@bastani/atomic 0.7.17 → 0.8.0

package/dist/core/package-manager.js

@@ -0,0 +1,1970 @@
+import { spawn, spawnSync } from "node:child_process";
+import { createHash } from "node:crypto";
+import { existsSync, mkdirSync, readdirSync, readFileSync, rmSync, statSync, writeFileSync } from "node:fs";
+import { homedir, tmpdir } from "node:os";
+function getEnv() {
+    if (process.platform !== "linux" || Object.keys(process.env).length > 0) {
+        return process.env;
+    }
+    try {
+        const data = readFileSync("/proc/self/environ", "utf-8");
+        const env = {};
+        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 { globSync } from "glob";
+import ignore from "ignore";
+import { minimatch } from "minimatch";
+import { CONFIG_DIR_NAME, ENV_OFFLINE } from "../config.js";
+import { shouldUseWindowsShell } from "../utils/child-process.js";
+import { parseGitUrl } from "../utils/git.js";
+import { canonicalizePath, isLocalPath } from "../utils/paths.js";
+import { isStdoutTakenOver } from "./output-guard.js";
+const NETWORK_TIMEOUT_MS = 10000;
+const UPDATE_CHECK_CONCURRENCY = 4;
+const GIT_UPDATE_CONCURRENCY = 4;
+function isOfflineModeEnabled() {
+    const value = process.env[ENV_OFFLINE];
+    if (!value)
+        return false;
+    return value === "1" || value.toLowerCase() === "true" || value.toLowerCase() === "yes";
+}
+/**
+ * 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) {
+    if (m.origin === "package")
+        return 4;
+    const scopeBase = m.scope === "project" ? 0 : 2;
+    return scopeBase + (m.source === "local" ? 0 : 1);
+}
+const RESOURCE_TYPES = ["extensions", "skills", "prompts", "themes"];
+const FILE_PATTERNS = {
+    extensions: /\.(ts|js)$/,
+    skills: /\.md$/,
+    prompts: /\.md$/,
+    themes: /\.json$/,
+};
+const IGNORE_FILE_NAMES = [".gitignore", ".ignore", ".fdignore"];
+function toPosixPath(p) {
+    return p.split(sep).join("/");
+}
+function getHomeDir() {
+    return process.env.HOME || homedir();
+}
+function prefixIgnorePattern(line, prefix) {
+    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 ? `!${prefixed}` : prefixed;
+}
+function addIgnoreRules(ig, dir, rootDir) {
+    const relativeDir = relative(rootDir, dir);
+    const prefix = relativeDir ? `${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) => Boolean(line));
+            if (patterns.length > 0) {
+                ig.add(patterns);
+            }
+        }
+        catch { }
+    }
+}
+function isPattern(s) {
+    return s.startsWith("!") || s.startsWith("+") || s.startsWith("-") || s.includes("*") || s.includes("?");
+}
+function isOverridePattern(s) {
+    return s.startsWith("!") || s.startsWith("+") || s.startsWith("-");
+}
+function hasGlobPattern(s) {
+    return s.includes("*") || s.includes("?");
+}
+function splitPatterns(entries) {
+    const plain = [];
+    const patterns = [];
+    for (const entry of entries) {
+        if (isPattern(entry)) {
+            patterns.push(entry);
+        }
+        else {
+            plain.push(entry);
+        }
+    }
+    return { plain, patterns };
+}
+function collectFiles(dir, filePattern, skipNodeModules = true, ignoreMatcher, rootDir) {
+    const files = [];
+    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;
+}
+function collectSkillEntries(dir, mode, ignoreMatcher, rootDir) {
+    const entries = [];
+    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, mode) {
+    return collectSkillEntries(dir, mode);
+}
+function findGitRepoRoot(startDir) {
+    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) {
+    const skillDirs = [];
+    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) {
+    const entries = [];
+    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) {
+    const entries = [];
+    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) {
+    try {
+        const content = readFileSync(packageJsonPath, "utf-8");
+        const pkg = JSON.parse(content);
+        return pkg.pi ?? null;
+    }
+    catch {
+        return null;
+    }
+}
+function resolveExtensionEntries(dir) {
+    const packageJsonPath = join(dir, "package.json");
+    if (existsSync(packageJsonPath)) {
+        const manifest = readPiManifestFile(packageJsonPath);
+        if (manifest?.extensions?.length) {
+            const entries = [];
+            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) {
+    const entries = [];
+    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, resourceType) {
+    if (resourceType === "skills") {
+        return collectSkillEntries(dir, "pi");
+    }
+    if (resourceType === "extensions") {
+        return collectAutoExtensionEntries(dir);
+    }
+    return collectFiles(dir, FILE_PATTERNS[resourceType]);
+}
+function matchesAnyPattern(filePath, patterns, baseDir) {
+    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) {
+    const normalized = pattern.startsWith("./") || pattern.startsWith(".\\") ? pattern.slice(2) : pattern;
+    return toPosixPath(normalized);
+}
+function matchesAnyExactPattern(filePath, patterns, baseDir) {
+    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) {
+    return entries.filter((pattern) => pattern.startsWith("!") || pattern.startsWith("+") || pattern.startsWith("-"));
+}
