMetadata;
-}
-
-export interface ResolvedPaths {
-	extensions: ResolvedResource[];
-	skills: ResolvedResource[];
-	prompts: ResolvedResource[];
-	themes: ResolvedResource[];
-}
-
-export type MissingSourceAction = "install" | "skip" | "error";
-
-export interface ProgressEvent {
-	type: "start" | "progress" | "complete" | "error";
-	action: "install" | "remove" | "update" | "clone" | "pull";
-	source: string;
-	message?: string;
-}
-
-export type ProgressCallback = (event: ProgressEvent) => void;
-
-export interface ConfiguredPackage {
-	source: string;
-	scope: "user" | "project";
-	filtered: boolean;
-	installedPath?: string;
-}
-
-export interface PackageManager {
-	resolve(onMissing?: (source: string) => Promise<MissingSourceAction>): Promise<ResolvedPaths>;
-	install(source: string, options?: { local?: boolean }): Promise<void>;
-	installAndPersist(source: string, options?: { local?: boolean }): Promise<void>;
-	remove(source: string, options?: { local?: boolean }): Promise<void>;
-	removeAndPersist(source: string, options?: { local?: boolean }): Promise<boolean>;
-	update(source?: string): Promise<void>;
-	listConfiguredPackages(): ConfiguredPackage[];
-	resolveExtensionSources(
-		sources: string[],
-		options?: { local?: boolean; temporary?: boolean },
-	): Promise<ResolvedPaths>;
-	addSourceToSettings(source: string, options?: { local?: boolean }): boolean;
-	removeSourceFromSettings(source: string, options?: { local?: boolean }): boolean;
-	setProgressCallback(callback: ProgressCallback | undefined): void;
-	getInstalledPath(source: string, scope: "user" | "project"): string | undefined;
-}
-
-interface PackageManagerOptions {
-	cwd: string;
-	agentDir: string;
-	settingsManager: SettingsManager;
-}
-
-type SourceScope = "user" | "project" | "temporary";
-
-type NpmSource = {
-	type: "npm";
-	spec: string;
-	name: string;
-	version?: string;
-	range?: string;
-	pinned: boolean;
-};
-
-type LocalSource = {
-	type: "local";
-	path: string;
-};
-
-type ParsedSource = NpmSource | GitSource | LocalSource;
-
-type InstalledSourceScope = Exclude<SourceScope, "temporary">;
-
-interface ConfiguredUpdateSource {
-	source: string;
-	scope: InstalledSourceScope;
-}
-
-interface NpmUpdateTarget extends ConfiguredUpdateSource {
-	parsed: NpmSource;
-}
-
-interface GitUpdateTarget extends ConfiguredUpdateSource {
-	parsed: GitSource;
-}
-
-interface AgentManifest {
-	extensions?: string[];
-	skills?: string[];
-	prompts?: string[];
-	themes?: string[];
-}
-
-interface ResourceAccumulator {
-	extensions: Map<string, { metadata: PathMetadata; enabled: boolean }>;
-	skills: Map<string, { metadata: PathMetadata; enabled: boolean }>;
-	prompts: Map<string, { metadata: PathMetadata; enabled: boolean }>;
-	themes: Map<string, { metadata: PathMetadata; enabled: boolean }>;
-}
-
-/**
- * Compute a numeric precedence rank for a resource based on its metadata.
- * Lower rank = higher precedence. Used to sort resolved resources so that
- * name-collision resolution ("first wins") produces the correct outcome.
- *
- * Precedence (highest to lowest):
- *   0  project + settings entry (source: "local", scope: "project")
- *   1  project + auto-discovered (source: "auto", scope: "project")
- *   2  user + settings entry (source: "local", scope: "user")
- *   3  user + auto-discovered (source: "auto", scope: "user")
- *   4  package resource (origin: "package")
- */
-function resourcePrecedenceRank(m: PathMetadata): number {
-	if (m.origin === "package") return 4;
-	const scopeBase = m.scope === "project" ? 0 : 2;
-	return scopeBase + (m.source === "local" ? 0 : 1);
-}
-
-interface PackageFilter {
-	autoload?: boolean;
-	extensions?: string[];
-	skills?: string[];
-	prompts?: string[];
-	themes?: string[];
-}
-
-type ResourceType = "extensions" | "skills" | "prompts" | "themes";
-
-const RESOURCE_TYPES: ResourceType[] = ["extensions", "skills", "prompts", "themes"];
-
-const FILE_PATTERNS: Record<ResourceType, RegExp> = {
-	extensions: /\.(ts|js)$/,
-	skills: /\.md$/,
-	prompts: /\.md$/,
-	themes: /\.json$/,
-};
-
-const IGNORE_FILE_NAMES = [".gitignore", ".ignore", ".fdignore"];
-
-type IgnoreMatcher = ReturnType<typeof ignore>;
-
-function toPosixPath(p: string): string {
-	return p.split(sep).join("/");
-}
-
-function getHomeDir(): string {
-	return process.env.HOME || homedir();
-}
-
-export function getExtensionTempFolder(agentDir: string): string {
-	const tempFolder = join(agentDir, "tmp", "extensions");
-	mkdirSync(tempFolder, { recursive: true, mode: 0o700 });
-	chmodSync(tempFolder, 0o700);
-	return tempFolder;
-}
-
-function prefixIgnorePattern(line: string, prefix: string): string | null {
-	const trimmed = line.trim();
-	if (!trimmed) return null;
-	if (trimmed.startsWith("#") && !trimmed.startsWith("\\#")) return null;
-
-	let pattern = line;
-	let negated = false;
-
-	if (pattern.startsWith("!")) {
-		negated = true;
-		pattern = pattern.slice(1);
-	} else if (pattern.startsWith("\\!")) {
-		pattern = pattern.slice(1);
-	}
-
-	if (pattern.startsWith("/")) {
-		pattern = pattern.slice(1);
-	}
-
-	const prefixed = prefix ? `${prefix}${pattern}` : pattern;
-	return negated ? `!${prefixed}` : prefixed;
-}
-
-function addIgnoreRules(ig: IgnoreMatcher, dir: string, rootDir: string): void {
-	const relativeDir = relative(rootDir, dir);
-	const prefix = relativeDir ? `${toPosixPath(relativeDir)}/` : "";
-
-	for (const filename of IGNORE_FILE_NAMES) {
-		const ignorePath = join(dir, filename);
-		if (!existsSync(ignorePath)) continue;
-		try {
-			const content = readFileSync(ignorePath, "utf-8");
-			const patterns = content
-				.split(/\r?\n/)
-				.map((line) => prefixIgnorePattern(line, prefix))
-				.filter((line): line is string => Boolean(line));
-			if (patterns.length > 0) {
-				ig.add(patterns);
-			}
-		} catch {}
-	}
-}
-
-function isPattern(s: string): boolean {
-	return s.startsWith("!") || s.startsWith("+") || s.startsWith("-") || s.includes("*") || s.includes("?");
-}
-
-function isOverridePattern(s: string): boolean {
-	return s.startsWith("!") || s.startsWith("+") || s.startsWith("-");
-}
-
-function hasGlobPattern(s: string): boolean {
-	return s.includes("*") || s.includes("?");
-}
-
-function splitPatterns(entries: string[]): { plain: string[]; patterns: string[] } {
-	const plain: string[] = [];
-	const patterns: string[] = [];
-	for (const entry of entries) {
-		if (isPattern(entry)) {
-			patterns.push(entry);
-		} else {
-			plain.push(entry);
-		}
-	}
-	return { plain, patterns };
-}
-
-function collectFiles(
-	dir: string,
-	filePattern: RegExp,
-	skipNodeModules = true,
-	ignoreMatcher?: IgnoreMatcher,
-	rootDir?: string,
-): string[] {
-	const files: string[] = [];
-	if (!existsSync(dir)) return files;
-
-	const root = rootDir ?? dir;
-	const ig = ignoreMatcher ?? ignore();
-	addIgnoreRules(ig, dir, root);
-
-	try {
-		const entries = readdirSync(dir, { withFileTypes: true });
-		for (const entry of entries) {
-			if (entry.name.startsWith(".")) continue;
-			if (skipNodeModules && entry.name === "node_modules") continue;
-
-			const fullPath = join(dir, entry.name);
-			let isDir = entry.isDirectory();
-			let isFile = entry.isFile();
-
-			if (entry.isSymbolicLink()) {
-				try {
-					const stats = statSync(fullPath);
-					isDir = stats.isDirectory();
-					isFile = stats.isFile();
-				} catch {
-					continue;
-				}
-			}
-
-			const relPath = toPosixPath(relative(root, fullPath));
-			const ignorePath = isDir ? `${relPath}/` : relPath;
-			if (ig.ignores(ignorePath)) continue;
-
-			if (isDir) {
-				files.push(...collectFiles(fullPath, filePattern, skipNodeModules, ig, root));
-			} else if (isFile && filePattern.test(entry.name)) {
-				files.push(fullPath);
-			}
-		}
-	} catch {
-		// Ignore errors
-	}
-
-	return files;
-}
-
-type SkillDiscoveryMode = "native" | "agents";
-
-function collectSkillEntries(
-	dir: string,
-	mode: SkillDiscoveryMode,
-	ignoreMatcher?: IgnoreMatcher,
-	rootDir?: string,
-): string[] {
-	const entries: string[] = [];
-	if (!existsSync(dir)) return entries;
-
-	const root = rootDir ?? dir;
-	const ig = ignoreMatcher ?? ignore();
-	addIgnoreRules(ig, dir, root);
-
-	try {
-		const dirEntries = readdirSync(dir, { withFileTypes: true });
-
-		for (const entry of dirEntries) {
-			if (entry.name !== "SKILL.md") {
-				continue;
-			}
-
-			const fullPath = join(dir, entry.name);
-			let isFile = entry.isFile();
-			if (entry.isSymbolicLink()) {
-				try {
-					isFile = statSync(fullPath).isFile();
-				} catch {
-					continue;
-				}
-			}
-
-			const relPath = toPosixPath(relative(root, fullPath));
-			if (isFile && !ig.ignores(relPath)) {
-				entries.push(fullPath);
-				return entries;
-			}
-		}
-
-		for (const entry of dirEntries) {
-			if (entry.name.startsWith(".")) continue;
-			if (entry.name === "node_modules") continue;
-
-			const fullPath = join(dir, entry.name);
-			let isDir = entry.isDirectory();
-			let isFile = entry.isFile();
-
-			if (entry.isSymbolicLink()) {
-				try {
-					const stats = statSync(fullPath);
-					isDir = stats.isDirectory();
-					isFile = stats.isFile();
-				} catch {
-					continue;
-				}
-			}
-
-			const relPath = toPosixPath(relative(root, fullPath));
