pi-oxidized 0.1.1

package/.references/pi/packages/coding-agent/test/package-manager.test.ts

@@ -0,0 +1,2512 @@
+import { EventEmitter } from "node:events";
+import { mkdirSync, rmSync, statSync, symlinkSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join, relative } from "node:path";
+import { PassThrough } from "node:stream";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+import { DefaultPackageManager, type ProgressEvent, type ResolvedResource } from "../src/core/package-manager.ts";
+import { SettingsManager } from "../src/core/settings-manager.ts";
+
+function normalizeForMatch(value: string): string {
+	return value.replace(/\\/g, "/");
+}
+
+function pathEndsWith(actualPath: string, suffix: string): boolean {
+	return normalizeForMatch(actualPath).endsWith(normalizeForMatch(suffix));
+}
+
+class MockSpawnedProcess extends EventEmitter {
+	stdout = new PassThrough();
+	stderr = new PassThrough();
+
+	kill(): boolean {
+		this.emit("close", null, "SIGTERM");
+		return true;
+	}
+}
+
+interface PackageManagerInternals {
+	runCommand(command: string, args: string[], options?: { cwd?: string }): Promise<void>;
+	runCommandCapture(
+		command: string,
+		args: string[],
+		options?: { cwd?: string; timeoutMs?: number; env?: Record<string, string> },
+	): Promise<string>;
+	getLocalGitUpdateTarget(installedPath: string): Promise<{ ref: string; head: string; fetchArgs: string[] }>;
+	parseSource(
+		source: string,
+	):
+		| { type: "npm"; spec: string; name: string; pinned: boolean }
+		| { type: "git"; repo: string; host: string; path: string; pinned: boolean; ref?: string }
+		| { type: "local"; path: string };
+	getNpmInstallPath(
+		source: { type: "npm"; spec: string; name: string; pinned: boolean },
+		scope: "user" | "project" | "temporary",
+	): string;
+	getGitInstallPath(
+		source: { type: "git"; repo: string; host: string; path: string; pinned: boolean; ref?: string },
+		scope: "user" | "project" | "temporary",
+	): string;
+}
+
+// Helper to check if a resource is enabled
+const isEnabled = (r: ResolvedResource, pathMatch: string, matchFn: "endsWith" | "includes" = "endsWith") => {
+	const normalizedPath = normalizeForMatch(r.path);
+	const normalizedMatch = normalizeForMatch(pathMatch);
+	return matchFn === "endsWith"
+		? normalizedPath.endsWith(normalizedMatch) && r.enabled
+		: normalizedPath.includes(normalizedMatch) && r.enabled;
+};
+
+const isDisabled = (r: ResolvedResource, pathMatch: string, matchFn: "endsWith" | "includes" = "endsWith") => {
+	const normalizedPath = normalizeForMatch(r.path);
+	const normalizedMatch = normalizeForMatch(pathMatch);
+	return matchFn === "endsWith"
+		? normalizedPath.endsWith(normalizedMatch) && !r.enabled
+		: normalizedPath.includes(normalizedMatch) && !r.enabled;
+};
+
+describe("DefaultPackageManager", () => {
+	let tempDir: string;
+	let agentDir: string;
+	let settingsManager: SettingsManager;
+	let packageManager: DefaultPackageManager;
+	let previousOfflineEnv: string | undefined;
+
+	beforeEach(() => {
+		previousOfflineEnv = process.env.PI_OFFLINE;
+		delete process.env.PI_OFFLINE;
+		tempDir = join(tmpdir(), `pm-test-${Date.now()}-${Math.random().toString(36).slice(2)}`);
+		mkdirSync(tempDir, { recursive: true });
+		agentDir = join(tempDir, "agent");
+		mkdirSync(agentDir, { recursive: true });
+
+		settingsManager = SettingsManager.inMemory();
+		packageManager = new DefaultPackageManager({
+			cwd: tempDir,
+			agentDir,
+			settingsManager,
+		});
+	});
+
+	afterEach(() => {
+		if (previousOfflineEnv === undefined) {
+			delete process.env.PI_OFFLINE;
+		} else {
+			process.env.PI_OFFLINE = previousOfflineEnv;
+		}
+		vi.restoreAllMocks();
+		vi.unstubAllGlobals();
+		rmSync(tempDir, { recursive: true, force: true });
+	});
+
+	describe("resolve", () => {
+		it("should return no package-sourced paths when no sources configured", async () => {
+			const result = await packageManager.resolve();
+			expect(result.extensions).toEqual([]);
+			expect(result.prompts).toEqual([]);
+			expect(result.themes).toEqual([]);
+			expect(result.skills.every((r) => r.metadata.source === "auto" && r.metadata.origin === "top-level")).toBe(
+				true,
+			);
+		});
+
+		it("should resolve local extension paths from settings", async () => {
+			const extDir = join(agentDir, "extensions");
+			mkdirSync(extDir, { recursive: true });
+			const extPath = join(extDir, "my-extension.ts");
+			writeFileSync(extPath, "export default function() {}");
+			settingsManager.setExtensionPaths(["extensions/my-extension.ts"]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => r.path === extPath && r.enabled)).toBe(true);
+		});
+
+		it("should resolve skill paths from settings", async () => {
+			const skillDir = join(agentDir, "skills", "my-skill");
+			mkdirSync(skillDir, { recursive: true });
+			const skillFile = join(skillDir, "SKILL.md");
+			writeFileSync(
+				skillFile,
+				`---
+name: test-skill
+description: A test skill
+---
+Content`,
+			);
+
+			settingsManager.setSkillPaths(["skills"]);
+
+			const result = await packageManager.resolve();
+			// Skills with SKILL.md are returned as file paths