+function isEnabledByOverrides(filePath, patterns, baseDir) {
+    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, patterns, baseDir) {
+    const includes = [];
+    const excludes = [];
+    const forceIncludes = [];
+    const forceExcludes = [];
+    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;
+    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);
+}
+export class DefaultPackageManager {
+    constructor(options) {
+        this.cwd = options.cwd;
+        this.agentDir = options.agentDir;
+        this.settingsManager = options.settingsManager;
+    }
+    setProgressCallback(callback) {
+        this.progressCallback = callback;
+    }
+    addSourceToSettings(source, options) {
+        const scope = 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 exists = currentPackages.some((existing) => this.packageSourcesMatch(existing, source, scope));
+        if (exists) {
+            return false;
+        }
+        const nextPackages = [...currentPackages, normalizedSource];
+        if (scope === "project") {
+            this.settingsManager.setProjectPackages(nextPackages);
+        }
+        else {
+            this.settingsManager.setPackages(nextPackages);
+        }
+        return true;
+    }
+    removeSourceFromSettings(source, options) {
+        const scope = 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, scope) {
+        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;
+    }
+    emitProgress(event) {
+        this.progressCallback?.(event);
+    }
+    async withProgress(action, source, message, operation) {
+        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) {
+        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 = [];
+        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] ?? []);
+            const projectEntries = (projectSettings[resourceType] ?? []);
+            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, options) {
+        const accumulator = this.createAccumulator();
+        const scope = options?.temporary ? "temporary" : options?.local ? "project" : "user";
+        const packageSources = sources.map((source) => ({ pkg: source, scope }));
+        await this.resolvePackageSources(packageSources, accumulator);
+        return this.toResolvedPaths(accumulator);
+    }
+    listConfiguredPackages() {
+        const globalSettings = this.settingsManager.getGlobalSettings();
+        const projectSettings = this.settingsManager.getProjectSettings();
+        const configuredPackages = [];
+        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, options) {
+        const parsed = this.parseSource(source);
+        const scope = options?.local ? "project" : "user";
+        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, options) {
+        await this.install(source, options);
+        this.addSourceToSettings(source, options);
+    }
+    async remove(source, options) {
+        const parsed = this.parseSource(source);
+        const scope = options?.local ? "project" : "user";
+        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, options) {
+        await this.remove(source, options);
+        return this.removeSourceFromSettings(source, options);
+    }
+    async update(source) {
+        const globalSettings = this.settingsManager.getGlobalSettings();
+        const projectSettings = this.settingsManager.getProjectSettings();
+        const identity = source ? this.getPackageIdentity(source) : undefined;
+        let matched = false;
+        const updateSources = [];
+        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);
+    }
+    async updateConfiguredSources(sources) {
+        if (isOfflineModeEnabled() || sources.length === 0) {
+            return;
+        }
+        const npmCandidates = [];
+        const gitCandidates = [];
+        for (const entry of sources) {
+            const parsed = this.parseSource(entry.source);
+            if (parsed.type === "local" || parsed.pinned) {
+                continue;
+            }
+            if (parsed.type === "npm") {
+                npmCandidates.push({ ...entry, parsed });
+                continue;
+            }
+            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 = [];
+        const projectNpmUpdates = [];
+        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 = [];
+        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 ${entry.source}...`, async () => {
+                await this.updateGit(entry.parsed, entry.scope);
+            }));
+            tasks.push(this.runWithConcurrency(gitTasks, GIT_UPDATE_CONCURRENCY).then(() => { }));
+        }
+        await Promise.all(tasks);
+    }
+    async shouldUpdateNpmSource(source, scope) {
+        const installedPath = this.getNpmInstallPath(source, scope);
+        const installedVersion = existsSync(installedPath) ? this.getInstalledNpmVersion(installedPath) : undefined;
+        if (!installedVersion) {
+            return true;
+        }
+        try {
+            const latestVersion = await this.getLatestNpmVersion(source.name);
+            return latestVersion !== installedVersion;
+        }
+        catch {
+            // Preserve existing update behavior when version lookup fails.