-			if (mode === "native" && dir === root && isFile && entry.name.endsWith(".md") && !ig.ignores(relPath)) {
-				entries.push(fullPath);
-				continue;
-			}
-
-			if (!isDir) continue;
-			if (ig.ignores(`${relPath}/`)) continue;
-
-			entries.push(...collectSkillEntries(fullPath, mode, ig, root));
-		}
-	} catch {
-		// Ignore errors
-	}
-
-	return entries;
-}
-
-function collectAutoSkillEntries(dir: string, mode: SkillDiscoveryMode): string[] {
-	return collectSkillEntries(dir, mode);
-}
-
-function findGitRepoRoot(startDir: string): string | null {
-	let dir = resolve(startDir);
-	while (true) {
-		if (existsSync(join(dir, ".git"))) {
-			return dir;
-		}
-		const parent = dirname(dir);
-		if (parent === dir) {
-			return null;
-		}
-		dir = parent;
-	}
-}
-
-function collectAncestorAgentsSkillDirs(startDir: string): string[] {
-	const skillDirs: string[] = [];
-	const resolvedStartDir = resolve(startDir);
-	const gitRepoRoot = findGitRepoRoot(resolvedStartDir);
-
-	let dir = resolvedStartDir;
-	while (true) {
-		skillDirs.push(join(dir, ".agents", "skills"));
-		if (gitRepoRoot && dir === gitRepoRoot) {
-			break;
-		}
-		const parent = dirname(dir);
-		if (parent === dir) {
-			break;
-		}
-		dir = parent;
-	}
-
-	return skillDirs;
-}
-
-function collectAutoPromptEntries(dir: string): string[] {
-	const entries: string[] = [];
-	if (!existsSync(dir)) return entries;
-
-	const ig = ignore();
-	addIgnoreRules(ig, dir, dir);
-
-	try {
-		const dirEntries = readdirSync(dir, { withFileTypes: true });
-		for (const entry of dirEntries) {
-			if (entry.name.startsWith(".")) continue;
-			if (entry.name === "node_modules") continue;
-
-			const fullPath = join(dir, entry.name);
-			let isFile = entry.isFile();
-			if (entry.isSymbolicLink()) {
-				try {
-					isFile = statSync(fullPath).isFile();
-				} catch {
-					continue;
-				}
-			}
-
-			const relPath = toPosixPath(relative(dir, fullPath));
-			if (ig.ignores(relPath)) continue;
-
-			if (isFile && entry.name.endsWith(".md")) {
-				entries.push(fullPath);
-			}
-		}
-	} catch {
-		// Ignore errors
-	}
-
-	return entries;
-}
-
-function collectAutoThemeEntries(dir: string): string[] {
-	const entries: string[] = [];
-	if (!existsSync(dir)) return entries;
-
-	const ig = ignore();
-	addIgnoreRules(ig, dir, dir);
-
-	try {
-		const dirEntries = readdirSync(dir, { withFileTypes: true });
-		for (const entry of dirEntries) {
-			if (entry.name.startsWith(".")) continue;
-			if (entry.name === "node_modules") continue;
-
-			const fullPath = join(dir, entry.name);
-			let isFile = entry.isFile();
-			if (entry.isSymbolicLink()) {
-				try {
-					isFile = statSync(fullPath).isFile();
-				} catch {
-					continue;
-				}
-			}
-
-			const relPath = toPosixPath(relative(dir, fullPath));
-			if (ig.ignores(relPath)) continue;
-
-			if (isFile && entry.name.endsWith(".json")) {
-				entries.push(fullPath);
-			}
-		}
-	} catch {
-		// Ignore errors
-	}
-
-	return entries;
-}
-
-function readAgentManifestFile(packageJsonPath: string): AgentManifest | null {
-	try {
-		const content = readFileSync(packageJsonPath, "utf-8");
-		const pkg = JSON.parse(content) as { agent?: AgentManifest };
-		return pkg.agent ?? null;
-	} catch {
-		return null;
-	}
-}
-
-function resolveExtensionEntries(dir: string): string[] | null {
-	const packageJsonPath = join(dir, "package.json");
-	if (existsSync(packageJsonPath)) {
-		const manifest = readAgentManifestFile(packageJsonPath);
-		if (manifest?.extensions?.length) {
-			const entries: string[] = [];
-			for (const extPath of manifest.extensions) {
-				const resolvedExtPath = resolve(dir, extPath);
-				if (existsSync(resolvedExtPath)) {
-					entries.push(resolvedExtPath);
-				}
-			}
-			if (entries.length > 0) {
-				return entries;
-			}
-		}
-	}
-
-	const indexTs = join(dir, "index.ts");
-	const indexJs = join(dir, "index.js");
-	if (existsSync(indexTs)) {
-		return [indexTs];
-	}
-	if (existsSync(indexJs)) {
-		return [indexJs];
-	}
-
-	return null;
-}
-
-function collectAutoExtensionEntries(dir: string): string[] {
-	const entries: string[] = [];
-	if (!existsSync(dir)) return entries;
-
-	// First check if this directory itself has explicit extension entries (package.json or index)
-	const rootEntries = resolveExtensionEntries(dir);
-	if (rootEntries) {
-		return rootEntries;
-	}
-
-	// Otherwise, discover extensions from directory contents
-	const ig = ignore();
-	addIgnoreRules(ig, dir, dir);
-
-	try {
-		const dirEntries = readdirSync(dir, { withFileTypes: true });
-		for (const entry of dirEntries) {
-			if (entry.name.startsWith(".")) continue;
-			if (entry.name === "node_modules") continue;
-
-			const fullPath = join(dir, entry.name);
-			let isDir = entry.isDirectory();
-			let isFile = entry.isFile();
-
-			if (entry.isSymbolicLink()) {
-				try {
-					const stats = statSync(fullPath);
-					isDir = stats.isDirectory();
-					isFile = stats.isFile();
-				} catch {
-					continue;
-				}
-			}
-
-			const relPath = toPosixPath(relative(dir, fullPath));
-			const ignorePath = isDir ? `${relPath}/` : relPath;
-			if (ig.ignores(ignorePath)) continue;
-
-			if (isFile && (entry.name.endsWith(".ts") || entry.name.endsWith(".js"))) {
-				entries.push(fullPath);
-			} else if (isDir) {
-				const resolvedEntries = resolveExtensionEntries(fullPath);
-				if (resolvedEntries) {
-					entries.push(...resolvedEntries);
-				}
-			}
-		}
-	} catch {
-		// Ignore errors
-	}
-
-	return entries;
-}
-
-/**
- * Collect resource files from a directory based on resource type.
- * Extensions use smart discovery (index.ts in subdirs), others use recursive collection.
- */
-function collectResourceFiles(dir: string, resourceType: ResourceType): string[] {
-	if (resourceType === "skills") {
-		return collectSkillEntries(dir, "native");
-	}
-	if (resourceType === "extensions") {
-		return collectAutoExtensionEntries(dir);
-	}
-	return collectFiles(dir, FILE_PATTERNS[resourceType]);
-}
-
-function matchesAnyPattern(filePath: string, patterns: string[], baseDir: string): boolean {
-	const rel = toPosixPath(relative(baseDir, filePath));
-	const name = basename(filePath);
-	const filePathPosix = toPosixPath(filePath);
-	const isSkillFile = name === "SKILL.md";
-	const parentDir = isSkillFile ? dirname(filePath) : undefined;
-	const parentRel = isSkillFile ? toPosixPath(relative(baseDir, parentDir!)) : undefined;
-	const parentName = isSkillFile ? basename(parentDir!) : undefined;
-	const parentDirPosix = isSkillFile ? toPosixPath(parentDir!) : undefined;
-
-	return patterns.some((pattern) => {
-		const normalizedPattern = toPosixPath(pattern);
-		if (
-			minimatch(rel, normalizedPattern) ||
-			minimatch(name, normalizedPattern) ||
-			minimatch(filePathPosix, normalizedPattern)
-		) {
-			return true;
-		}
-		if (!isSkillFile) return false;
-		return (
-			minimatch(parentRel!, normalizedPattern) ||
-			minimatch(parentName!, normalizedPattern) ||
-			minimatch(parentDirPosix!, normalizedPattern)
-		);
-	});
-}
-
-function normalizeExactPattern(pattern: string): string {
-	const normalized = pattern.startsWith("./") || pattern.startsWith(".\\") ? pattern.slice(2) : pattern;
-	return toPosixPath(normalized);
-}
-
-function matchesAnyExactPattern(filePath: string, patterns: string[], baseDir: string): boolean {
-	if (patterns.length === 0) return false;
-	const rel = toPosixPath(relative(baseDir, filePath));
-	const name = basename(filePath);
-	const filePathPosix = toPosixPath(filePath);
-	const isSkillFile = name === "SKILL.md";
-	const parentDir = isSkillFile ? dirname(filePath) : undefined;
-	const parentRel = isSkillFile ? toPosixPath(relative(baseDir, parentDir!)) : undefined;
-	const parentDirPosix = isSkillFile ? toPosixPath(parentDir!) : undefined;
-
-	return patterns.some((pattern) => {
-		const normalized = normalizeExactPattern(pattern);
-		if (normalized === rel || normalized === filePathPosix) {
-			return true;
-		}
-		if (!isSkillFile) return false;
-		return normalized === parentRel || normalized === parentDirPosix;
-	});
-}
-
-function getOverridePatterns(entries: string[]): string[] {
-	return entries.filter((pattern) => pattern.startsWith("!") || pattern.startsWith("+") || pattern.startsWith("-"));
-}
-
-function isEnabledByOverrides(filePath: string, patterns: string[], baseDir: string): boolean {
-	const overrides = getOverridePatterns(patterns);
-	const excludes = overrides.filter((pattern) => pattern.startsWith("!")).map((pattern) => pattern.slice(1));
-	const forceIncludes = overrides.filter((pattern) => pattern.startsWith("+")).map((pattern) => pattern.slice(1));
-	const forceExcludes = overrides.filter((pattern) => pattern.startsWith("-")).map((pattern) => pattern.slice(1));
-
-	let enabled = true;
-	if (excludes.length > 0 && matchesAnyPattern(filePath, excludes, baseDir)) {
-		enabled = false;
-	}
-	if (forceIncludes.length > 0 && matchesAnyExactPattern(filePath, forceIncludes, baseDir)) {
-		enabled = true;
-	}
-	if (forceExcludes.length > 0 && matchesAnyExactPattern(filePath, forceExcludes, baseDir)) {
-		enabled = false;
-	}
-	return enabled;
-}
-
-/**
- * Apply patterns to paths and return a Set of enabled paths.