+			expect(result.skills.some((r) => r.path === skillFile && r.enabled)).toBe(true);
+		});
+
+		it("should auto-discover root markdown skills from .pi skill dirs", async () => {
+			const skillFile = join(agentDir, "skills", "single-file.md");
+			mkdirSync(join(agentDir, "skills"), { recursive: true });
+			writeFileSync(
+				skillFile,
+				`---
+name: single-file
+description: A root markdown skill
+---
+Content`,
+			);
+
+			const result = await packageManager.resolve();
+			expect(result.skills.some((r) => r.path === skillFile && r.enabled)).toBe(true);
+		});
+
+		it("should resolve project paths relative to .pi", async () => {
+			const extDir = join(tempDir, ".pi", "extensions");
+			mkdirSync(extDir, { recursive: true });
+			const extPath = join(extDir, "project-ext.ts");
+			writeFileSync(extPath, "export default function() {}");
+
+			settingsManager.setProjectExtensionPaths(["extensions/project-ext.ts"]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => r.path === extPath && r.enabled)).toBe(true);
+		});
+
+		it("should auto-discover user prompts with overrides", async () => {
+			const promptsDir = join(agentDir, "prompts");
+			mkdirSync(promptsDir, { recursive: true });
+			const promptPath = join(promptsDir, "auto.md");
+			writeFileSync(promptPath, "Auto prompt");
+
+			settingsManager.setPromptTemplatePaths(["!prompts/auto.md"]);
+
+			const result = await packageManager.resolve();
+			expect(result.prompts.some((r) => r.path === promptPath && !r.enabled)).toBe(true);
+		});
+
+		it("should resolve symlinked user and project resources once", async () => {
+			const previousHome = process.env.HOME;
+			process.env.HOME = tempDir;
+
+			try {
+				const sharedDir = join(tempDir, "shared-resources");
+				const sharedExtensionsDir = join(sharedDir, "extensions");
+				const sharedSkillsDir = join(sharedDir, "skills");
+				const sharedPromptsDir = join(sharedDir, "prompts");
+				const sharedThemesDir = join(sharedDir, "themes");
+				mkdirSync(sharedExtensionsDir, { recursive: true });
+				mkdirSync(sharedSkillsDir, { recursive: true });
+				mkdirSync(sharedPromptsDir, { recursive: true });
+				mkdirSync(sharedThemesDir, { recursive: true });
+
+				writeFileSync(join(sharedExtensionsDir, "shared.ts"), "export default function() {}");
+				mkdirSync(join(sharedSkillsDir, "shared-skill"), { recursive: true });
+				writeFileSync(
+					join(sharedSkillsDir, "shared-skill", "SKILL.md"),
+					`---
+name: shared-skill
+description: Shared skill
+---
+Content`,
+				);
+				writeFileSync(join(sharedPromptsDir, "shared.md"), "Shared prompt");
+				writeFileSync(join(sharedThemesDir, "shared.json"), JSON.stringify({ name: "shared-theme" }));
+
+				mkdirSync(join(agentDir), { recursive: true });
+				mkdirSync(join(tempDir, ".pi"), { recursive: true });
+				symlinkSync(sharedExtensionsDir, join(agentDir, "extensions"), "dir");
+				symlinkSync(sharedSkillsDir, join(agentDir, "skills"), "dir");
+				symlinkSync(sharedPromptsDir, join(agentDir, "prompts"), "dir");
+				symlinkSync(sharedThemesDir, join(agentDir, "themes"), "dir");
+				symlinkSync(sharedExtensionsDir, join(tempDir, ".pi", "extensions"), "dir");
+				symlinkSync(sharedSkillsDir, join(tempDir, ".pi", "skills"), "dir");
+				symlinkSync(sharedPromptsDir, join(tempDir, ".pi", "prompts"), "dir");
+				symlinkSync(sharedThemesDir, join(tempDir, ".pi", "themes"), "dir");
+
+				const result = await packageManager.resolve();
+
+				expect({
+					extensions: result.extensions.length,
+					skills: result.skills.length,
+					prompts: result.prompts.length,
+					themes: result.themes.length,
+				}).toEqual({
+					extensions: 1,
+					skills: 1,
+					prompts: 1,
+					themes: 1,
+				});
+
+				// Project auto-discovered has higher precedence than user auto-discovered,
+				// so the surviving entry should be scoped to project.
+				expect(result.extensions[0].metadata.scope).toBe("project");
+				expect(result.skills[0].metadata.scope).toBe("project");
+				expect(result.prompts[0].metadata.scope).toBe("project");
+				expect(result.themes[0].metadata.scope).toBe("project");
+			} finally {
+				if (previousHome === undefined) {
+					delete process.env.HOME;
+				} else {
+					process.env.HOME = previousHome;
+				}
+			}
+		});
+
+		it("should auto-discover project prompts with overrides", async () => {
+			const promptsDir = join(tempDir, ".pi", "prompts");
+			mkdirSync(promptsDir, { recursive: true });
+			const promptPath = join(promptsDir, "is.md");
+			writeFileSync(promptPath, "Is prompt");
+
+			settingsManager.setProjectPromptTemplatePaths(["!prompts/is.md"]);
+
+			const result = await packageManager.resolve();
+			expect(result.prompts.some((r) => r.path === promptPath && !r.enabled)).toBe(true);
+		});
+
+		it("should resolve directory with package.json pi.extensions in extensions setting", async () => {
+			// Create a package with pi.extensions in package.json
+			const pkgDir = join(tempDir, "my-extensions-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(
+				join(pkgDir, "package.json"),
+				JSON.stringify({
+					name: "my-extensions-pkg",