+            return true;
+        }
+    }
+    async updateNpmBatch(sources, scope) {
+        if (sources.length === 0) {
+            return;
+        }
+        const sourceLabel = sources.length === 1 ? sources[0].source : `${scope} npm packages`;
+        const message = sources.length === 1 ? `Updating ${sources[0].source}...` : `Updating ${scope} npm packages...`;
+        const specs = sources.map((entry) => `${entry.parsed.name}@latest`);
+        await this.withProgress("update", sourceLabel, message, async () => {
+            await this.installNpmBatch(specs, scope);
+        });
+    }
+    async installNpmBatch(specs, scope) {
+        if (scope === "user") {
+            await this.runNpmCommand(["install", "-g", ...specs]);
+            return;
+        }
+        const installRoot = this.getNpmInstallRoot(scope, false);
+        this.ensureNpmProject(installRoot);
+        await this.runNpmCommand(["install", ...specs, "--prefix", installRoot]);
+    }
+    async checkForAvailableUpdates() {
+        if (isOfflineModeEnabled()) {
+            return [];
+        }
+        const globalSettings = this.settingsManager.getGlobalSettings();
+        const projectSettings = this.settingsManager.getProjectSettings();
+        const allPackages = [];
+        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.scope !== "temporary")
+            .map((entry) => async () => {
+            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 !== undefined);
+    }
+    async resolvePackageSources(sources, accumulator, onMissing) {
+        for (const { pkg, scope } of sources) {
+            const sourceStr = typeof pkg === "string" ? pkg : pkg.source;
+            const filter = typeof pkg === "object" ? pkg : undefined;
+            const parsed = this.parseSource(sourceStr);
+            const metadata = { source: sourceStr, scope, origin: "package" };
+            if (parsed.type === "local") {
+                const baseDir = this.getBaseDirForScope(scope);
+                this.resolveLocalExtensionSource(parsed, accumulator, filter, metadata, baseDir);
+                continue;
+            }
+            const installMissing = async () => {
+                if (isOfflineModeEnabled()) {
+                    return false;
+                }
+                if (!onMissing) {
+                    await this.installParsedSource(parsed, scope);
+                    return true;
+                }
+                const action = await onMissing(sourceStr);
+                if (action === "skip")
+                    return false;
+                if (action === "error")
+                    throw new Error(`Missing source: ${sourceStr}`);
+                await this.installParsedSource(parsed, scope);
+                return true;
+            };
+            if (parsed.type === "npm") {
+                const installedPath = this.getNpmInstallPath(parsed, scope);
+                const needsInstall = !existsSync(installedPath) ||
+                    (parsed.pinned && !(await this.installedNpmMatchesPinnedVersion(parsed, installedPath)));
+                if (needsInstall) {
+                    const installed = await installMissing();
+                    if (!installed)
+                        continue;
+                }
+                metadata.baseDir = installedPath;
+                this.collectPackageResources(installedPath, accumulator, filter, metadata);
+                continue;
+            }
+            if (parsed.type === "git") {
+                const installedPath = this.getGitInstallPath(parsed, scope);
+                if (!existsSync(installedPath)) {
+                    const installed = await installMissing();
+                    if (!installed)
+                        continue;
+                }
+                else if (scope === "temporary" && !parsed.pinned && !isOfflineModeEnabled()) {
+                    await this.refreshTemporaryGitSource(parsed, sourceStr);
+                }
+                metadata.baseDir = installedPath;
+                this.collectPackageResources(installedPath, accumulator, filter, metadata);
+            }
+        }
+    }
+    resolveLocalExtensionSource(source, accumulator, filter, metadata, baseDir) {
+        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;
+        }
+    }
+    async installParsedSource(parsed, scope) {
+        if (parsed.type === "npm") {
+            await this.installNpm(parsed, scope, scope === "temporary");
+            return;
+        }
+        if (parsed.type === "git") {
+            await this.installGit(parsed, scope);
+            return;
+        }
+    }