- * Pattern types:
- * - Plain patterns: include matching paths
- * - `!pattern`: exclude matching paths
- * - `+path`: force-include exact path (overrides exclusions)
- * - `-path`: force-exclude exact path (overrides force-includes)
- */
-function applyPatterns(allPaths: string[], patterns: string[], baseDir: string): Set<string> {
-	const includes: string[] = [];
-	const excludes: string[] = [];
-	const forceIncludes: string[] = [];
-	const forceExcludes: string[] = [];
-
-	for (const p of patterns) {
-		if (p.startsWith("+")) {
-			forceIncludes.push(p.slice(1));
-		} else if (p.startsWith("-")) {
-			forceExcludes.push(p.slice(1));
-		} else if (p.startsWith("!")) {
-			excludes.push(p.slice(1));
-		} else {
-			includes.push(p);
-		}
-	}
-
-	// Step 1: Apply includes (or all if no includes)
-	let result: string[];
-	if (includes.length === 0) {
-		result = [...allPaths];
-	} else {
-		result = allPaths.filter((filePath) => matchesAnyPattern(filePath, includes, baseDir));
-	}
-
-	// Step 2: Apply excludes
-	if (excludes.length > 0) {
-		result = result.filter((filePath) => !matchesAnyPattern(filePath, excludes, baseDir));
-	}
-
-	// Step 3: Force-include (add back from allPaths, overriding exclusions)
-	if (forceIncludes.length > 0) {
-		for (const filePath of allPaths) {
-			if (!result.includes(filePath) && matchesAnyExactPattern(filePath, forceIncludes, baseDir)) {
-				result.push(filePath);
-			}
-		}
-	}
-
-	// Step 4: Force-exclude (remove even if included or force-included)
-	if (forceExcludes.length > 0) {
-		result = result.filter((filePath) => !matchesAnyExactPattern(filePath, forceExcludes, baseDir));
-	}
-
-	return new Set(result);
-}
-
-function applyAutoloadDisabledPatterns(allPaths: string[], patterns: string[], baseDir: string): Map<string, boolean> {
-	const result = new Map<string, boolean>();
-	for (const pattern of patterns) {
-		const target = pattern.slice(
-			pattern.startsWith("+") || pattern.startsWith("-") || pattern.startsWith("!") ? 1 : 0,
-		);
-		const enabled = !pattern.startsWith("-") && !pattern.startsWith("!");
-		const exact = pattern.startsWith("+") || pattern.startsWith("-");
-		for (const filePath of allPaths) {
-			if (
-				exact ? matchesAnyExactPattern(filePath, [target], baseDir) : matchesAnyPattern(filePath, [target], baseDir)
-			) {
-				result.set(filePath, enabled);
-			}
-		}
-	}
-	return result;
-}
-
-export class DefaultPackageManager implements PackageManager {
-	private cwd: string;
-	private agentDir: string;
-	private settingsManager: SettingsManager;
-	private globalNpmRoot: string | undefined;
-	private globalNpmRootCommandKey: string | undefined;
-	private progressCallback: ProgressCallback | undefined;
-
-	constructor(options: PackageManagerOptions) {
-		this.cwd = resolvePath(options.cwd);
-		this.agentDir = resolvePath(options.agentDir);
-		this.settingsManager = options.settingsManager;
-	}
-
-	setProgressCallback(callback: ProgressCallback | undefined): void {
-		this.progressCallback = callback;
-	}
-
-	addSourceToSettings(source: string, options?: { local?: boolean }): boolean {
-		const scope: SourceScope = options?.local ? "project" : "user";
-		const currentSettings =
-			scope === "project" ? this.settingsManager.getProjectSettings() : this.settingsManager.getGlobalSettings();
-		const currentPackages = currentSettings.packages ?? [];
-		const normalizedSource = this.normalizePackageSourceForSettings(source, scope);
-		const matchIndex = currentPackages.findIndex((existing) => this.packageSourcesMatch(existing, source, scope));
-		if (matchIndex !== -1) {
-			const existing = currentPackages[matchIndex];
-			if (this.getPackageSourceString(existing) === normalizedSource) {
-				return false;
-			}
-			const nextPackages = [...currentPackages];
-			nextPackages[matchIndex] =
-				typeof existing === "string" ? normalizedSource : { ...existing, source: normalizedSource };
-			if (scope === "project") {
-				this.settingsManager.setProjectPackages(nextPackages);
-			} else {
-				this.settingsManager.setPackages(nextPackages);
-			}
-			return true;
-		}
-		const nextPackages = [...currentPackages, normalizedSource];
-		if (scope === "project") {
-			this.settingsManager.setProjectPackages(nextPackages);
-		} else {
-			this.settingsManager.setPackages(nextPackages);
-		}
-		return true;
-	}
-
-	removeSourceFromSettings(source: string, options?: { local?: boolean }): boolean {
-		const scope: SourceScope = options?.local ? "project" : "user";
-		const currentSettings =
-			scope === "project" ? this.settingsManager.getProjectSettings() : this.settingsManager.getGlobalSettings();
-		const currentPackages = currentSettings.packages ?? [];
-		const nextPackages = currentPackages.filter((existing) => !this.packageSourcesMatch(existing, source, scope));
-		const changed = nextPackages.length !== currentPackages.length;
-		if (!changed) {
-			return false;
-		}
-		if (scope === "project") {
-			this.settingsManager.setProjectPackages(nextPackages);
-		} else {
-			this.settingsManager.setPackages(nextPackages);
-		}
-		return true;
-	}
-
-	getInstalledPath(source: string, scope: "user" | "project"): string | undefined {
-		const parsed = this.parseSource(source);
-		if (parsed.type === "npm") {
-			const path = this.getNpmInstallPath(parsed, scope);
-			return existsSync(path) ? path : undefined;
-		}
-		if (parsed.type === "git") {
-			const path = this.getGitInstallPath(parsed, scope);
-			return existsSync(path) ? path : undefined;
-		}
-		if (parsed.type === "local") {
-			const baseDir = this.getBaseDirForScope(scope);
-			const path = this.resolvePathFromBase(parsed.path, baseDir);
-			return existsSync(path) ? path : undefined;
-		}
-		return undefined;
-	}
-
-	private emitProgress(event: ProgressEvent): void {
-		this.progressCallback?.(event);
-	}
-
-	private async withProgress(
-		action: ProgressEvent["action"],
-		source: string,
-		message: string,
-		operation: () => Promise<void>,
-	): Promise<void> {
-		this.emitProgress({ type: "start", action, source, message });
-		try {
-			await operation();
-			this.emitProgress({ type: "complete", action, source });
-		} catch (error) {
-			const errorMessage = error instanceof Error ? error.message : String(error);
-			this.emitProgress({ type: "error", action, source, message: errorMessage });
-			throw error;
-		}
-	}
-
-	async resolve(onMissing?: (source: string) => Promise<MissingSourceAction>): Promise<ResolvedPaths> {
-		const accumulator = this.createAccumulator();
-		const globalSettings = this.settingsManager.getGlobalSettings();
-		const projectSettings = this.settingsManager.getProjectSettings();
-
-		// Collect all packages with scope (project first so cwd resources win collisions)
-		const allPackages: Array<{ pkg: PackageSource; scope: SourceScope }> = [];
-		for (const pkg of projectSettings.packages ?? []) {
-			allPackages.push({ pkg, scope: "project" });
-		}
-		for (const pkg of globalSettings.packages ?? []) {
-			allPackages.push({ pkg, scope: "user" });
-		}
-
-		// Dedupe: project scope wins over global for same package identity
-		const packageSources = this.dedupePackages(allPackages);
-		await this.resolvePackageSources(packageSources, accumulator, onMissing);
-
-		const globalBaseDir = this.agentDir;
-		const projectBaseDir = join(this.cwd, CONFIG_DIR_NAME);
-
-		for (const resourceType of RESOURCE_TYPES) {
-			const target = this.getTargetMap(accumulator, resourceType);
-			const globalEntries = (globalSettings[resourceType] ?? []) as string[];
-			const projectEntries = (projectSettings[resourceType] ?? []) as string[];
-			this.resolveLocalEntries(
-				projectEntries,
-				resourceType,
-				target,
-				{
-					source: "local",
-					scope: "project",
-					origin: "top-level",
-				},
-				projectBaseDir,
-			);
-			this.resolveLocalEntries(
-				globalEntries,
-				resourceType,
-				target,
-				{
-					source: "local",
-					scope: "user",
-					origin: "top-level",
-				},
-				globalBaseDir,
-			);
-		}
-
-		this.addAutoDiscoveredResources(accumulator, globalSettings, projectSettings, globalBaseDir, projectBaseDir);
-
-		return this.toResolvedPaths(accumulator);
-	}
-
-	async resolveExtensionSources(
-		sources: string[],
-		options?: { local?: boolean; temporary?: boolean },
-	): Promise<ResolvedPaths> {
-		const accumulator = this.createAccumulator();
-		const scope: SourceScope = options?.temporary ? "temporary" : options?.local ? "project" : "user";
-		const packageSources = sources.map((source) => ({ pkg: source as PackageSource, scope }));
-		await this.resolvePackageSources(packageSources, accumulator);
-		return this.toResolvedPaths(accumulator);
-	}
-
-	listConfiguredPackages(): ConfiguredPackage[] {
-		const globalSettings = this.settingsManager.getGlobalSettings();
-		const projectSettings = this.settingsManager.getProjectSettings();
-		const configuredPackages: ConfiguredPackage[] = [];
-
-		for (const pkg of globalSettings.packages ?? []) {
-			const source = typeof pkg === "string" ? pkg : pkg.source;
-			configuredPackages.push({
-				source,
-				scope: "user",
-				filtered: typeof pkg === "object",
-				installedPath: this.getInstalledPath(source, "user"),
-			});
-		}
-
-		for (const pkg of projectSettings.packages ?? []) {
-			const source = typeof pkg === "string" ? pkg : pkg.source;
-			configuredPackages.push({
-				source,
-				scope: "project",
-				filtered: typeof pkg === "object",
-				installedPath: this.getInstalledPath(source, "project"),
-			});
-		}
-
-		return configuredPackages;
-	}
-
-	async install(source: string, options?: { local?: boolean }): Promise<void> {
-		const parsed = this.parseSource(source);
-		const scope: SourceScope = options?.local ? "project" : "user";
-		this.assertProjectTrustedForScope(scope);
-		await this.withProgress("install", source, `Installing ${source}...`, async () => {
-			if (parsed.type === "npm") {
-				await this.installNpm(parsed, scope, false);
-				return;
-			}
-			if (parsed.type === "git") {
-				await this.installGit(parsed, scope);
-				return;
-			}
-			if (parsed.type === "local") {
-				const resolved = this.resolvePath(parsed.path);
-				if (!existsSync(resolved)) {
-					throw new Error(`Path does not exist: ${resolved}`);
-				}
-				return;
-			}
-			throw new Error(`Unsupported install source: ${source}`);
-		});
-	}
-
-	async installAndPersist(source: string, options?: { local?: boolean }): Promise<void> {
-		await this.install(source, options);
-		this.addSourceToSettings(source, options);
-	}
-
-	async remove(source: string, options?: { local?: boolean }): Promise<void> {
-		const parsed = this.parseSource(source);
-		const scope: SourceScope = options?.local ? "project" : "user";
-		this.assertProjectTrustedForScope(scope);
-		await this.withProgress("remove", source, `Removing ${source}...`, async () => {
-			if (parsed.type === "npm") {
-				await this.uninstallNpm(parsed, scope);
-				return;
-			}
-			if (parsed.type === "git") {
-				await this.removeGit(parsed, scope);
-				return;
-			}
-			if (parsed.type === "local") {
-				return;
-			}
-			throw new Error(`Unsupported remove source: ${source}`);
-		});
-	}
-
-	async removeAndPersist(source: string, options?: { local?: boolean }): Promise<boolean> {
-		await this.remove(source, options);
-		return this.removeSourceFromSettings(source, options);
-	}
-
-	async update(source?: string): Promise<void> {
-		const globalSettings = this.settingsManager.getGlobalSettings();
-		const projectSettings = this.settingsManager.getProjectSettings();
-		const identity = source ? this.getPackageIdentity(source) : undefined;
-		let matched = false;
-		const updateSources: ConfiguredUpdateSource[] = [];
-
-		for (const pkg of globalSettings.packages ?? []) {
-			const sourceStr = typeof pkg === "string" ? pkg : pkg.source;
-			if (identity && this.getPackageIdentity(sourceStr, "user") !== identity) continue;
-			matched = true;
-			updateSources.push({ source: sourceStr, scope: "user" });
-		}
-		for (const pkg of projectSettings.packages ?? []) {
-			const sourceStr = typeof pkg === "string" ? pkg : pkg.source;
-			if (identity && this.getPackageIdentity(sourceStr, "project") !== identity) continue;
-			matched = true;
-			updateSources.push({ source: sourceStr, scope: "project" });
-		}
-
-		if (source && !matched) {
-			throw new Error(
-				this.buildNoMatchingPackageMessage(source, [
-					...(globalSettings.packages ?? []),
-					...(projectSettings.packages ?? []),
-				]),
-			);
-		}
-
-		await this.updateConfiguredSources(updateSources);
-	}
-
-	private async updateConfiguredSources(sources: ConfiguredUpdateSource[]): Promise<void> {
-		if (sources.length === 0) {
-			return;
-		}
-
-		const npmCandidates: NpmUpdateTarget[] = [];
-		const gitCandidates: GitUpdateTarget[] = [];
-
-		for (const entry of sources) {
-			const parsed = this.parseSource(entry.source);
-			// Pinned npm versions are fixed. Pinned git refs are configured checkout targets,
-			// so include them to reconcile an existing clone when the configured ref changes.