+					pi: {
+						extensions: ["./extensions/clip.ts", "./extensions/cost.ts"],
+					},
+				}),
+			);
+			writeFileSync(join(pkgDir, "extensions", "clip.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "cost.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "helper.ts"), "export const x = 1;"); // Not in manifest, shouldn't be loaded
+
+			// Add the directory to extensions setting (not packages setting)
+			settingsManager.setExtensionPaths([pkgDir]);
+
+			const result = await packageManager.resolve();
+
+			// Should find the extensions declared in package.json pi.extensions
+			expect(result.extensions.some((r) => r.path === join(pkgDir, "extensions", "clip.ts") && r.enabled)).toBe(
+				true,
+			);
+			expect(result.extensions.some((r) => r.path === join(pkgDir, "extensions", "cost.ts") && r.enabled)).toBe(
+				true,
+			);
+
+			// Should NOT find helper.ts (not declared in manifest)
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "helper.ts"))).toBe(false);
+		});
+	});
+
+	describe("auto-discovered skill metadata", () => {
+		it("should use the agent dir as baseDir for user .pi/agent skills", async () => {
+			const skillPath = join(agentDir, "skills", "user-pi", "SKILL.md");
+			mkdirSync(join(agentDir, "skills", "user-pi"), { recursive: true });
+			writeFileSync(skillPath, "---\nname: user-pi\ndescription: user pi\n---\n");
+
+			const result = await packageManager.resolve();
+			const skill = result.skills.find((r) => r.path === skillPath);
+
+			expect(skill?.metadata.source).toBe("auto");
+			expect(skill?.metadata.scope).toBe("user");
+			expect(skill?.metadata.baseDir).toBe(agentDir);
+		});
+
+		it("should use the project .pi dir as baseDir for project .pi skills", async () => {
+			const projectBaseDir = join(tempDir, ".pi");
+			const skillPath = join(projectBaseDir, "skills", "project-pi", "SKILL.md");
+			mkdirSync(join(projectBaseDir, "skills", "project-pi"), { recursive: true });
+			writeFileSync(skillPath, "---\nname: project-pi\ndescription: project pi\n---\n");
+
+			const result = await packageManager.resolve();
+			const skill = result.skills.find((r) => r.path === skillPath);
+
+			expect(skill?.metadata.source).toBe("auto");
+			expect(skill?.metadata.scope).toBe("project");
+			expect(skill?.metadata.baseDir).toBe(projectBaseDir);
+		});
+
+		it("should use ~/.agents as baseDir for user .agents skills", async () => {
+			const previousHome = process.env.HOME;
+			process.env.HOME = tempDir;
+
+			try {
+				const agentsBaseDir = join(tempDir, ".agents");
+				const skillPath = join(agentsBaseDir, "skills", "user-agents", "SKILL.md");
+				mkdirSync(join(agentsBaseDir, "skills", "user-agents"), { recursive: true });
+				writeFileSync(skillPath, "---\nname: user-agents\ndescription: user agents\n---\n");
+
+				const result = await packageManager.resolve();
+				const skill = result.skills.find((r) => r.path === skillPath);
+
+				expect(skill?.metadata.source).toBe("auto");
+				expect(skill?.metadata.scope).toBe("user");
+				expect(skill?.metadata.baseDir).toBe(agentsBaseDir);
+			} finally {
+				if (previousHome === undefined) {
+					delete process.env.HOME;
+				} else {
+					process.env.HOME = previousHome;
+				}
+			}
+		});
+
+		it("should use each project .agents dir as baseDir for project .agents skills", async () => {
+			const repoRoot = join(tempDir, "repo");
+			const nestedCwd = join(repoRoot, "packages", "feature");
+			mkdirSync(nestedCwd, { recursive: true });
+			mkdirSync(join(repoRoot, ".git"), { recursive: true });
+
+			const repoAgentsBaseDir = join(repoRoot, ".agents");
+			const repoSkill = join(repoAgentsBaseDir, "skills", "repo", "SKILL.md");
+			mkdirSync(join(repoAgentsBaseDir, "skills", "repo"), { recursive: true });
+			writeFileSync(repoSkill, "---\nname: repo\ndescription: repo\n---\n");
+
+			const packageAgentsBaseDir = join(repoRoot, "packages", ".agents");
+			const packageSkill = join(packageAgentsBaseDir, "skills", "package", "SKILL.md");
+			mkdirSync(join(packageAgentsBaseDir, "skills", "package"), { recursive: true });
+			writeFileSync(packageSkill, "---\nname: package\ndescription: package\n---\n");
+
+			const pm = new DefaultPackageManager({
+				cwd: nestedCwd,
+				agentDir,
+				settingsManager,
+			});
+
+			const result = await pm.resolve();
+			const resolvedRepoSkill = result.skills.find((r) => r.path === repoSkill);
+			const resolvedPackageSkill = result.skills.find((r) => r.path === packageSkill);
+
+			expect(resolvedRepoSkill?.metadata.source).toBe("auto");
+			expect(resolvedRepoSkill?.metadata.scope).toBe("project");
+			expect(resolvedRepoSkill?.metadata.baseDir).toBe(repoAgentsBaseDir);
+			expect(resolvedPackageSkill?.metadata.source).toBe("auto");
+			expect(resolvedPackageSkill?.metadata.scope).toBe("project");
+			expect(resolvedPackageSkill?.metadata.baseDir).toBe(packageAgentsBaseDir);
+		});
+	});
+
+	describe(".agents/skills auto-discovery", () => {
+		it("should scan .agents/skills from cwd up to git repo root", async () => {
+			const repoRoot = join(tempDir, "repo");
+			const nestedCwd = join(repoRoot, "packages", "feature");