+    getPackageSourceString(pkg) {
+        return typeof pkg === "string" ? pkg : pkg.source;
+    }
+    getSourceMatchKeyForInput(source) {
+        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:${this.resolvePath(parsed.path)}`;
+    }
+    getSourceMatchKeyForSettings(source, scope) {
+        const parsed = this.parseSource(source);
+        if (parsed.type === "npm") {
+            return `npm:${parsed.name}`;
+        }
+        if (parsed.type === "git") {
+            return `git:${parsed.host}/${parsed.path}`;
+        }
+        const baseDir = this.getBaseDirForScope(scope);
+        return `local:${this.resolvePathFromBase(parsed.path, baseDir)}`;
+    }
+    buildNoMatchingPackageMessage(source, configuredPackages) {
+        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 ${suggestion}?`;
+    }
+    findSuggestedConfiguredSource(source, configuredPackages) {
+        const trimmedSource = source.trim();
+        const suggestions = new Set();
+        for (const pkg of configuredPackages) {
+            const sourceStr = this.getPackageSourceString(pkg);
+            const parsed = this.parseSource(sourceStr);
+            if (parsed.type === "npm") {
+                if (trimmedSource === parsed.name || trimmedSource === parsed.spec) {
+                    suggestions.add(sourceStr);
+                }
+                continue;
+            }
+            if (parsed.type === "git") {
+                const shorthand = `${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;
+    }
+    packageSourcesMatch(existing, inputSource, scope) {
+        const left = this.getSourceMatchKeyForSettings(this.getPackageSourceString(existing), scope);
+        const right = this.getSourceMatchKeyForInput(inputSource);
+        return left === right;
+    }
+    normalizePackageSourceForSettings(source, scope) {
+        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 || ".";
+    }
+    parseSource(source) {
+        if (source.startsWith("npm:")) {
+            const spec = source.slice("npm:".length).trim();
+            const { name, version } = this.parseNpmSpec(spec);
+            return {
+                type: "npm",
+                spec,
+                name,
+                pinned: Boolean(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 };
+    }
+    async installedNpmMatchesPinnedVersion(source, installedPath) {
+        const installedVersion = this.getInstalledNpmVersion(installedPath);
+        if (!installedVersion) {
+            return false;
+        }
+        const { version: pinnedVersion } = this.parseNpmSpec(source.spec);
+        if (!pinnedVersion) {
+            return true;
+        }
+        return installedVersion === pinnedVersion;
+    }
+    async npmHasAvailableUpdate(source, installedPath) {
+        if (isOfflineModeEnabled()) {
+            return false;
+        }
+        const installedVersion = this.getInstalledNpmVersion(installedPath);
+        if (!installedVersion) {
+            return false;
+        }
+        try {
+            const latestVersion = await this.getLatestNpmVersion(source.name);
+            return latestVersion !== installedVersion;
+        }
+        catch {
+            return false;
+        }
+    }
+    getInstalledNpmVersion(installedPath) {
+        const packageJsonPath = join(installedPath, "package.json");
+        if (!existsSync(packageJsonPath))
+            return undefined;
+        try {
+            const content = readFileSync(packageJsonPath, "utf-8");
+            const pkg = JSON.parse(content);
+            return pkg.version;
+        }
+        catch {
+            return undefined;
+        }
+    }
+    async getLatestNpmVersion(packageName) {
+        const npmCommand = this.getNpmCommand();
+        const stdout = await this.runCommandCapture(npmCommand.command, [...npmCommand.args, "view", packageName, "version", "--json"], { cwd: this.cwd, timeoutMs: NETWORK_TIMEOUT_MS });
+        const raw = stdout.trim();
+        if (!raw)
+            throw new Error("Empty response from npm view");
+        return JSON.parse(raw);
+    }
+    async gitHasAvailableUpdate(installedPath) {
+        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;
+        }
+    }
+    async getRemoteGitHead(installedPath) {
+        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];
+    }
+    async getLocalGitUpdateTarget(installedPath) {
+        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/${branch}`,
+                    ],
+                };
+            }
+            return {
+                ref: "origin/HEAD",
+                head,