-			if (parsed.type === "npm") {
-				if (!parsed.pinned) {
-					npmCandidates.push({ ...entry, parsed });
-				}
-			} else if (parsed.type === "git") {
-				gitCandidates.push({ ...entry, parsed });
-			}
-		}
-
-		const userNpmUpdates: NpmUpdateTarget[] = [];
-		const projectNpmUpdates: NpmUpdateTarget[] = [];
-		for (const entry of npmCandidates) {
-			if (entry.scope === "user") {
-				userNpmUpdates.push(entry);
-			} else {
-				projectNpmUpdates.push(entry);
-			}
-		}
-
-		const tasks: Promise<void>[] = [];
-		if (userNpmUpdates.length > 0) {
-			tasks.push(this.updateNpmBatch(userNpmUpdates, "user"));
-		}
-		if (projectNpmUpdates.length > 0) {
-			tasks.push(this.updateNpmBatch(projectNpmUpdates, "project"));
-		}
-		if (gitCandidates.length > 0) {
-			const gitTasks = gitCandidates.map(
-				(entry) => async () =>
-					this.withProgress("update", entry.source, `Updating ${entry.source}...`, async () => {
-						await this.updateGit(entry.parsed, entry.scope);
-					}),
-			);
-			tasks.push(this.runWithConcurrency(gitTasks, GIT_UPDATE_CONCURRENCY).then(() => {}));
-		}
-
-		await Promise.all(tasks);
-	}
-
-	private async updateNpmBatch(sources: NpmUpdateTarget[], scope: InstalledSourceScope): Promise<void> {
-		if (sources.length === 0) {
-			return;
-		}
-
-		const sourceLabel = sources.length === 1 ? sources[0].source : `${scope} npm packages`;
-		const message = sources.length === 1 ? `Updating ${sources[0].source}...` : `Updating ${scope} npm packages...`;
-		const specs = sources.map((entry) => (entry.parsed.version ? entry.parsed.spec : `${entry.parsed.name}@latest`));
-
-		await this.withProgress("update", sourceLabel, message, async () => {
-			await this.installNpmBatch(specs, scope);
-		});
-	}
-
-	private async installNpmBatch(specs: string[], scope: InstalledSourceScope): Promise<void> {
-		const installRoot = this.getNpmInstallRoot(scope, false);
-		this.ensureNpmProject(installRoot);
-		await this.runNpmCommand(this.getNpmInstallArgs(specs, installRoot));
-	}
-
-	private async resolvePackageSources(
-		sources: Array<{ pkg: PackageSource; scope: SourceScope }>,
-		accumulator: ResourceAccumulator,
-		onMissing?: (source: string) => Promise<MissingSourceAction>,
-	): Promise<void> {
-		for (const { pkg, scope } of sources) {
-			const sourceStr = typeof pkg === "string" ? pkg : pkg.source;
-			const filter = typeof pkg === "object" ? pkg : undefined;
-			const deltaBase = this.findAutoloadDeltaBase(pkg, scope, sources);
-			const resolvedSource = deltaBase?.source ?? sourceStr;
-			const resolvedScope = deltaBase?.scope ?? scope;
-			const parsed = this.parseSource(resolvedSource);
-			const metadata: PathMetadata = { source: sourceStr, scope, origin: "package" };
-
-			if (parsed.type === "local") {
-				const baseDir = this.getBaseDirForScope(resolvedScope);
-				this.resolveLocalExtensionSource(parsed, accumulator, filter, metadata, baseDir);
-				continue;
-			}
-
-			const installMissing = async (): Promise<boolean> => {
-				if (!onMissing) {
-					await this.installParsedSource(parsed, resolvedScope);
-					return true;
-				}
-				const action = await onMissing(resolvedSource);
-				if (action === "skip") return false;
-				if (action === "error") throw new Error(`Missing source: ${resolvedSource}`);
-				await this.installParsedSource(parsed, resolvedScope);
-				return true;
-			};
-
-			if (parsed.type === "npm") {
-				let installedPath = this.getNpmInstallPath(parsed, resolvedScope);
-				const needsInstall =
-					!existsSync(installedPath) || !(await this.installedNpmMatchesConfiguredVersion(parsed, installedPath));
-				if (needsInstall) {
-					const installed = await installMissing();
-					if (!installed) continue;
-					installedPath = this.getNpmInstallPath(parsed, resolvedScope);
-				}
-				metadata.baseDir = installedPath;
-				this.collectPackageResources(installedPath, accumulator, filter, metadata);
-				continue;
-			}
-
-			if (parsed.type === "git") {
-				const installedPath = this.getGitInstallPath(parsed, resolvedScope);
-				if (!existsSync(installedPath)) {
-					const installed = await installMissing();
-					if (!installed) continue;
-				} else if (resolvedScope === "temporary" && !parsed.pinned) {
-					await this.refreshTemporaryGitSource(parsed, resolvedSource);
-				}
-				metadata.baseDir = installedPath;
-				this.collectPackageResources(installedPath, accumulator, filter, metadata);
-			}
-		}
-	}
-
-	private findAutoloadDeltaBase(
-		pkg: PackageSource,
-		scope: SourceScope,
-		sources: Array<{ pkg: PackageSource; scope: SourceScope }>,
-	): { source: string; scope: SourceScope } | undefined {
-		if (scope !== "project" || typeof pkg !== "object" || pkg.autoload !== false) return undefined;
-		const identity = this.getPackageIdentity(pkg.source, scope);
-		const userEntry = sources.find(
-			(entry) =>
-				entry.scope === "user" &&
-				this.getPackageIdentity(this.getPackageSourceString(entry.pkg), "user") === identity,
-		);
-		return userEntry ? { source: this.getPackageSourceString(userEntry.pkg), scope: "user" } : undefined;
-	}
-
-	private resolveLocalExtensionSource(
-		source: LocalSource,
-		accumulator: ResourceAccumulator,
-		filter: PackageFilter | undefined,
-		metadata: PathMetadata,
-		baseDir: string,
-	): void {
-		const resolved = this.resolvePathFromBase(source.path, baseDir);
-		if (!existsSync(resolved)) {
-			return;
-		}
-
-		try {
-			const stats = statSync(resolved);
-			if (stats.isFile()) {
-				metadata.baseDir = dirname(resolved);
-				this.addResource(accumulator.extensions, resolved, metadata, true);
-				return;
-			}
-			if (stats.isDirectory()) {
-				metadata.baseDir = resolved;
-				const resources = this.collectPackageResources(resolved, accumulator, filter, metadata);
-				if (!resources) {
-					this.addResource(accumulator.extensions, resolved, metadata, true);
-				}
-			}
-		} catch {
-			return;
-		}
-	}
-
-	private async installParsedSource(parsed: ParsedSource, scope: SourceScope): Promise<void> {
-		if (parsed.type === "npm") {
-			await this.installNpm(parsed, scope, scope === "temporary");
-			return;
-		}
-		if (parsed.type === "git") {
-			await this.installGit(parsed, scope);
-			return;
-		}
-	}
-
-	private getPackageSourceString(pkg: PackageSource): string {
-		return typeof pkg === "string" ? pkg : pkg.source;
-	}
-
-	private getSourceMatchKeyForInput(source: string): string {
-		const parsed = this.parseSource(source);
-		if (parsed.type === "npm") {
-			return `npm:${parsed.name}`;
-		}
-		if (parsed.type === "git") {
-			return `git:${parsed.host}/${parsed.path}`;
-		}
-		return `local:${this.resolvePath(parsed.path)}`;
-	}
-
-	private getSourceMatchKeyForSettings(source: string, scope: SourceScope): string {
-		const parsed = this.parseSource(source);
-		if (parsed.type === "npm") {
-			return `npm:${parsed.name}`;
-		}
-		if (parsed.type === "git") {
-			return `git:${parsed.host}/${parsed.path}`;
-		}
-		const baseDir = this.getBaseDirForScope(scope);
-		return `local:${this.resolvePathFromBase(parsed.path, baseDir)}`;
-	}
-
-	private buildNoMatchingPackageMessage(source: string, configuredPackages: PackageSource[]): string {
-		const suggestion = this.findSuggestedConfiguredSource(source, configuredPackages);
-		if (!suggestion) {
-			return `No matching package found for ${source}`;
-		}
-		return `No matching package found for ${source}. Did you mean ${suggestion}?`;
-	}
-
-	private findSuggestedConfiguredSource(source: string, configuredPackages: PackageSource[]): string | undefined {
-		const trimmedSource = source.trim();
-		const suggestions = new Set<string>();
-
-		for (const pkg of configuredPackages) {
-			const sourceStr = this.getPackageSourceString(pkg);
-			const parsed = this.parseSource(sourceStr);
-			if (parsed.type === "npm") {
-				if (trimmedSource === parsed.name || trimmedSource === parsed.spec) {
-					suggestions.add(sourceStr);
-				}
-				continue;
-			}
-			if (parsed.type === "git") {
-				const shorthand = `${parsed.host}/${parsed.path}`;
-				const shorthandWithRef = parsed.ref ? `${shorthand}@${parsed.ref}` : undefined;
-				if (trimmedSource === shorthand || (shorthandWithRef && trimmedSource === shorthandWithRef)) {
-					suggestions.add(sourceStr);
-				}
-			}
-		}
-
-		return suggestions.values().next().value;
-	}
-
-	private packageSourcesMatch(existing: PackageSource, inputSource: string, scope: SourceScope): boolean {
-		const left = this.getSourceMatchKeyForSettings(this.getPackageSourceString(existing), scope);