+			mkdirSync(nestedCwd, { recursive: true });
+			mkdirSync(join(repoRoot, ".git"), { recursive: true });
+
+			const aboveRepoSkill = join(tempDir, ".agents", "skills", "above-repo", "SKILL.md");
+			mkdirSync(join(tempDir, ".agents", "skills", "above-repo"), { recursive: true });
+			writeFileSync(aboveRepoSkill, "---\nname: above-repo\ndescription: above\n---\n");
+
+			const repoRootSkill = join(repoRoot, ".agents", "skills", "repo-root", "SKILL.md");
+			mkdirSync(join(repoRoot, ".agents", "skills", "repo-root"), { recursive: true });
+			writeFileSync(repoRootSkill, "---\nname: repo-root\ndescription: repo\n---\n");
+
+			const nestedSkill = join(repoRoot, "packages", ".agents", "skills", "nested", "SKILL.md");
+			mkdirSync(join(repoRoot, "packages", ".agents", "skills", "nested"), { recursive: true });
+			writeFileSync(nestedSkill, "---\nname: nested\ndescription: nested\n---\n");
+
+			const pm = new DefaultPackageManager({
+				cwd: nestedCwd,
+				agentDir,
+				settingsManager,
+			});
+
+			const result = await pm.resolve();
+			expect(result.skills.some((r) => r.path === repoRootSkill && r.enabled)).toBe(true);
+			expect(result.skills.some((r) => r.path === nestedSkill && r.enabled)).toBe(true);
+			expect(result.skills.some((r) => r.path === aboveRepoSkill)).toBe(false);
+		});
+
+		it("should scan .agents/skills up to filesystem root when not in a git repo", async () => {
+			const nonRepoRoot = join(tempDir, "non-repo");
+			const nestedCwd = join(nonRepoRoot, "a", "b");
+			mkdirSync(nestedCwd, { recursive: true });
+
+			const rootSkill = join(nonRepoRoot, ".agents", "skills", "root", "SKILL.md");
+			mkdirSync(join(nonRepoRoot, ".agents", "skills", "root"), { recursive: true });
+			writeFileSync(rootSkill, "---\nname: root\ndescription: root\n---\n");
+
+			const middleSkill = join(nonRepoRoot, "a", ".agents", "skills", "middle", "SKILL.md");
+			mkdirSync(join(nonRepoRoot, "a", ".agents", "skills", "middle"), { recursive: true });
+			writeFileSync(middleSkill, "---\nname: middle\ndescription: middle\n---\n");
+
+			const pm = new DefaultPackageManager({
+				cwd: nestedCwd,
+				agentDir,
+				settingsManager,
+			});
+
+			const result = await pm.resolve();
+			expect(result.skills.some((r) => r.path === rootSkill && r.enabled)).toBe(true);
+			expect(result.skills.some((r) => r.path === middleSkill && r.enabled)).toBe(true);
+		});
+
+		it("should ignore root markdown files in .agents/skills", async () => {
+			const agentsSkillsDir = join(tempDir, ".agents", "skills");
+			mkdirSync(join(agentsSkillsDir, "nested-skill"), { recursive: true });
+			const rootSkill = join(agentsSkillsDir, "root-file.md");
+			const nestedSkill = join(agentsSkillsDir, "nested-skill", "SKILL.md");
+			writeFileSync(rootSkill, "---\nname: root-file\ndescription: Root markdown file\n---\n");
+			writeFileSync(nestedSkill, "---\nname: nested-skill\ndescription: Nested skill\n---\n");
+
+			const pm = new DefaultPackageManager({
+				cwd: join(tempDir, "work"),
+				agentDir,
+				settingsManager,
+			});
+			mkdirSync(join(tempDir, "work"), { recursive: true });
+
+			const result = await pm.resolve();
+			expect(result.skills.some((r) => r.path === rootSkill)).toBe(false);
+			expect(result.skills.some((r) => r.path === nestedSkill && r.enabled)).toBe(true);
+		});
+
+		it("should keep ~/.agents/skills user-scoped when cwd is under home in a non-git directory", async () => {
+			const previousHome = process.env.HOME;
+			process.env.HOME = tempDir;
+
+			try {
+				const cwd = join(tempDir, "scratch", "nested");
+				const localAgentDir = join(tempDir, ".pi", "agent");
+				const localSettingsManager = SettingsManager.inMemory();
+				mkdirSync(cwd, { recursive: true });
+				mkdirSync(localAgentDir, { recursive: true });
+
+				const homeSkill = join(tempDir, ".agents", "skills", "home-skill", "SKILL.md");
+				mkdirSync(join(tempDir, ".agents", "skills", "home-skill"), { recursive: true });
+				writeFileSync(homeSkill, "---\nname: home-skill\ndescription: home\n---\n");
+
+				const pm = new DefaultPackageManager({
+					cwd,
+					agentDir: localAgentDir,
+					settingsManager: localSettingsManager,
+				});
+
+				const result = await pm.resolve();
+				const matchingSkills = result.skills.filter((r) => r.path === homeSkill);
+				expect(matchingSkills).toHaveLength(1);
+				expect(matchingSkills[0]?.enabled).toBe(true);
+				expect(matchingSkills[0]?.metadata.scope).toBe("user");
+				expect(matchingSkills[0]?.metadata.source).toBe("auto");
+			} finally {
+				if (previousHome === undefined) {
+					delete process.env.HOME;
+				} else {
+					process.env.HOME = previousHome;
+				}
+			}
+		});
+
+		it("should dedupe user skill entries when ~/.pi/agent/skills is a symlink to ~/.agents/skills", async () => {
+			const previousHome = process.env.HOME;
+			process.env.HOME = tempDir;
+
+			try {
+				const agentSkillsDir = join(agentDir, "skills");
+				const agentsSkillsDir = join(tempDir, ".agents", "skills");
+				mkdirSync(agentsSkillsDir, { recursive: true });
+				// Use junction on Windows to avoid EPERM when symlink privileges are unavailable.