+                fetchArgs: ["fetch", "--prune", "--no-tags", "origin", "+HEAD:refs/remotes/origin/HEAD"],
+            };
+        }
+    }
+    async getGitUpstreamRef(installedPath) {
+        try {
+            const upstream = await this.runCommandCapture("git", ["rev-parse", "--abbrev-ref", "@{upstream}"], {
+                cwd: installedPath,
+                timeoutMs: NETWORK_TIMEOUT_MS,
+            });
+            const trimmed = upstream.trim();
+            if (!trimmed.startsWith("origin/")) {
+                return undefined;
+            }
+            const branch = trimmed.slice("origin/".length);
+            return branch ? `refs/heads/${branch}` : undefined;
+        }
+        catch {
+            return undefined;
+        }
+    }
+    runGitRemoteCommand(installedPath, args) {
+        return this.runCommandCapture("git", args, {
+            cwd: installedPath,
+            timeoutMs: NETWORK_TIMEOUT_MS,
+            env: {
+                GIT_TERMINAL_PROMPT: "0",
+            },
+        });
+    }
+    async runWithConcurrency(tasks, limit) {
+        if (tasks.length === 0) {
+            return [];
+        }
+        const results = 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.
+     */
+    getPackageIdentity(source, scope) {
+        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).
+     */
+    dedupePackages(packages) {
+        const seen = new Map();
+        for (const entry of packages) {
+            const sourceStr = typeof entry.pkg === "string" ? entry.pkg : entry.pkg.source;
+            const identity = this.getPackageIdentity(sourceStr, entry.scope);
+            const existing = seen.get(identity);
+            if (!existing) {
+                seen.set(identity, entry);
+            }
+            else if (entry.scope === "project" && existing.scope === "user") {
+                // Project wins over user
+                seen.set(identity, entry);
+            }
+            // If existing is project and new is global, keep existing (project)
+            // If both are same scope, keep first one
+        }
+        return Array.from(seen.values());
+    }
+    parseNpmSpec(spec) {
+        const versionSeparator = spec.startsWith("@") ? spec.indexOf("@", spec.indexOf("/") + 1) : spec.indexOf("@");
+        if (versionSeparator <= 0) {
+            return { name: spec };
+        }
+        return {
+            name: spec.slice(0, versionSeparator),
+            version: spec.slice(versionSeparator + 1),
+        };
+    }
+    getNpmCommand() {
+        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 };
+    }
+    async runNpmCommand(args, options) {
+        const npmCommand = this.getNpmCommand();
+        await this.runCommand(npmCommand.command, [...npmCommand.args, ...args], options);
+    }
+    getGitDependencyInstallArgs() {
+        const configuredCommand = this.settingsManager.getNpmCommand();
+        if (configuredCommand && configuredCommand.length > 0) {
+            return ["install"];
+        }
+        return ["install", "--omit=dev"];
+    }
+    runNpmCommandSync(args) {
+        const npmCommand = this.getNpmCommand();
+        return this.runCommandSync(npmCommand.command, [...npmCommand.args, ...args]);
+    }
+    async installNpm(source, scope, temporary) {
+        if (scope === "user" && !temporary) {
+            await this.runNpmCommand(["install", "-g", source.spec]);
+            return;
+        }
+        const installRoot = this.getNpmInstallRoot(scope, temporary);
+        this.ensureNpmProject(installRoot);
+        await this.runNpmCommand(["install", source.spec, "--prefix", installRoot]);
+    }
+    async uninstallNpm(source, scope) {
+        if (scope === "user") {
+            await this.runNpmCommand(["uninstall", "-g", source.name]);
+            return;
+        }
+        const installRoot = this.getNpmInstallRoot(scope, false);
+        if (!existsSync(installRoot)) {
+            return;
+        }
+        await this.runNpmCommand(["uninstall", source.name, "--prefix", installRoot]);
+    }
+    async installGit(source, scope) {
+        const targetDir = this.getGitInstallPath(source, scope);
+        if (existsSync(targetDir)) {
+            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 });
+        }
+    }
+    async updateGit(source, scope) {
+        const targetDir = this.getGitInstallPath(source, scope);
+        if (!existsSync(targetDir)) {
+            await this.installGit(source, scope);
+            return;
+        }
+        const target = await this.getLocalGitUpdateTarget(targetDir);
+        // Fetch only the ref we will reset to, avoiding unrelated branch/tag noise.
