pi-oxidized 0.1.1

package/.references/pi/packages/coding-agent/src/core/package-manager.ts

@@ -0,0 +1,2650 @@
+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 { maxSatisfying, rcompare, 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 UPDATE_CHECK_CONCURRENCY = 4;
+const GIT_UPDATE_CONCURRENCY = 4;
+
+function isOfflineModeEnabled(): boolean {
+	const value = process.env.PI_OFFLINE;
+	if (!value) return false;
+	return value === "1" || value.toLowerCase() === "true" || value.toLowerCase() === "yes";
+}
+
+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 PackageUpdate {
+	source: string;
+	displayName: string;
+	type: "npm" | "git";
+	scope: Exclude<SourceScope, "temporary">;
+}
+
+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 PiManifest {
+	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 ? `${relPath}/` : relPath;
+			if (ig.ignores(ignorePath)) continue;
+
+			if (isDir) {
+				files.push(...collectFiles(fullPath, filePattern, skipNodeModules, ig, root));
+			} else if (isFile && filePattern.test(entry.name)) {
+				files.push(fullPath);
+			}
+		}
+	} catch {
+		// Ignore errors
+	}
+
+	return files;
+}
+
+type SkillDiscoveryMode = "pi" | "agents";
+
+function collectSkillEntries(
+	dir: string,
+	mode: SkillDiscoveryMode,
+	ignoreMatcher?: IgnoreMatcher,
+	rootDir?: string,
+): string[] {
+	const entries: string[] = [];
+	if (!existsSync(dir)) return entries;
+
+	const root = rootDir ?? dir;
+	const ig = ignoreMatcher ?? ignore();
+	addIgnoreRules(ig, dir, root);
+
+	try {
+		const dirEntries = readdirSync(dir, { withFileTypes: true });
+
+		for (const entry of dirEntries) {
+			if (entry.name !== "SKILL.md") {
+				continue;
+			}
+
+			const fullPath = join(dir, entry.name);
+			let isFile = entry.isFile();
+			if (entry.isSymbolicLink()) {
+				try {
+					isFile = statSync(fullPath).isFile();
+				} catch {
+					continue;
+				}
+			}
+
+			const relPath = toPosixPath(relative(root, fullPath));
+			if (isFile && !ig.ignores(relPath)) {
+				entries.push(fullPath);
+				return entries;
+			}
+		}
+
+		for (const entry of dirEntries) {
+			if (entry.name.startsWith(".")) continue;
+			if (entry.name === "node_modules") continue;
+
+			const fullPath = join(dir, entry.name);
+			let isDir = entry.isDirectory();
+			let isFile = entry.isFile();
+
+			if (entry.isSymbolicLink()) {
+				try {
+					const stats = statSync(fullPath);
+					isDir = stats.isDirectory();
+					isFile = stats.isFile();
+				} catch {
+					continue;
+				}
+			}
+
+			const relPath = toPosixPath(relative(root, fullPath));
+			if (mode === "pi" && dir === root && isFile && entry.name.endsWith(".md") && !ig.ignores(relPath)) {
+				entries.push(fullPath);
+				continue;
+			}
+
+			if (!isDir) continue;
+			if (ig.ignores(`${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 readPiManifestFile(packageJsonPath: string): PiManifest | null {
+	try {
+		const content = readFileSync(packageJsonPath, "utf-8");
+		const pkg = JSON.parse(content) as { pi?: PiManifest };
+		return pkg.pi ?? null;
+	} catch {
+		return null;
+	}
+}
+
+function resolveExtensionEntries(dir: string): string[] | null {
+	const packageJsonPath = join(dir, "package.json");
+	if (existsSync(packageJsonPath)) {
+		const manifest = readPiManifestFile(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, "pi");
+	}
+	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 (isOfflineModeEnabled() || 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 npmCheckTasks = npmCandidates.map((entry) => async () => ({
+			entry,
+			shouldUpdate: await this.shouldUpdateNpmSource(entry.parsed, entry.scope),
+		}));
+		const npmCheckResults = await this.runWithConcurrency(npmCheckTasks, UPDATE_CHECK_CONCURRENCY);
+		const userNpmUpdates: NpmUpdateTarget[] = [];
+		const projectNpmUpdates: NpmUpdateTarget[] = [];
+		for (const result of npmCheckResults) {
+			if (!result.shouldUpdate) {
+				continue;
+			}
+			if (result.entry.scope === "user") {
+				userNpmUpdates.push(result.entry);
+			} else {
+				projectNpmUpdates.push(result.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 ${entry.source}...`, async () => {
+						await this.updateGit(entry.parsed, entry.scope);
+					}),
+			);
+			tasks.push(this.runWithConcurrency(gitTasks, GIT_UPDATE_CONCURRENCY).then(() => {}));
+		}
+
+		await Promise.all(tasks);
+	}
+
+	private async shouldUpdateNpmSource(source: NpmSource, scope: InstalledSourceScope): Promise<boolean> {
+		const installedPath = this.getManagedNpmInstallPath(source, scope);
+		const installedVersion = existsSync(installedPath) ? this.getInstalledNpmVersion(installedPath) : undefined;
+		if (!installedVersion) {
+			return true;
+		}
+
+		try {
+			const targetVersion = await this.getLatestNpmVersion(source.version ? source.spec : source.name, source.range);
+			return targetVersion !== installedVersion;
+		} catch {
+			// Preserve existing update behavior when version lookup fails.