+				const directoryLinkType = process.platform === "win32" ? "junction" : "dir";
+				symlinkSync(agentsSkillsDir, agentSkillsDir, directoryLinkType);
+
+				const skillPath = join(agentsSkillsDir, "foo", "SKILL.md");
+				mkdirSync(join(agentsSkillsDir, "foo"), { recursive: true });
+				writeFileSync(skillPath, "---\nname: foo\ndescription: foo\n---\n");
+
+				const result = await packageManager.resolve();
+				const fooSkills = result.skills.filter((r) => pathEndsWith(r.path, "foo/SKILL.md"));
+
+				expect(fooSkills).toHaveLength(1);
+			} finally {
+				if (previousHome === undefined) {
+					delete process.env.HOME;
+				} else {
+					process.env.HOME = previousHome;
+				}
+			}
+		});
+	});
+
+	describe("ignore files", () => {
+		it("should respect .gitignore in skill directories", async () => {
+			const skillsDir = join(agentDir, "skills");
+			mkdirSync(skillsDir, { recursive: true });
+			writeFileSync(join(skillsDir, ".gitignore"), "venv\n__pycache__\n");
+
+			const goodSkillDir = join(skillsDir, "good-skill");
+			mkdirSync(goodSkillDir, { recursive: true });
+			writeFileSync(join(goodSkillDir, "SKILL.md"), "---\nname: good-skill\ndescription: Good\n---\nContent");
+
+			const ignoredSkillDir = join(skillsDir, "venv", "bad-skill");
+			mkdirSync(ignoredSkillDir, { recursive: true });
+			writeFileSync(join(ignoredSkillDir, "SKILL.md"), "---\nname: bad-skill\ndescription: Bad\n---\nContent");
+
+			settingsManager.setSkillPaths(["skills"]);
+
+			const result = await packageManager.resolve();
+			expect(result.skills.some((r) => r.path.includes("good-skill") && r.enabled)).toBe(true);
+			expect(result.skills.some((r) => r.path.includes("venv") && r.enabled)).toBe(false);
+		});
+
+		it("should not apply parent .gitignore to .pi auto-discovery", async () => {
+			writeFileSync(join(tempDir, ".gitignore"), ".pi\n");
+
+			const skillDir = join(tempDir, ".pi", "skills", "auto-skill");
+			mkdirSync(skillDir, { recursive: true });
+			const skillPath = join(skillDir, "SKILL.md");
+			writeFileSync(skillPath, "---\nname: auto-skill\ndescription: Auto\n---\nContent");
+
+			const result = await packageManager.resolve();
+			expect(result.skills.some((r) => r.path === skillPath && r.enabled)).toBe(true);
+		});
+	});
+
+	describe("resolveExtensionSources", () => {
+		it("should resolve local paths", async () => {
+			const extPath = join(tempDir, "ext.ts");
+			writeFileSync(extPath, "export default function() {}");
+
+			const result = await packageManager.resolveExtensionSources([extPath]);
+			expect(result.extensions.some((r) => r.path === extPath && r.enabled)).toBe(true);
+		});
+
+		it("should handle directories with pi manifest", async () => {
+			const pkgDir = join(tempDir, "my-package");
+			mkdirSync(pkgDir, { recursive: true });
+			writeFileSync(
+				join(pkgDir, "package.json"),
+				JSON.stringify({
+					name: "my-package",
+					pi: {
+						extensions: ["./src/index.ts"],
+						skills: ["./skills"],
+					},
+				}),
+			);
+			mkdirSync(join(pkgDir, "src"), { recursive: true });
+			writeFileSync(join(pkgDir, "src", "index.ts"), "export default function() {}");
+			mkdirSync(join(pkgDir, "skills", "my-skill"), { recursive: true });
+			writeFileSync(
+				join(pkgDir, "skills", "my-skill", "SKILL.md"),
+				"---\nname: my-skill\ndescription: Test\n---\nContent",
+			);
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+			expect(result.extensions.some((r) => r.path === join(pkgDir, "src", "index.ts") && r.enabled)).toBe(true);
+			// Skills with SKILL.md are returned as file paths
+			expect(result.skills.some((r) => r.path === join(pkgDir, "skills", "my-skill", "SKILL.md") && r.enabled)).toBe(
+				true,
+			);
+		});
+
+		it("should keep pi manifest entries with leading tilde package-relative", async () => {
+			const pkgDir = join(tempDir, "tilde-manifest-package");
+			const directExtensionPath = join(pkgDir, "~extensions", "main.ts");
+			const slashExtensionPath = join(pkgDir, "~", "extensions", "alt.ts");
+			const directSkillPath = join(pkgDir, "~skills", "direct-skill", "SKILL.md");
+			const slashSkillPath = join(pkgDir, "~", "skills", "slash-skill", "SKILL.md");
+
+			mkdirSync(join(pkgDir, "~extensions"), { recursive: true });
+			mkdirSync(join(pkgDir, "~", "extensions"), { recursive: true });
+			mkdirSync(join(pkgDir, "~skills", "direct-skill"), { recursive: true });
+			mkdirSync(join(pkgDir, "~", "skills", "slash-skill"), { recursive: true });
+			writeFileSync(directExtensionPath, "export default function() {}");
+			writeFileSync(slashExtensionPath, "export default function() {}");
+			writeFileSync(directSkillPath, "---\nname: direct-skill\ndescription: Direct\n---\nContent");
+			writeFileSync(slashSkillPath, "---\nname: slash-skill\ndescription: Slash\n---\nContent");
+			writeFileSync(
+				join(pkgDir, "package.json"),
+				JSON.stringify({
+					name: "tilde-manifest-package",
+					pi: {
+						extensions: ["~extensions/main.ts", "~/extensions/alt.ts"],
+						skills: ["~skills", "~/skills"],
+					},
+				}),
+			);
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+
+			expect(result.extensions.some((r) => r.path === directExtensionPath && r.enabled)).toBe(true);
+			expect(result.extensions.some((r) => r.path === slashExtensionPath && r.enabled)).toBe(true);
+			expect(result.skills.some((r) => r.path === directSkillPath && r.enabled)).toBe(true);
+			expect(result.skills.some((r) => r.path === slashSkillPath && r.enabled)).toBe(true);
+		});
+
+		it("should handle directories with auto-discovery layout", async () => {