+        await this.runCommand("git", target.fetchArgs, { cwd: targetDir });
+        const localHead = await this.runCommandCapture("git", ["rev-parse", "HEAD"], {
+            cwd: targetDir,
+            timeoutMs: NETWORK_TIMEOUT_MS,
+        });
+        const refreshedTargetHead = await this.runCommandCapture("git", ["rev-parse", target.ref], {
+            cwd: targetDir,
+            timeoutMs: NETWORK_TIMEOUT_MS,
+        });
+        if (localHead.trim() === refreshedTargetHead.trim()) {
+            return;
+        }
+        await this.runCommand("git", ["reset", "--hard", target.ref], { 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 });
+        }
+    }
+    async refreshTemporaryGitSource(source, sourceStr) {
+        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.
+        }
+    }
+    async removeGit(source, scope) {
+        const targetDir = this.getGitInstallPath(source, scope);
+        if (!existsSync(targetDir))
+            return;
+        rmSync(targetDir, { recursive: true, force: true });
+        this.pruneEmptyGitParents(targetDir, this.getGitInstallRoot(scope));
+    }
+    pruneEmptyGitParents(targetDir, installRoot) {
+        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);
+        }
+    }
+    ensureNpmProject(installRoot) {
+        if (!existsSync(installRoot)) {
+            mkdirSync(installRoot, { recursive: true });
+        }
+        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");
+        }
+    }
+    ensureGitIgnore(dir) {
+        if (!existsSync(dir)) {
+            mkdirSync(dir, { recursive: true });
+        }
+        const ignorePath = join(dir, ".gitignore");
+        if (!existsSync(ignorePath)) {
+            writeFileSync(ignorePath, "*\n!.gitignore\n", "utf-8");
+        }
+    }
+    getNpmInstallRoot(scope, temporary) {
+        if (temporary) {
+            return this.getTemporaryDir("npm");
+        }
+        if (scope === "project") {
+            return join(this.cwd, CONFIG_DIR_NAME, "npm");
+        }
+        return join(this.getGlobalNpmRoot(), "..");
+    }
+    getGlobalNpmRoot() {
+        const npmCommand = this.getNpmCommand();
+        const commandKey = [npmCommand.command, ...npmCommand.args].join("\0");
+        if (this.globalNpmRoot && this.globalNpmRootCommandKey === commandKey) {
+            return this.globalNpmRoot;
+        }
+        const isBunPackageManager = npmCommand.command === "bun";
+        if (isBunPackageManager) {
+            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;
+    }
+    getNpmInstallPath(source, scope) {
+        if (scope === "temporary") {
+            return join(this.getTemporaryDir("npm"), "node_modules", source.name);
+        }
+        if (scope === "project") {
+            return join(this.cwd, CONFIG_DIR_NAME, "npm", "node_modules", source.name);
+        }
+        return join(this.getGlobalNpmRoot(), source.name);
+    }
+    getGitInstallPath(source, scope) {
+        if (scope === "temporary") {
+            return this.getTemporaryDir(`git-${source.host}`, source.path);
+        }
+        if (scope === "project") {
+            return join(this.cwd, CONFIG_DIR_NAME, "git", source.host, source.path);
+        }
+        return join(this.agentDir, "git", source.host, source.path);
+    }
+    getGitInstallRoot(scope) {
+        if (scope === "temporary") {
+            return undefined;
+        }
+        if (scope === "project") {
+            return join(this.cwd, CONFIG_DIR_NAME, "git");
+        }
+        return join(this.agentDir, "git");
+    }
+    getTemporaryDir(prefix, suffix) {
+        const hash = createHash("sha256")
+            .update(`${prefix}-${suffix ?? ""}`)
+            .digest("hex")
+            .slice(0, 8);
+        return join(tmpdir(), "pi-extensions", prefix, hash, suffix ?? "");
+    }
+    getBaseDirForScope(scope) {
+        if (scope === "project") {
+            return join(this.cwd, CONFIG_DIR_NAME);
+        }
+        if (scope === "user") {
+            return this.agentDir;
+        }
+        return this.cwd;
+    }
+    resolvePath(input) {