-		const right = this.getSourceMatchKeyForInput(inputSource);
-		return left === right;
-	}
-
-	private normalizePackageSourceForSettings(source: string, scope: SourceScope): string {
-		const parsed = this.parseSource(source);
-		if (parsed.type !== "local") {
-			return source;
-		}
-		const baseDir = this.getBaseDirForScope(scope);
-		const resolved = this.resolvePath(parsed.path);
-		const rel = relative(baseDir, resolved);
-		return rel || ".";
-	}
-
-	private parseSource(source: string): ParsedSource {
-		if (source.startsWith("npm:")) {
-			const spec = source.slice("npm:".length).trim();
-			const { name, version } = this.parseNpmSpec(spec);
-			return {
-				type: "npm",
-				spec,
-				name,
-				version,
-				range: getNpmVersionRange(version),
-				pinned: isExactNpmVersion(version),
-			};
-		}
-
-		if (isLocalPath(source)) {
-			return { type: "local", path: source };
-		}
-
-		// Try parsing as git URL
-		const gitParsed = parseGitUrl(source);
-		if (gitParsed) {
-			return gitParsed;
-		}
-
-		return { type: "local", path: source };
-	}
-
-	private async installedNpmMatchesConfiguredVersion(source: NpmSource, installedPath: string): Promise<boolean> {
-		const installedVersion = this.getInstalledNpmVersion(installedPath);
-		if (!installedVersion) {
-			return false;
-		}
-		return source.range ? satisfies(installedVersion, source.range) : true;
-	}
-
-	private getInstalledNpmVersion(installedPath: string): string | undefined {
-		const packageJsonPath = join(installedPath, "package.json");
-		if (!existsSync(packageJsonPath)) return undefined;
-		try {
-			const content = readFileSync(packageJsonPath, "utf-8");
-			const pkg = JSON.parse(content) as { version?: string };
-			return pkg.version;
-		} catch {
-			return undefined;
-		}
-	}
-
-	private async getLocalGitUpdateTarget(
-		installedPath: string,
-	): Promise<{ ref: string; head: string; fetchArgs: string[] }> {
-		try {
-			const upstream = await this.runCommandCapture("git", ["rev-parse", "--abbrev-ref", "@{upstream}"], {
-				cwd: installedPath,
-				timeoutMs: NETWORK_TIMEOUT_MS,
-			});
-			const trimmedUpstream = upstream.trim();
-			if (!trimmedUpstream.startsWith("origin/")) {
-				throw new Error(`Unsupported upstream remote: ${trimmedUpstream}`);
-			}
-			const branch = trimmedUpstream.slice("origin/".length);
-			if (!branch) {
-				throw new Error("Missing upstream branch name");
-			}
-			const head = await this.runCommandCapture("git", ["rev-parse", "@{upstream}"], {
-				cwd: installedPath,
-				timeoutMs: NETWORK_TIMEOUT_MS,
-			});
-			return {
-				ref: "@{upstream}",
-				head,
-				fetchArgs: [
-					"fetch",
-					"--prune",
-					"--no-tags",
-					"origin",
-					`+refs/heads/${branch}:refs/remotes/origin/${branch}`,
-				],
-			};
-		} catch {
-			await this.runCommand("git", ["remote", "set-head", "origin", "-a"], { cwd: installedPath }).catch(() => {});
-			const head = await this.runCommandCapture("git", ["rev-parse", "origin/HEAD"], {
-				cwd: installedPath,
-				timeoutMs: NETWORK_TIMEOUT_MS,
-			});
-			const originHeadRef = await this.runCommandCapture("git", ["symbolic-ref", "refs/remotes/origin/HEAD"], {
-				cwd: installedPath,
-				timeoutMs: NETWORK_TIMEOUT_MS,
-			}).catch(() => "");
-			const branch = originHeadRef.trim().replace(/^refs\/remotes\/origin\//, "");
-			if (branch) {
-				return {
-					ref: "origin/HEAD",
-					head,
-					fetchArgs: [
-						"fetch",
-						"--prune",
-						"--no-tags",
-						"origin",
-						`+refs/heads/${branch}:refs/remotes/origin/${branch}`,
-					],
-				};
-			}
-			return {
-				ref: "origin/HEAD",
-				head,
-				fetchArgs: ["fetch", "--prune", "--no-tags", "origin", "+HEAD:refs/remotes/origin/HEAD"],
-			};
-		}
-	}
-
-	private async runWithConcurrency<T>(tasks: Array<() => Promise<T>>, limit: number): Promise<T[]> {
-		if (tasks.length === 0) {
-			return [];
-		}
-
-		const results: T[] = new Array(tasks.length);
-		let nextIndex = 0;
-		const workerCount = Math.max(1, Math.min(limit, tasks.length));
-
-		const worker = async () => {
-			while (true) {
-				const index = nextIndex;
-				nextIndex += 1;
-				if (index >= tasks.length) {
-					return;
-				}
-				results[index] = await tasks[index]();
-			}
-		};
-
-		await Promise.all(Array.from({ length: workerCount }, () => worker()));
-		return results;
-	}
-
-	/**
-	 * Get a unique identity for a package, ignoring version/ref.
-	 * Used to detect when the same package is in both global and project settings.
-	 * For git packages, uses normalized host/path to ensure SSH and HTTPS URLs
-	 * for the same repository are treated as identical.
-	 */
-	private getPackageIdentity(source: string, scope?: SourceScope): string {
-		const parsed = this.parseSource(source);
-		if (parsed.type === "npm") {
-			return `npm:${parsed.name}`;
-		}
-		if (parsed.type === "git") {
-			// Use host/path for identity to normalize SSH and HTTPS
-			return `git:${parsed.host}/${parsed.path}`;
-		}
-		if (scope) {
-			const baseDir = this.getBaseDirForScope(scope);
-			return `local:${this.resolvePathFromBase(parsed.path, baseDir)}`;
-		}
-		return `local:${this.resolvePath(parsed.path)}`;
-	}
-
-	/**
-	 * Dedupe packages: if same package identity appears in both global and project,
-	 * keep only the project one (project wins). A project entry with autoload=false
-	 * is a delta over the global entry, so both are kept (delta first).
-	 */
-	private dedupePackages(
-		packages: Array<{ pkg: PackageSource; scope: SourceScope }>,
-	): Array<{ pkg: PackageSource; scope: SourceScope }> {
-		const result: Array<{ pkg: PackageSource; scope: SourceScope }> = [];
-		const seen = new Map<string, number>();
-		for (const entry of packages) {
-			const identity = this.getPackageIdentity(this.getPackageSourceString(entry.pkg), entry.scope);
-			const index = seen.get(identity);
-			if (index === undefined) {
-				seen.set(identity, result.length);
-				result.push(entry);
-				continue;
-			}
-			const existing = result[index];
-			if (existing?.scope === "project" && entry.scope === "user") {
-				if (typeof existing.pkg === "object" && existing.pkg.autoload === false) result.push(entry);
-			} else if (entry.scope === "project") {
-				result[index] = entry;
-			}
-		}
-		return result;
-	}
-
-	private parseNpmSpec(spec: string): { name: string; version?: string } {
-		const match = spec.match(/^(@?[^@]+(?:\/[^@]+)?)(?:@(.+))?$/);
-		if (!match) {
-			return { name: spec };
-		}
-		const name = match[1] ?? spec;
-		const version = match[2];
-		return { name, version };
-	}
-
-	private assertProjectTrustedForScope(scope: SourceScope): void {
-		if (scope === "project" && !this.settingsManager.isProjectTrusted()) {
-			throw new Error("Project is not trusted; refusing to access project package storage");
-		}
-	}
-
-	private getNpmCommand(): { command: string; args: string[] } {
-		const configuredCommand = this.settingsManager.getNpmCommand();
-		if (!configuredCommand || configuredCommand.length === 0) {
-			return { command: "npm", args: [] };
-		}
-		const [command, ...args] = configuredCommand;
-		if (!command) {
-			throw new Error("Invalid npmCommand: first array entry must be a non-empty command");
-		}
-		return { command, args };
-	}
-
-	private getPackageManagerName(): string {
-		const npmCommand = this.getNpmCommand();
-		const commandParts = [npmCommand.command, ...npmCommand.args];
-		const separatorIndex = commandParts.lastIndexOf("--");
-		const packageManagerCommand = separatorIndex >= 0 ? commandParts[separatorIndex + 1] : npmCommand.command;
-		return packageManagerCommand ? basename(packageManagerCommand).replace(/\.(cmd|exe)$/i, "") : "";
-	}
-
-	private async runNpmCommand(args: string[], options?: { cwd?: string }): Promise<void> {
-		const npmCommand = this.getNpmCommand();
-		await this.runCommand(npmCommand.command, [...npmCommand.args, ...args], options);
-	}
-
-	private getGitDependencyInstallArgs(): string[] {
-		const configuredCommand = this.settingsManager.getNpmCommand();
-		if (configuredCommand && configuredCommand.length > 0) {
-			return ["install"];
-		}
-		return ["install", "--omit=dev"];
-	}
-
-	private runNpmCommandSync(args: string[]): string {
-		const npmCommand = this.getNpmCommand();
-		return this.runCommandSync(npmCommand.command, [...npmCommand.args, ...args]);
-	}
-
-	private getNpmInstallArgs(specs: string[], installRoot: string): string[] {
-		const packageManagerName = this.getPackageManagerName();
-		// Erweiterungen laufen im Agenten und lösen dessen APIs über die Loader-Aliase auf.