+			const pkgDir = join(tempDir, "auto-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			mkdirSync(join(pkgDir, "themes"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "main.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "themes", "dark.json"), "{}");
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "main.ts") && r.enabled)).toBe(true);
+			expect(result.themes.some((r) => pathEndsWith(r.path, "dark.json") && r.enabled)).toBe(true);
+		});
+
+		it("should stop recursing when a package skill directory contains SKILL.md", async () => {
+			const pkgDir = join(tempDir, "skill-root-pkg");
+			mkdirSync(join(pkgDir, "skills", "root-skill", "nested-skill"), { recursive: true });
+			const rootSkill = join(pkgDir, "skills", "root-skill", "SKILL.md");
+			const nestedSkill = join(pkgDir, "skills", "root-skill", "nested-skill", "SKILL.md");
+			writeFileSync(rootSkill, "---\nname: root-skill\ndescription: Root skill\n---\n");
+			writeFileSync(nestedSkill, "---\nname: nested-skill\ndescription: Nested skill\n---\n");
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+			expect(result.skills.some((r) => r.path === rootSkill && r.enabled)).toBe(true);
+			expect(result.skills.some((r) => r.path === nestedSkill)).toBe(false);
+		});
+	});
+
+	describe("progress callback", () => {
+		it("should emit progress events", async () => {
+			const events: ProgressEvent[] = [];
+			packageManager.setProgressCallback((event) => events.push(event));
+
+			const extPath = join(tempDir, "ext.ts");
+			writeFileSync(extPath, "export default function() {}");
+
+			// Local paths don't trigger install progress, but we can verify the callback is set
+			await packageManager.resolveExtensionSources([extPath]);
+
+			// For now just verify no errors - npm/git would trigger actual events
+			expect(events.length).toBe(0);
+		});
+	});
+
+	describe("command spawning", () => {
+		it("should preserve argv entries containing spaces", () => {
+			const managerWithInternals = packageManager as unknown as {
+				runCommandSync(command: string, args: string[]): string;
+			};
+			const valueWithSpace = "C:\\Users\\A B\\.pi\\npm";
+			const output = managerWithInternals.runCommandSync(process.execPath, [
+				"-e",
+				"console.log(process.argv[1])",
+				valueWithSpace,
+			]);
+
+			expect(output).toBe(valueWithSpace);
+		});
+	});
+
+	describe("npmCommand", () => {
+		it("should use npmCommand argv for npm installs", async () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["mise", "exec", "node@20", "--", "npm"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const runCommandSpy = vi.spyOn(packageManager as any, "runCommand").mockResolvedValue(undefined);
+
+			await packageManager.install("npm:@scope/pkg");
+
+			expect(runCommandSpy).toHaveBeenCalledWith(
+				"mise",
+				[
+					"exec",
+					"node@20",
+					"--",
+					"npm",
+					"install",
+					"@scope/pkg",
+					"--prefix",
+					join(agentDir, "npm"),
+					"--legacy-peer-deps",
+				],
+				undefined,
+			);
+		});
+
+		it("should pass legacy peer deps when uninstalling npm packages", async () => {
+			mkdirSync(join(agentDir, "npm"), { recursive: true });
+			const runCommandSpy = vi.spyOn(packageManager as any, "runCommand").mockResolvedValue(undefined);
+
+			await packageManager.remove("npm:@scope/pkg");
+
+			expect(runCommandSpy).toHaveBeenCalledWith(
+				"npm",
+				["uninstall", "@scope/pkg", "--prefix", join(agentDir, "npm"), "--legacy-peer-deps"],
+				undefined,
+			);
+		});
+
+		it("should use bun --cwd for npm package installs", async () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["mise", "exec", "bun@1", "--", "bun"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const runCommandSpy = vi.spyOn(packageManager as any, "runCommand").mockResolvedValue(undefined);
+
+			await packageManager.install("npm:@scope/pkg");
+
+			expect(runCommandSpy).toHaveBeenCalledWith(
+				"mise",
+				["exec", "bun@1", "--", "bun", "install", "@scope/pkg", "--cwd", join(agentDir, "npm"), "--omit=peer"],
+				undefined,
+			);
+		});
+
+		it("should install git package dependencies with --omit=dev", async () => {
+			const source = "git:github.com/user/repo";
+			const targetDir = join(agentDir, "git", "github.com", "user", "repo");
+			const runCommandSpy = vi
+				.spyOn(packageManager as any, "runCommand")
+				.mockImplementation(async (...callArgs: unknown[]) => {
+					const [command, args] = callArgs as [string, string[]];
+					if (command === "git" && args[0] === "clone") {
+						mkdirSync(targetDir, { recursive: true });
+						writeFileSync(join(targetDir, "package.json"), JSON.stringify({ name: "repo", version: "1.0.0" }));
+					}
+				});
+
+			await packageManager.install(source);
+
+			expect(runCommandSpy).toHaveBeenCalledWith("npm", ["install", "--omit=dev"], { cwd: targetDir });
+		});
+
+		it("should reconcile an existing git checkout to a pinned ref during install", async () => {
+			const source = "git:github.com/user/repo@v2";
+			const targetDir = join(agentDir, "git", "github.com", "user", "repo");
+			mkdirSync(targetDir, { recursive: true });
+			writeFileSync(join(targetDir, "package.json"), JSON.stringify({ name: "repo", version: "1.0.0" }));
+
+			const managerWithInternals = packageManager as unknown as PackageManagerInternals;
+			vi.spyOn(managerWithInternals, "runCommandCapture").mockImplementation(async (_command, args) => {
+				if (args[0] === "rev-parse" && args[1] === "HEAD") {
+					return "old-head";
+				}
+				if (args[0] === "rev-parse" && args[1] === "FETCH_HEAD^{commit}") {
+					return "new-head";
+				}
+				throw new Error(`Unexpected runCommandCapture args: ${args.join(" ")}`);
+			});
+			const runCommandSpy = vi.spyOn(managerWithInternals, "runCommand").mockResolvedValue(undefined);
+