+        const trimmed = input.trim();
+        if (trimmed === "~")
+            return getHomeDir();
+        if (trimmed.startsWith("~/"))
+            return join(getHomeDir(), trimmed.slice(2));
+        if (trimmed.startsWith("~"))
+            return join(getHomeDir(), trimmed.slice(1));
+        return resolve(this.cwd, trimmed);
+    }
+    resolvePathFromBase(input, baseDir) {
+        const trimmed = input.trim();
+        if (trimmed === "~")
+            return getHomeDir();
+        if (trimmed.startsWith("~/"))
+            return join(getHomeDir(), trimmed.slice(2));
+        if (trimmed.startsWith("~"))
+            return join(getHomeDir(), trimmed.slice(1));
+        return resolve(baseDir, trimmed);
+    }
+    collectPackageResources(packageRoot, accumulator, filter, metadata) {
+        if (filter) {
+            for (const resourceType of RESOURCE_TYPES) {
+                const patterns = filter[resourceType];
+                const target = this.getTargetMap(accumulator, resourceType);
+                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];
+                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;
+    }
+    collectDefaultResources(packageRoot, resourceType, target, metadata) {
+        const manifest = this.readPiManifest(packageRoot);
+        const entries = manifest?.[resourceType];
+        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);
+            }
+        }
+    }
+    applyPackageFilter(packageRoot, userPatterns, resourceType, target, metadata) {
+        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);
+        }
+    }
+    /**
+     * 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.
+     */
+    collectManifestFiles(packageRoot, resourceType) {
+        const manifest = this.readPiManifest(packageRoot);
+        const entries = manifest?.[resourceType];
+        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) };
+    }
+    readPiManifest(packageRoot) {
+        const packageJsonPath = join(packageRoot, "package.json");
+        if (!existsSync(packageJsonPath)) {
+            return null;
+        }
+        try {
+            const content = readFileSync(packageJsonPath, "utf-8");
+            const pkg = JSON.parse(content);
+            return pkg.pi ?? null;
+        }
+        catch {
+            return null;
+        }
+    }
+    addManifestEntries(entries, root, resourceType, target, metadata) {
+        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);
+            }
+        }
+    }
+    collectFilesFromManifestEntries(entries, root, resourceType) {
+        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);
+    }
+    resolveLocalEntries(entries, resourceType, target, metadata, baseDir) {
+        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));
+        }
+    }
+    addAutoDiscoveredResources(accumulator, globalSettings, projectSettings, globalBaseDir, projectBaseDir) {
+        const userMetadata = {
+            source: "auto",
+            scope: "user",
+            origin: "top-level",
+            baseDir: globalBaseDir,
+        };
+        const projectMetadata = {
+            source: "auto",
+            scope: "project",
+            origin: "top-level",
+            baseDir: projectBaseDir,
+        };
+        const userOverrides = {
+            extensions: (globalSettings.extensions ?? []),
+            skills: (globalSettings.skills ?? []),
+            prompts: (globalSettings.prompts ?? []),
+            themes: (globalSettings.themes ?? []),
+        };
+        const projectOverrides = {
+            extensions: (projectSettings.extensions ?? []),
+            skills: (projectSettings.skills ?? []),
+            prompts: (projectSettings.prompts ?? []),
+            themes: (projectSettings.themes ?? []),
+        };
+        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 projectAgentsSkillDirs = collectAncestorAgentsSkillDirs(this.cwd).filter((dir) => resolve(dir) !== resolve(userAgentsSkillsDir));
+        const addResources = (resourceType, paths, metadata, overrides, baseDir) => {