+			return true;
+		}
+	}
+
+	private async updateNpmBatch(sources: NpmUpdateTarget[], scope: InstalledSourceScope): Promise<void> {
+		if (sources.length === 0) {
+			return;
+		}
+
+		const sourceLabel = sources.length === 1 ? sources[0].source : `${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));
+	}
+
+	async checkForAvailableUpdates(): Promise<PackageUpdate[]> {
+		if (isOfflineModeEnabled()) {
+			return [];
+		}
+
+		const globalSettings = this.settingsManager.getGlobalSettings();
+		const projectSettings = this.settingsManager.getProjectSettings();
+		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" });
+		}
+
+		const packageSources = this.dedupePackages(allPackages);
+		const checks = packageSources
+			.filter(
+				(entry): entry is { pkg: PackageSource; scope: Exclude<SourceScope, "temporary"> } =>
+					entry.scope !== "temporary",
+			)
+			.map((entry) => async (): Promise<PackageUpdate | undefined> => {
+				const source = typeof entry.pkg === "string" ? entry.pkg : entry.pkg.source;
+				const parsed = this.parseSource(source);
+				if (parsed.type === "local" || parsed.pinned) {
+					return undefined;
+				}
+
+				if (parsed.type === "npm") {
+					const installedPath = this.getNpmInstallPath(parsed, entry.scope);
+					if (!existsSync(installedPath)) {
+						return undefined;
+					}
+					const hasUpdate = await this.npmHasAvailableUpdate(parsed, installedPath);
+					if (!hasUpdate) {
+						return undefined;
+					}
+					return {
+						source,
+						displayName: parsed.name,
+						type: "npm",
+						scope: entry.scope,
+					};
+				}
+
+				const installedPath = this.getGitInstallPath(parsed, entry.scope);
+				if (!existsSync(installedPath)) {
+					return undefined;
+				}
+				const hasUpdate = await this.gitHasAvailableUpdate(installedPath);
+				if (!hasUpdate) {
+					return undefined;
+				}
+				return {
+					source,
+					displayName: `${parsed.host}/${parsed.path}`,
+					type: "git",
+					scope: entry.scope,
+				};
+			});
+
+		const results = await this.runWithConcurrency(checks, UPDATE_CHECK_CONCURRENCY);
+		return results.filter((result): result is PackageUpdate => result !== undefined);
+	}
+
+	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 (isOfflineModeEnabled()) return false;
+				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 && !isOfflineModeEnabled()) {
+					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 async npmHasAvailableUpdate(source: NpmSource, installedPath: string): Promise<boolean> {
+		if (isOfflineModeEnabled()) {
+			return false;
+		}
+
+		const installedVersion = this.getInstalledNpmVersion(installedPath);
+		if (!installedVersion) {
+			return false;
+		}
+
+		try {
+			const targetVersion = await this.getLatestNpmVersion(source.version ? source.spec : source.name, source.range);
+			return targetVersion !== installedVersion;
+		} catch {
+			return false;
+		}
+	}
+
+	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 getLatestNpmVersion(packageSpec: string, range?: string): Promise<string> {
+		const npmCommand = this.getNpmCommand();
+		const stdout = await this.runCommandCapture(
+			npmCommand.command,
+			[...npmCommand.args, "view", packageSpec, "version", "--json"],
+			{ cwd: this.cwd, timeoutMs: NETWORK_TIMEOUT_MS },
+		);
+		const raw = stdout.trim();
+		if (!raw) throw new Error("Empty response from npm view");
+		const parsed = JSON.parse(raw) as unknown;
+		if (typeof parsed === "string") {
+			return parsed;
+		}
+		if (Array.isArray(parsed)) {
+			const versions = parsed.filter((value): value is string => typeof value === "string" && value.length > 0);
+			const latest = range ? maxSatisfying(versions, range) : [...versions].sort(rcompare)[0];
+			if (latest) return latest;
+		}
+		throw new Error("Unexpected response from npm view");
+	}
+
+	private async gitHasAvailableUpdate(installedPath: string): Promise<boolean> {
+		if (isOfflineModeEnabled()) {
+			return false;
+		}
+
+		try {
+			const localHead = await this.runCommandCapture("git", ["rev-parse", "HEAD"], {