+			await packageManager.install(source);
+
+			expect(runCommandSpy).toHaveBeenCalledWith("git", ["fetch", "origin", "v2"], { cwd: targetDir });
+			expect(runCommandSpy).toHaveBeenCalledWith("git", ["reset", "--hard", "FETCH_HEAD^{commit}"], {
+				cwd: targetDir,
+			});
+			expect(runCommandSpy).toHaveBeenCalledWith("git", ["clean", "-fdx"], { cwd: targetDir });
+			expect(runCommandSpy).toHaveBeenCalledWith("npm", ["install", "--omit=dev"], { cwd: targetDir });
+		});
+
+		it("should reconcile an existing git checkout to its update target when installing without a ref", async () => {
+			const source = "git:github.com/user/repo";
+			const targetDir = join(agentDir, "git", "github.com", "user", "repo");
+			const fetchArgs = ["fetch", "--prune", "--no-tags", "origin", "+refs/heads/main:refs/remotes/origin/main"];
+			mkdirSync(targetDir, { recursive: true });
+
+			const managerWithInternals = packageManager as unknown as PackageManagerInternals;
+			vi.spyOn(managerWithInternals, "getLocalGitUpdateTarget").mockResolvedValue({
+				ref: "origin/HEAD",
+				head: "new-head",
+				fetchArgs,
+			});
+			vi.spyOn(managerWithInternals, "runCommandCapture").mockImplementation(async (_command, args) => {
+				if (args[0] === "rev-parse" && args[1] === "HEAD") {
+					return "old-head";
+				}
+				if (args[0] === "rev-parse" && args[1] === "origin/HEAD^{commit}") {
+					return "new-head";
+				}
+				throw new Error(`Unexpected runCommandCapture args: ${args.join(" ")}`);
+			});
+			const runCommandSpy = vi.spyOn(managerWithInternals, "runCommand").mockResolvedValue(undefined);
+
+			await packageManager.install(source);
+
+			expect(runCommandSpy).toHaveBeenCalledWith("git", fetchArgs, { cwd: targetDir });
+			expect(runCommandSpy).toHaveBeenCalledWith("git", ["reset", "--hard", "origin/HEAD^{commit}"], {
+				cwd: targetDir,
+			});
+			expect(runCommandSpy).toHaveBeenCalledWith("git", ["clean", "-fdx"], { cwd: targetDir });
+		});
+
+		it("should use plain install for git package dependencies when npmCommand is configured", async () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["pnpm"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const source = "git:github.com/user/repo";
+			const targetDir = join(agentDir, "git", "github.com", "user", "repo");
+			const runCommandSpy = vi
+				.spyOn(packageManager as any, "runCommand")
+				.mockImplementation(async (...callArgs: unknown[]) => {
+					const [command, args] = callArgs as [string, string[]];
+					if (command === "git" && args[0] === "clone") {
+						mkdirSync(targetDir, { recursive: true });
+						writeFileSync(join(targetDir, "package.json"), JSON.stringify({ name: "repo", version: "1.0.0" }));
+					}
+				});
+
+			await packageManager.install(source);
+
+			expect(runCommandSpy).toHaveBeenCalledWith("pnpm", ["install"], { cwd: targetDir });
+		});
+
+		it("should update git package dependencies with --omit=dev", async () => {
+			const source = "git:github.com/user/repo";
+			const targetDir = join(tempDir, ".pi", "git", "github.com", "user", "repo");
+			mkdirSync(targetDir, { recursive: true });
+			writeFileSync(join(targetDir, "package.json"), JSON.stringify({ name: "repo", version: "1.0.0" }));
+			settingsManager.setProjectPackages([source]);
+
+			vi.spyOn(packageManager as any, "runCommandCapture").mockImplementation(async (...callArgs: unknown[]) => {
+				const [_command, args] = callArgs as [string, string[]];
+				if (args[0] === "rev-parse" && args[1] === "--abbrev-ref" && args[2] === "@{upstream}") {
+					return "origin/main";
+				}
+				if (args[0] === "rev-parse" && (args[1] === "@{upstream}" || args[1] === "@{upstream}^{commit}")) {
+					return "remote-head";
+				}
+				if (args[0] === "rev-parse" && args[1] === "HEAD") {
+					return "local-head";
+				}
+				throw new Error(`Unexpected runCommandCapture args: ${args.join(" ")}`);
+			});
+			const runCommandSpy = vi.spyOn(packageManager as any, "runCommand").mockResolvedValue(undefined);
+
+			await packageManager.update(source);
+
+			expect(runCommandSpy).toHaveBeenCalledWith("npm", ["install", "--omit=dev"], { cwd: targetDir });
+		});
+
+		it("should use plain install through npmCommand argv when updating git package dependencies", async () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["mise", "exec", "node@20", "--", "pnpm"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const source = "git:github.com/user/repo";
+			const targetDir = join(tempDir, ".pi", "git", "github.com", "user", "repo");
+			mkdirSync(targetDir, { recursive: true });
+			writeFileSync(join(targetDir, "package.json"), JSON.stringify({ name: "repo", version: "1.0.0" }));
+			settingsManager.setProjectPackages([source]);
+
+			vi.spyOn(packageManager as any, "runCommandCapture").mockImplementation(async (...callArgs: unknown[]) => {
+				const [_command, args] = callArgs as [string, string[]];
+				if (args[0] === "rev-parse" && args[1] === "--abbrev-ref" && args[2] === "@{upstream}") {
+					return "origin/main";
+				}
+				if (args[0] === "rev-parse" && (args[1] === "@{upstream}" || args[1] === "@{upstream}^{commit}")) {
+					return "remote-head";
+				}
+				if (args[0] === "rev-parse" && args[1] === "HEAD") {
+					return "local-head";
+				}
+				throw new Error(`Unexpected runCommandCapture args: ${args.join(" ")}`);
+			});
+			const runCommandSpy = vi.spyOn(packageManager as any, "runCommand").mockResolvedValue(undefined);
+
+			await packageManager.update(source);
+
+			expect(runCommandSpy).toHaveBeenCalledWith("mise", ["exec", "node@20", "--", "pnpm", "install"], {
+				cwd: targetDir,
+			});
+		});
+