-		// Peer-Auflösung bei verwalteten Installationen abschalten, damit Paketmanager keine
-		// vom Host bereitgestellten Peers nachinstallieren.
-		if (packageManagerName === "bun") {
-			return ["install", ...specs, "--cwd", installRoot, "--omit=peer"];
-		}
-		if (packageManagerName === "pnpm") {
-			return [
-				"install",
-				...specs,
-				"--prefix",
-				installRoot,
-				"--config.auto-install-peers=false",
-				"--config.strict-peer-dependencies=false",
-				"--config.strict-dep-builds=false",
-			];
-		}
-		return ["install", ...specs, "--prefix", installRoot, "--legacy-peer-deps"];
-	}
-
-	private async installNpm(source: NpmSource, scope: SourceScope, temporary: boolean): Promise<void> {
-		const installRoot = this.getNpmInstallRoot(scope, temporary);
-		this.ensureNpmProject(installRoot);
-		await this.runNpmCommand(this.getNpmInstallArgs([source.spec], installRoot));
-	}
-
-	private async uninstallNpm(source: NpmSource, scope: SourceScope): Promise<void> {
-		const installRoot = this.getNpmInstallRoot(scope, false);
-		if (!existsSync(installRoot)) {
-			return;
-		}
-		const packageManagerName = this.getPackageManagerName();
-		if (packageManagerName === "bun") {
-			await this.runNpmCommand(["uninstall", source.name, "--cwd", installRoot]);
-			return;
-		}
-		const args = ["uninstall", source.name, "--prefix", installRoot];
-		if (packageManagerName !== "pnpm") {
-			args.push("--legacy-peer-deps");
-		}
-		await this.runNpmCommand(args);
-	}
-
-	private async installGit(source: GitSource, scope: SourceScope): Promise<void> {
-		const targetDir = this.getGitInstallPath(source, scope);
-		if (existsSync(targetDir)) {
-			if (source.ref) {
-				await this.ensureGitRef(targetDir, ["fetch", "origin", source.ref], "FETCH_HEAD");
-				return;
-			}
-			const target = await this.getLocalGitUpdateTarget(targetDir);
-			await this.ensureGitRef(targetDir, target.fetchArgs, target.ref);
-			return;
-		}
-		const gitRoot = this.getGitInstallRoot(scope);
-		if (gitRoot) {
-			this.ensureGitIgnore(gitRoot);
-		}
-		mkdirSync(dirname(targetDir), { recursive: true });
-
-		await this.runCommand("git", ["clone", source.repo, targetDir]);
-		if (source.ref) {
-			await this.runCommand("git", ["checkout", source.ref], { cwd: targetDir });
-		}
-		const packageJsonPath = join(targetDir, "package.json");
-		if (existsSync(packageJsonPath)) {
-			await this.runNpmCommand(this.getGitDependencyInstallArgs(), { cwd: targetDir });
-		}
-	}
-
-	private async updateGit(source: GitSource, scope: SourceScope): Promise<void> {
-		const targetDir = this.getGitInstallPath(source, scope);
-		if (!existsSync(targetDir)) {
-			await this.installGit(source, scope);
-			return;
-		}
-
-		if (source.ref) {
-			await this.ensureGitRef(targetDir, ["fetch", "origin", source.ref], "FETCH_HEAD");
-			return;
-		}
-
-		const target = await this.getLocalGitUpdateTarget(targetDir);
-		await this.ensureGitRef(targetDir, target.fetchArgs, target.ref);
-	}
-
-	private async ensureGitRef(targetDir: string, fetchArgs: string[], ref: string): Promise<void> {
-		// Fetch only the ref we will reset to, avoiding unrelated branch/tag noise.
-		await this.runCommand("git", fetchArgs, { cwd: targetDir });
-
-		const localHead = await this.runCommandCapture("git", ["rev-parse", "HEAD"], {
-			cwd: targetDir,
-			timeoutMs: NETWORK_TIMEOUT_MS,
-		});
-		const commitRef = `${ref}^{commit}`;
-		const targetHead = await this.runCommandCapture("git", ["rev-parse", commitRef], {
-			cwd: targetDir,
-			timeoutMs: NETWORK_TIMEOUT_MS,
-		});
-		if (localHead.trim() === targetHead.trim()) {
-			return;
-		}
-
-		await this.runCommand("git", ["reset", "--hard", commitRef], { cwd: targetDir });
-
-		// Clean untracked files (extensions should be pristine)
-		await this.runCommand("git", ["clean", "-fdx"], { cwd: targetDir });
-
-		const packageJsonPath = join(targetDir, "package.json");
-		if (existsSync(packageJsonPath)) {
-			await this.runNpmCommand(this.getGitDependencyInstallArgs(), { cwd: targetDir });
-		}
-	}
-
-	private async refreshTemporaryGitSource(source: GitSource, sourceStr: string): Promise<void> {
-		try {
-			await this.withProgress("pull", sourceStr, `Refreshing ${sourceStr}...`, async () => {
-				await this.updateGit(source, "temporary");
-			});
-		} catch {
-			// Keep cached temporary checkout if refresh fails.
-		}
-	}
-
-	private async removeGit(source: GitSource, scope: SourceScope): Promise<void> {
-		const targetDir = this.getGitInstallPath(source, scope);
-		if (!existsSync(targetDir)) return;
-		rmSync(targetDir, { recursive: true, force: true });
-		this.pruneEmptyGitParents(targetDir, this.getGitInstallRoot(scope));
-	}
-
-	private pruneEmptyGitParents(targetDir: string, installRoot: string | undefined): void {
-		if (!installRoot) return;
-		const resolvedRoot = resolve(installRoot);
-		let current = dirname(targetDir);
-		while (current.startsWith(resolvedRoot) && current !== resolvedRoot) {
-			if (!existsSync(current)) {
-				current = dirname(current);
-				continue;
-			}
-			const entries = readdirSync(current);
-			if (entries.length > 0) {
-				break;
-			}
-			try {
-				rmSync(current, { recursive: true, force: true });
-			} catch {
-				break;
-			}
-			current = dirname(current);
-		}
-	}
-
-	private ensureNpmProject(installRoot: string): void {
-		if (!existsSync(installRoot)) {
-			mkdirSync(installRoot, { recursive: true });
-		}
-		markPathIgnoredByCloudSync(installRoot);
-		this.ensureGitIgnore(installRoot);
-		const packageJsonPath = join(installRoot, "package.json");
-		if (!existsSync(packageJsonPath)) {
-			const pkgJson = { name: "agent-extensions", private: true };
-			writeFileSync(packageJsonPath, JSON.stringify(pkgJson, null, 2), "utf-8");
-		}
-	}
-
-	private ensureGitIgnore(dir: string): void {
-		if (!existsSync(dir)) {
-			mkdirSync(dir, { recursive: true });
-		}
-		const ignorePath = join(dir, ".gitignore");
-		if (!existsSync(ignorePath)) {
-			writeFileSync(ignorePath, "*\n!.gitignore\n", "utf-8");
-		}
-	}
-
-	private getNpmInstallRoot(scope: SourceScope, temporary: boolean): string {
-		if (temporary) {
-			return this.getTemporaryDir("npm");
-		}
-		if (scope === "project") {
-			this.assertProjectTrustedForScope(scope);
-			return join(this.cwd, CONFIG_DIR_NAME, "npm");
-		}
-		return join(this.agentDir, "npm");
-	}
-
-	private getGlobalNpmRoot(): string {
-		const npmCommand = this.getNpmCommand();
-		const commandKey = [npmCommand.command, ...npmCommand.args].join("\0");
-		if (this.globalNpmRoot && this.globalNpmRootCommandKey === commandKey) {
-			return this.globalNpmRoot;
-		}
-		if (this.getPackageManagerName() === "bun") {
-			const binDir = this.runNpmCommandSync(["pm", "bin", "-g"]).trim();
-			this.globalNpmRoot = join(dirname(binDir), "install", "global", "node_modules");
-		} else {
-			this.globalNpmRoot = this.runNpmCommandSync(["root", "-g"]).trim();
-		}
-		this.globalNpmRootCommandKey = commandKey;
-		return this.globalNpmRoot;
-	}
-
-	private getPnpmGlobalPackagePath(packageName: string): string | undefined {
-		if (this.getPackageManagerName() !== "pnpm") {
-			return undefined;
-		}
-
-		const output = this.runNpmCommandSync(["list", "-g", "--depth", "0", "--json"]);
-		const entries = JSON.parse(output) as Array<{ dependencies?: Record<string, { path?: string }> }>;
-		for (const entry of entries) {
-			const path = entry.dependencies?.[packageName]?.path;
-			if (path) return path;
-		}
-		return undefined;
-	}
-
-	private getManagedNpmInstallPath(source: NpmSource, scope: SourceScope): string {
-		if (scope === "temporary") {
-			return join(this.getTemporaryDir("npm"), "node_modules", source.name);
-		}
-		if (scope === "project") {
-			this.assertProjectTrustedForScope(scope);
-			return join(this.cwd, CONFIG_DIR_NAME, "npm", "node_modules", source.name);
-		}
-		return join(this.agentDir, "npm", "node_modules", source.name);
-	}
-
-	private getLegacyGlobalNpmInstallPath(source: NpmSource): string | undefined {
-		try {
-			return this.getPnpmGlobalPackagePath(source.name) ?? join(this.getGlobalNpmRoot(), source.name);
-		} catch {
-			return undefined;
-		}
-	}
-
-	private getNpmInstallPath(source: NpmSource, scope: SourceScope): string {
-		const managedPath = this.getManagedNpmInstallPath(source, scope);
-		if (scope !== "user" || existsSync(managedPath)) {
-			return managedPath;
-		}
-		const legacyPath = this.getLegacyGlobalNpmInstallPath(source);
-		return legacyPath && existsSync(legacyPath) ? legacyPath : managedPath;
-	}
-
-	private getGitInstallPath(source: GitSource, scope: SourceScope): string {
-		if (scope === "temporary") {
-			return this.getTemporaryDir(`git-${source.host}`, source.path);
-		}
-		const installRoot = this.getGitInstallRoot(scope);
-		if (!installRoot) {
-			throw new Error("Missing git install root");
-		}
-		return this.resolveManagedPath(installRoot, source.host, source.path);
-	}
-
-	private getGitInstallRoot(scope: SourceScope): string | undefined {
-		if (scope === "temporary") {
-			return undefined;
-		}
-		if (scope === "project") {
-			this.assertProjectTrustedForScope(scope);
-			return join(this.cwd, CONFIG_DIR_NAME, "git");
-		}
-		return join(this.agentDir, "git");