+            const target = this.getTargetMap(accumulator, resourceType);
+            for (const path of paths) {
+                const enabled = isEnabledByOverrides(path, overrides, baseDir);
+                this.addResource(target, path, metadata, enabled);
+            }
+        };
+        // Project extensions from .atomic/
+        addResources("extensions", collectAutoExtensionEntries(projectDirs.extensions), projectMetadata, projectOverrides.extensions, projectBaseDir);
+        // Project skills from .atomic/
+        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 = {
+                ...projectMetadata,
+                baseDir: agentsBaseDir,
+            };
+            addResources("skills", collectAutoSkillEntries(agentsSkillsDir, "agents"), agentsMetadata, projectOverrides.skills, agentsBaseDir);
+        }
+        addResources("prompts", collectAutoPromptEntries(projectDirs.prompts), projectMetadata, projectOverrides.prompts, projectBaseDir);
+        addResources("themes", collectAutoThemeEntries(projectDirs.themes), projectMetadata, projectOverrides.themes, projectBaseDir);
+        // User extensions from ~/.atomic/agent/
+        addResources("extensions", collectAutoExtensionEntries(userDirs.extensions), userMetadata, userOverrides.extensions, globalBaseDir);
+        // User skills from ~/.atomic/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 = {
+            ...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);
+    }
+    collectFilesFromPaths(paths, resourceType) {
+        const files = [];
+        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;
+    }
+    getTargetMap(accumulator, resourceType) {
+        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}`);
+        }
+    }
+    addResource(map, path, metadata, enabled) {
+        if (!path)
+            return;
+        if (!map.has(path)) {
+            map.set(path, { metadata, enabled });
+        }
+    }
+    createAccumulator() {
+        return {
+            extensions: new Map(),
+            skills: new Map(),
+            prompts: new Map(),
+            themes: new Map(),
+        };
+    }
+    toResolvedPaths(accumulator) {
+        const mapToResolved = (entries) => {
+            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();
+            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),
+        };
+    }
+    spawnCommand(command, args, options) {
+        return spawn(command, args, {
+            cwd: options?.cwd,
+            stdio: isStdoutTakenOver() ? ["ignore", 2, 2] : "inherit",
+            shell: shouldUseWindowsShell(command),
+            env: getEnv(),
+        });
+    }
+    spawnCaptureCommand(command, args, options) {
+        const baseEnv = getEnv();
+        return spawn(command, args, {
+            cwd: options?.cwd,
+            stdio: ["ignore", "pipe", "pipe"],
+            shell: shouldUseWindowsShell(command),
+            env: options?.env ? { ...baseEnv, ...options.env } : baseEnv,
+        });
+    }
+    runCommandCapture(command, args, options) {
+        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}: ${stderr || stdout}`));
+            });
+        });
+    }
+    runCommand(command, args, options) {
+        return new Promise((resolvePromise, reject) => {
+            const child = this.spawnCommand(command, args, options);
+            child.on("error", reject);
+            child.on("exit", (code) => {
+                if (code === 0) {
+                    resolvePromise();
+                }
+                else {
+                    reject(new Error(`${command} ${args.join(" ")} failed with code ${code}`));
+                }
+            });
+        });
+    }
+    runCommandSync(command, args) {
+        const result = spawnSync(command, args, {
+            stdio: ["ignore", "pipe", "pipe"],
+            encoding: "utf-8",
+            shell: shouldUseWindowsShell(command),
+            env: getEnv(),
+        });
+        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();
+    }
+}
+//# sourceMappingURL=package-manager.js.map