+				cwd: installedPath,
+				timeoutMs: NETWORK_TIMEOUT_MS,
+			});
+			const remoteHead = await this.getRemoteGitHead(installedPath);
+			return localHead.trim() !== remoteHead.trim();
+		} catch {
+			return false;
+		}
+	}
+
+	private async getRemoteGitHead(installedPath: string): Promise<string> {
+		const upstreamRef = await this.getGitUpstreamRef(installedPath);
+		if (upstreamRef) {
+			const remoteHead = await this.runGitRemoteCommand(installedPath, ["ls-remote", "origin", upstreamRef]);
+			const match = remoteHead.match(/^([0-9a-f]{40})\s+/m);
+			if (match?.[1]) {
+				return match[1];
+			}
+		}
+
+		const remoteHead = await this.runGitRemoteCommand(installedPath, ["ls-remote", "origin", "HEAD"]);
+		const match = remoteHead.match(/^([0-9a-f]{40})\s+HEAD$/m);
+		if (!match?.[1]) {
+			throw new Error("Failed to determine remote HEAD");
+		}
+		return match[1];
+	}
+
+	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/${branch}`,
+					],
+				};
+			}
+			return {
+				ref: "origin/HEAD",
+				head,
+				fetchArgs: ["fetch", "--prune", "--no-tags", "origin", "+HEAD:refs/remotes/origin/HEAD"],
+			};
+		}
+	}
+
+	private async getGitUpstreamRef(installedPath: string): Promise<string | undefined> {
+		try {
+			const upstream = await this.runCommandCapture("git", ["rev-parse", "--abbrev-ref", "@{upstream}"], {
+				cwd: installedPath,
+				timeoutMs: NETWORK_TIMEOUT_MS,
+			});
+			const trimmed = upstream.trim();
+			if (!trimmed.startsWith("origin/")) {
+				return undefined;
+			}
+			const branch = trimmed.slice("origin/".length);
+			return branch ? `refs/heads/${branch}` : undefined;
+		} catch {
+			return undefined;
+		}
+	}
+
+	private runGitRemoteCommand(installedPath: string, args: string[]): Promise<string> {
+		return this.runCommandCapture("git", args, {
+			cwd: installedPath,
+			timeoutMs: NETWORK_TIMEOUT_MS,
+			env: {
+				GIT_TERMINAL_PROMPT: "0",
+			},
+		});
+	}
+
+	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();
+		// Extension packages run inside pi and resolve pi APIs through loader aliases/virtual modules.
+		// Disable peer dependency resolution for managed installs (npm's --legacy-peer-deps, and
+		// equivalent bun/pnpm settings) so package managers do not install or solve host-provided
+		// @earendil-works/pi-* peers. Stale auto-installed pi peers can otherwise block updates.
+		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> {
+		if (isOfflineModeEnabled()) {
+			return;
+		}
+		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: "pi-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.readPiManifest(packageRoot);
+		if (manifest) {
+			for (const resourceType of RESOURCE_TYPES) {
+				const entries = manifest[resourceType as keyof PiManifest];
+				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.readPiManifest(packageRoot);
+		const entries = manifest?.[resourceType as keyof PiManifest];
+		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.readPiManifest(packageRoot);
+		const entries = manifest?.[resourceType as keyof PiManifest];
+		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 readPiManifest(packageRoot: string): PiManifest | 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 { pi?: PiManifest };
+			return pkg.pi ?? 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 .pi/
+			addResources(
+				"extensions",
+				collectAutoExtensionEntries(projectDirs.extensions),
+				projectMetadata,
+				projectOverrides.extensions,
+				projectBaseDir,
+			);
+
+			// Project skills from .pi/
+			addResources(
+				"skills",
+				collectAutoSkillEntries(projectDirs.skills, "pi"),
+				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 ~/.pi/agent/
+		addResources(
+			"extensions",
+			collectAutoExtensionEntries(userDirs.extensions),
+			userMetadata,
+			userOverrides.extensions,
+			globalBaseDir,
+		);
+
+		// User skills from ~/.pi/agent/
+		addResources(
+			"skills",
+			collectAutoSkillEntries(userDirs.skills, "pi"),
+			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();
+	}
+}