-	}
-
-	private getTemporaryDir(prefix: string, suffix?: string): string {
-		const root = this.resolveManagedPath(getExtensionTempFolder(this.agentDir), prefix);
-		const hash = createHash("sha256")
-			.update(`${prefix}-${suffix ?? ""}`)
-			.digest("hex")
-			.slice(0, 8);
-		return this.resolveManagedPath(root, hash, suffix ?? "");
-	}
-
-	private resolveManagedPath(root: string, ...parts: string[]): string {
-		const resolvedRoot = resolve(root);
-		const resolvedPath = resolve(resolvedRoot, ...parts);
-		if (resolvedPath !== resolvedRoot && !resolvedPath.startsWith(`${resolvedRoot}${sep}`)) {
-			throw new Error(`Refusing to use path outside package install root: ${resolvedPath}`);
-		}
-		return resolvedPath;
-	}
-
-	private getBaseDirForScope(scope: SourceScope): string {
-		if (scope === "project") {
-			this.assertProjectTrustedForScope(scope);
-			return join(this.cwd, CONFIG_DIR_NAME);
-		}
-		if (scope === "user") {
-			return this.agentDir;
-		}
-		return this.cwd;
-	}
-
-	private resolvePath(input: string): string {
-		return resolvePath(input, this.cwd, { homeDir: getHomeDir(), trim: true });
-	}
-
-	private resolvePathFromBase(input: string, baseDir: string): string {
-		return resolvePath(input, baseDir, { homeDir: getHomeDir(), trim: true });
-	}
-
-	private collectPackageResources(
-		packageRoot: string,
-		accumulator: ResourceAccumulator,
-		filter: PackageFilter | undefined,
-		metadata: PathMetadata,
-	): boolean {
-		if (filter) {
-			for (const resourceType of RESOURCE_TYPES) {
-				const patterns = filter[resourceType];
-				const target = this.getTargetMap(accumulator, resourceType);
-				if (filter.autoload === false) {
-					this.applyPackageDeltaFilter(packageRoot, patterns ?? [], resourceType, target, metadata);
-				} else if (patterns !== undefined) {
-					this.applyPackageFilter(packageRoot, patterns, resourceType, target, metadata);
-				} else {
-					this.collectDefaultResources(packageRoot, resourceType, target, metadata);
-				}
-			}
-			return true;
-		}
-
-		const manifest = this.readAgentManifest(packageRoot);
-		if (manifest) {
-			for (const resourceType of RESOURCE_TYPES) {
-				const entries = manifest[resourceType as keyof AgentManifest];
-				this.addManifestEntries(
-					entries,
-					packageRoot,
-					resourceType,
-					this.getTargetMap(accumulator, resourceType),
-					metadata,
-				);
-			}
-			return true;
-		}
-
-		let hasAnyDir = false;
-		for (const resourceType of RESOURCE_TYPES) {
-			const dir = join(packageRoot, resourceType);
-			if (existsSync(dir)) {
-				// Collect all files from the directory (all enabled by default)
-				const files = collectResourceFiles(dir, resourceType);
-				for (const f of files) {
-					this.addResource(this.getTargetMap(accumulator, resourceType), f, metadata, true);
-				}
-				hasAnyDir = true;
-			}
-		}
-		return hasAnyDir;
-	}
-
-	private collectDefaultResources(
-		packageRoot: string,
-		resourceType: ResourceType,
-		target: Map<string, { metadata: PathMetadata; enabled: boolean }>,
-		metadata: PathMetadata,
-	): void {
-		const manifest = this.readAgentManifest(packageRoot);
-		const entries = manifest?.[resourceType as keyof AgentManifest];
-		if (entries) {
-			this.addManifestEntries(entries, packageRoot, resourceType, target, metadata);
-			return;
-		}
-		const dir = join(packageRoot, resourceType);
-		if (existsSync(dir)) {
-			// Collect all files from the directory (all enabled by default)
-			const files = collectResourceFiles(dir, resourceType);
-			for (const f of files) {
-				this.addResource(target, f, metadata, true);
-			}
-		}
-	}
-
-	private applyPackageFilter(
-		packageRoot: string,
-		userPatterns: string[],
-		resourceType: ResourceType,
-		target: Map<string, { metadata: PathMetadata; enabled: boolean }>,
-		metadata: PathMetadata,
-	): void {
-		const { allFiles } = this.collectManifestFiles(packageRoot, resourceType);
-
-		if (userPatterns.length === 0) {
-			// Empty array explicitly disables all resources of this type
-			for (const f of allFiles) {
-				this.addResource(target, f, metadata, false);
-			}
-			return;
-		}
-
-		// Apply user patterns
-		const enabledByUser = applyPatterns(allFiles, userPatterns, packageRoot);
-
-		for (const f of allFiles) {
-			const enabled = enabledByUser.has(f);
-			this.addResource(target, f, metadata, enabled);
-		}
-	}
-
-	private applyPackageDeltaFilter(
-		packageRoot: string,
-		userPatterns: string[],
-		resourceType: ResourceType,
-		target: Map<string, { metadata: PathMetadata; enabled: boolean }>,
-		metadata: PathMetadata,
-	): void {
-		if (userPatterns.length === 0) {
-			return;
-		}
-
-		const { allFiles } = this.collectManifestFiles(packageRoot, resourceType);
-		const enabledByUser = applyAutoloadDisabledPatterns(allFiles, userPatterns, packageRoot);
-		for (const [filePath, enabled] of enabledByUser) {
-			this.addResource(target, filePath, metadata, enabled);
-		}
-	}
-
-	/**
-	 * Collect all files from a package for a resource type, applying manifest patterns.
-	 * Returns { allFiles, enabledByManifest } where enabledByManifest is the set of files
-	 * that pass the manifest's own patterns.
-	 */
-	private collectManifestFiles(
-		packageRoot: string,
-		resourceType: ResourceType,
-	): { allFiles: string[]; enabledByManifest: Set<string> } {
-		const manifest = this.readAgentManifest(packageRoot);
-		const entries = manifest?.[resourceType as keyof AgentManifest];
-		if (entries && entries.length > 0) {
-			const allFiles = this.collectFilesFromManifestEntries(entries, packageRoot, resourceType);
-			const manifestPatterns = entries.filter(isOverridePattern);
-			const enabledByManifest =
-				manifestPatterns.length > 0 ? applyPatterns(allFiles, manifestPatterns, packageRoot) : new Set(allFiles);
-			return { allFiles: Array.from(enabledByManifest), enabledByManifest };
-		}
-
-		const conventionDir = join(packageRoot, resourceType);
-		if (!existsSync(conventionDir)) {
-			return { allFiles: [], enabledByManifest: new Set() };
-		}
-		const allFiles = collectResourceFiles(conventionDir, resourceType);
-		return { allFiles, enabledByManifest: new Set(allFiles) };
-	}
-
-	private readAgentManifest(packageRoot: string): AgentManifest | null {
-		const packageJsonPath = join(packageRoot, "package.json");
-		if (!existsSync(packageJsonPath)) {
-			return null;
-		}
-
-		try {
-			const content = readFileSync(packageJsonPath, "utf-8");
-			const pkg = JSON.parse(content) as { agent?: AgentManifest };
-			return pkg.agent ?? null;
-		} catch {
-			return null;
-		}
-	}
-
-	private addManifestEntries(
-		entries: string[] | undefined,
-		root: string,
-		resourceType: ResourceType,
-		target: Map<string, { metadata: PathMetadata; enabled: boolean }>,
-		metadata: PathMetadata,
-	): void {
-		if (!entries) return;
-
-		const allFiles = this.collectFilesFromManifestEntries(entries, root, resourceType);
-		const patterns = entries.filter(isOverridePattern);
-		const enabledPaths = applyPatterns(allFiles, patterns, root);
-
-		for (const f of allFiles) {
-			if (enabledPaths.has(f)) {
-				this.addResource(target, f, metadata, true);
-			}
-		}
-	}
-
-	private collectFilesFromManifestEntries(entries: string[], root: string, resourceType: ResourceType): string[] {
-		const sourceEntries = entries.filter((entry) => !isOverridePattern(entry));
-		const resolved = sourceEntries.flatMap((entry) => {
-			if (!hasGlobPattern(entry)) {
-				return [resolve(root, entry)];
-			}
-
-			return globSync(entry, {
-				cwd: root,
-				absolute: true,
-				dot: false,
-				nodir: false,
-			}).map((match) => resolve(match));
-		});
-		return this.collectFilesFromPaths(resolved, resourceType);
-	}
-
-	private resolveLocalEntries(
-		entries: string[],
-		resourceType: ResourceType,
-		target: Map<string, { metadata: PathMetadata; enabled: boolean }>,
-		metadata: PathMetadata,
-		baseDir: string,
-	): void {
-		if (entries.length === 0) return;
-
-		// Collect all files from plain entries (non-pattern entries)
-		const { plain, patterns } = splitPatterns(entries);
-		const resolvedPlain = plain.map((p) => this.resolvePathFromBase(p, baseDir));
-		const allFiles = this.collectFilesFromPaths(resolvedPlain, resourceType);
-
-		// Determine which files are enabled based on patterns
-		const enabledPaths = applyPatterns(allFiles, patterns, baseDir);
-
-		// Add all files with their enabled state
-		for (const f of allFiles) {
-			this.addResource(target, f, metadata, enabledPaths.has(f));
-		}
-	}
-
-	private addAutoDiscoveredResources(
-		accumulator: ResourceAccumulator,
-		globalSettings: ReturnType<SettingsManager["getGlobalSettings"]>,
-		projectSettings: ReturnType<SettingsManager["getProjectSettings"]>,
-		globalBaseDir: string,
-		projectBaseDir: string,
-	): void {
-		const userMetadata: PathMetadata = {
-			source: "auto",
-			scope: "user",
-			origin: "top-level",
-			baseDir: globalBaseDir,
-		};
-		const projectMetadata: PathMetadata = {
-			source: "auto",
-			scope: "project",
-			origin: "top-level",
-			baseDir: projectBaseDir,
-		};
-
-		const userOverrides = {
-			extensions: (globalSettings.extensions ?? []) as string[],
-			skills: (globalSettings.skills ?? []) as string[],
-			prompts: (globalSettings.prompts ?? []) as string[],
-			themes: (globalSettings.themes ?? []) as string[],
-		};
-		const projectOverrides = {
-			extensions: (projectSettings.extensions ?? []) as string[],
-			skills: (projectSettings.skills ?? []) as string[],
-			prompts: (projectSettings.prompts ?? []) as string[],
-			themes: (projectSettings.themes ?? []) as string[],
-		};
-
-		const userDirs = {
-			extensions: join(globalBaseDir, "extensions"),
-			skills: join(globalBaseDir, "skills"),
-			prompts: join(globalBaseDir, "prompts"),
-			themes: join(globalBaseDir, "themes"),
-		};
-		const projectDirs = {
-			extensions: join(projectBaseDir, "extensions"),
-			skills: join(projectBaseDir, "skills"),
-			prompts: join(projectBaseDir, "prompts"),
-			themes: join(projectBaseDir, "themes"),
-		};
-		const userAgentsSkillsDir = join(getHomeDir(), ".agents", "skills");
-		const projectTrusted = this.settingsManager.isProjectTrusted();
-		const projectAgentsSkillDirs = projectTrusted
-			? collectAncestorAgentsSkillDirs(this.cwd).filter((dir) => resolve(dir) !== resolve(userAgentsSkillsDir))
-			: [];
-
-		const addResources = (
-			resourceType: ResourceType,
-			paths: string[],
-			metadata: PathMetadata,
-			overrides: string[],
-			baseDir: string,
-		) => {
-			const target = this.getTargetMap(accumulator, resourceType);
-			for (const path of paths) {
-				const enabled = isEnabledByOverrides(path, overrides, baseDir);
-				this.addResource(target, path, metadata, enabled);
-			}
-		};
-
-		if (projectTrusted) {
-			// Project extensions from the project config dir
-			addResources(
-				"extensions",
-				collectAutoExtensionEntries(projectDirs.extensions),
-				projectMetadata,
-				projectOverrides.extensions,
-				projectBaseDir,
-			);
-
-			// Project skills from the project config dir
-			addResources(
-				"skills",
-				collectAutoSkillEntries(projectDirs.skills, "native"),
-				projectMetadata,
-				projectOverrides.skills,
-				projectBaseDir,
-			);
-		}
-
-		// Project skills from .agents/ (each with its own baseDir)
-		for (const agentsSkillsDir of projectAgentsSkillDirs) {
-			const agentsBaseDir = dirname(agentsSkillsDir); // the .agents directory
-			const agentsMetadata: PathMetadata = {
-				...projectMetadata,
-				baseDir: agentsBaseDir,
-			};
-			addResources(
-				"skills",
-				collectAutoSkillEntries(agentsSkillsDir, "agents"),
-				agentsMetadata,
-				projectOverrides.skills,
-				agentsBaseDir,
-			);
-		}
-
-		if (projectTrusted) {
-			addResources(
-				"prompts",
-				collectAutoPromptEntries(projectDirs.prompts),
-				projectMetadata,
-				projectOverrides.prompts,
-				projectBaseDir,
-			);
-			addResources(
-				"themes",
-				collectAutoThemeEntries(projectDirs.themes),
-				projectMetadata,
-				projectOverrides.themes,
-				projectBaseDir,
-			);
-		}
-
-		// User extensions from the user config dir
-		addResources(
-			"extensions",
-			collectAutoExtensionEntries(userDirs.extensions),
-			userMetadata,
-			userOverrides.extensions,
-			globalBaseDir,
-		);
-
-		// User skills from the user config dir
-		addResources(
-			"skills",
-			collectAutoSkillEntries(userDirs.skills, "native"),
-			userMetadata,
-			userOverrides.skills,
-			globalBaseDir,
-		);
-
-		// User skills from ~/.agents/ (with its own baseDir)
-		const userAgentsBaseDir = dirname(userAgentsSkillsDir);
-		const userAgentsMetadata: PathMetadata = {
-			...userMetadata,
-			baseDir: userAgentsBaseDir,
-		};
-		addResources(
-			"skills",
-			collectAutoSkillEntries(userAgentsSkillsDir, "agents"),
-			userAgentsMetadata,
-			userOverrides.skills,
-			userAgentsBaseDir,
-		);
-
-		addResources(
-			"prompts",
-			collectAutoPromptEntries(userDirs.prompts),
-			userMetadata,
-			userOverrides.prompts,
-			globalBaseDir,
-		);
-		addResources(
-			"themes",
-			collectAutoThemeEntries(userDirs.themes),
-			userMetadata,
-			userOverrides.themes,
-			globalBaseDir,
-		);
-	}
-
-	private collectFilesFromPaths(paths: string[], resourceType: ResourceType): string[] {
-		const files: string[] = [];
-		for (const p of paths) {
-			if (!existsSync(p)) continue;
-
-			try {
-				const stats = statSync(p);
-				if (stats.isFile()) {
-					files.push(p);
-				} else if (stats.isDirectory()) {
-					files.push(...collectResourceFiles(p, resourceType));
-				}
-			} catch {
-				// Ignore errors
-			}
-		}
-		return files;
-	}
-
-	private getTargetMap(
-		accumulator: ResourceAccumulator,
-		resourceType: ResourceType,
-	): Map<string, { metadata: PathMetadata; enabled: boolean }> {
-		switch (resourceType) {
-			case "extensions":
-				return accumulator.extensions;
-			case "skills":
-				return accumulator.skills;
-			case "prompts":
-				return accumulator.prompts;
-			case "themes":
-				return accumulator.themes;
-			default:
-				throw new Error(`Unknown resource type: ${resourceType}`);
-		}
-	}
-
-	private addResource(
-		map: Map<string, { metadata: PathMetadata; enabled: boolean }>,
-		path: string,
-		metadata: PathMetadata,
-		enabled: boolean,
-	): void {
-		if (!path) return;
-		if (!map.has(path)) {
-			map.set(path, { metadata, enabled });
-		}
-	}
-
-	private createAccumulator(): ResourceAccumulator {
-		return {
-			extensions: new Map(),
-			skills: new Map(),
-			prompts: new Map(),
-			themes: new Map(),
-		};
-	}
-
-	private toResolvedPaths(accumulator: ResourceAccumulator): ResolvedPaths {
-		const mapToResolved = (
-			entries: Map<string, { metadata: PathMetadata; enabled: boolean }>,
-		): ResolvedResource[] => {
-			const resolved = Array.from(entries.entries()).map(([path, { metadata, enabled }]) => ({
-				path,
-				enabled,
-				metadata,
-			}));
-			resolved.sort((a, b) => resourcePrecedenceRank(a.metadata) - resourcePrecedenceRank(b.metadata));
-
-			const seen = new Set<string>();
-			return resolved.filter((entry) => {
-				const canonicalPath = canonicalizePath(entry.path);
-				if (seen.has(canonicalPath)) return false;
-				seen.add(canonicalPath);
-				return true;
-			});
-		};
-
-		return {
-			extensions: mapToResolved(accumulator.extensions),
-			skills: mapToResolved(accumulator.skills),
-			prompts: mapToResolved(accumulator.prompts),
-			themes: mapToResolved(accumulator.themes),
-		};
-	}
-
-	private spawnCommand(command: string, args: string[], options?: { cwd?: string }): ChildProcess {
-		const env = getEnv();
-		return spawnProcess(command, args, {
-			cwd: options?.cwd,
-			stdio: isStdoutTakenOver() ? ["ignore", 2, 2] : "inherit",
-			env,
-		});
-	}
-
-	private spawnCaptureCommand(
-		command: string,
-		args: string[],
-		options?: { cwd?: string; env?: Record<string, string> },
-	): ChildProcessByStdio<null, Readable, Readable> {
-		const baseEnv = getEnv();
-		const env = options?.env ? { ...baseEnv, ...options.env } : baseEnv;
-		return spawnProcess(command, args, {
-			cwd: options?.cwd,
-			stdio: ["ignore", "pipe", "pipe"],
-			env,
-		});
-	}
-
-	private runCommandCapture(
-		command: string,
-		args: string[],
-		options?: { cwd?: string; timeoutMs?: number; env?: Record<string, string> },
-	): Promise<string> {
-		return new Promise((resolvePromise, reject) => {
-			const child = this.spawnCaptureCommand(command, args, options);
-			let stdout = "";
-			let stderr = "";
-			let timedOut = false;
-			const timeout =
-				typeof options?.timeoutMs === "number"
-					? setTimeout(() => {
-							timedOut = true;
-							child.kill();
-						}, options.timeoutMs)
-					: undefined;
-
-			child.stdout?.on("data", (data) => {
-				stdout += data.toString();
-			});
-			child.stderr?.on("data", (data) => {
-				stderr += data.toString();
-			});
-			child.once("error", (error) => {
-				if (timeout) clearTimeout(timeout);
-				reject(error);
-			});
-			child.once("close", (code, signal) => {
-				if (timeout) clearTimeout(timeout);
-				if (timedOut) {
-					reject(new Error(`${command} ${args.join(" ")} timed out after ${options?.timeoutMs}ms`));
-					return;
-				}
-				if (code === 0) {
-					resolvePromise(stdout.trim());
-					return;
-				}
-				const exitStatus = code === null ? `signal ${signal ?? "unknown"}` : `code ${code}`;
-				reject(new Error(`${command} ${args.join(" ")} failed with ${exitStatus}: ${stderr || stdout}`));
-			});
-		});
-	}
-
-	private runCommand(command: string, args: string[], options?: { cwd?: string }): Promise<void> {
-		return new Promise((resolvePromise, reject) => {
-			const child = this.spawnCommand(command, args, options);
-			child.on("error", reject);
-			child.on("exit", (code) => {
-				if (code === 0) {
-					resolvePromise();
-				} else {
-					reject(new Error(`${command} ${args.join(" ")} failed with code ${code}`));
-				}
-			});
-		});
-	}
-
-	private runCommandSync(command: string, args: string[]): string {
-		const env = getEnv();
-		const result = spawnProcessSync(command, args, {
-			stdio: ["ignore", "pipe", "pipe"],
-			encoding: "utf-8",
-			env,
-		});
-		if (result.error || result.status !== 0) {
-			throw new Error(
-				`Failed to run ${command} ${args.join(" ")}: ${result.error?.message || result.stderr || result.stdout}`,
-			);
-		}
-		return (result.stdout || result.stderr || "").trim();
-	}
-}