+		it("should use npmCommand argv for npm root lookup and invalidate cached root when npmCommand changes", () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["mise", "exec", "node@20", "--", "npm"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const root20 = join(tempDir, "node20", "lib", "node_modules");
+			const root22 = join(tempDir, "node22", "lib", "node_modules");
+			mkdirSync(join(root20, "@scope", "pkg"), { recursive: true });
+
+			const runCommandSyncSpy = vi
+				.spyOn(packageManager as any, "runCommandSync")
+				.mockImplementation((...callArgs: unknown[]) => {
+					const [command, args] = callArgs as [string, string[]];
+					if (command !== "mise") {
+						throw new Error(`unexpected command ${command}`);
+					}
+					if (args[1] === "node@20") {
+						return root20;
+					}
+					if (args[1] === "node@22") {
+						return root22;
+					}
+					throw new Error(`unexpected args ${args.join(" ")}`);
+				});
+
+			expect(packageManager.getInstalledPath("npm:@scope/pkg", "user")).toBe(join(root20, "@scope", "pkg"));
+			expect(runCommandSyncSpy).toHaveBeenNthCalledWith(1, "mise", ["exec", "node@20", "--", "npm", "root", "-g"]);
+
+			settingsManager.setNpmCommand(["mise", "exec", "node@22", "--", "npm"]);
+
+			expect(packageManager.getInstalledPath("npm:@scope/pkg", "user")).toBeUndefined();
+			expect(runCommandSyncSpy).toHaveBeenNthCalledWith(2, "mise", ["exec", "node@22", "--", "npm", "root", "-g"]);
+		});
+
+		it("should install user npm packages into the pi-managed npm root", async () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["pnpm"],
+				packages: ["npm:pnpm-pkg"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const packagePath = join(agentDir, "npm", "node_modules", "pnpm-pkg");
+			vi.spyOn(packageManager as any, "runCommandSync").mockImplementation(() => {
+				throw new Error("legacy lookup unavailable");
+			});
+			const runCommandSpy = vi
+				.spyOn(packageManager as any, "runCommand")
+				.mockImplementation(async (...callArgs: unknown[]) => {
+					const [command, args] = callArgs as [string, string[]];
+					expect(command).toBe("pnpm");
+					expect(args).toEqual([
+						"install",
+						"pnpm-pkg",
+						"--prefix",
+						join(agentDir, "npm"),
+						"--config.auto-install-peers=false",
+						"--config.strict-peer-dependencies=false",
+						"--config.strict-dep-builds=false",
+					]);
+					mkdirSync(join(packagePath, "extensions"), { recursive: true });
+					writeFileSync(join(packagePath, "package.json"), JSON.stringify({ name: "pnpm-pkg", version: "1.0.0" }));
+					writeFileSync(join(packagePath, "extensions", "index.ts"), "export default function() {};");
+				});
+
+			const first = await packageManager.resolve();
+			const second = await packageManager.resolve();
+
+			expect(first.extensions.some((r) => r.path === join(packagePath, "extensions", "index.ts") && r.enabled)).toBe(
+				true,
+			);
+			expect(
+				second.extensions.some((r) => r.path === join(packagePath, "extensions", "index.ts") && r.enabled),
+			).toBe(true);
+			expect(runCommandSpy).toHaveBeenCalledTimes(1);
+			expect(packageManager.getInstalledPath("npm:pnpm-pkg", "user")).toBe(packagePath);
+		});
+
+		it("should load legacy pnpm global package paths from pnpm list output", async () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["pnpm"],
+				packages: ["npm:pnpm-pkg"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const pnpmRoot = join(tempDir, "pnpm", "global", "v11");
+			const packagePath = join(pnpmRoot, "20-hash", "node_modules", "pnpm-pkg");
+			mkdirSync(join(packagePath, "extensions"), { recursive: true });
+			writeFileSync(join(packagePath, "package.json"), JSON.stringify({ name: "pnpm-pkg", version: "1.0.0" }));
+			writeFileSync(join(packagePath, "extensions", "index.ts"), "export default function() {};");
+
+			vi.spyOn(packageManager as any, "runCommandSync").mockImplementation((...callArgs: unknown[]) => {
+				const [command, args] = callArgs as [string, string[]];
+				if (command !== "pnpm") {
+					throw new Error(`unexpected command ${command}`);
+				}
+				if (args.join(" ") === "list -g --depth 0 --json") {
+					return JSON.stringify([
+						{
+							path: pnpmRoot,
+							dependencies: { "pnpm-pkg": { version: "1.0.0", path: packagePath } },
+						},
+					]);
+				}
+				throw new Error(`unexpected args ${args.join(" ")}`);
+			});
+			const runCommandSpy = vi.spyOn(packageManager as any, "runCommand").mockResolvedValue(undefined);
+
+			const result = await packageManager.resolve();
+
+			expect(
+				result.extensions.some((r) => r.path === join(packagePath, "extensions", "index.ts") && r.enabled),
+			).toBe(true);
+			expect(runCommandSpy).not.toHaveBeenCalled();
+			expect(packageManager.getInstalledPath("npm:pnpm-pkg", "user")).toBe(packagePath);
+		});
+
+		it("should resolve wrapped pnpm global package paths from pnpm list output", () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["mise", "exec", "node@20", "--", "pnpm"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const pnpmRoot = join(tempDir, "pnpm", "global", "v11");
+			const packagePath = join(pnpmRoot, "20-hash", "node_modules", "pnpm-pkg");
+			mkdirSync(packagePath, { recursive: true });
+
+			vi.spyOn(packageManager as any, "runCommandSync").mockImplementation((...callArgs: unknown[]) => {
+				const [command, args] = callArgs as [string, string[]];
+				expect(command).toBe("mise");
+				if (args.join(" ") === "exec node@20 -- pnpm list -g --depth 0 --json") {
+					return JSON.stringify([{ path: pnpmRoot, dependencies: { "pnpm-pkg": { path: packagePath } } }]);
+				}
+				throw new Error(`unexpected args ${args.join(" ")}`);
+			});
+
+			expect(packageManager.getInstalledPath("npm:pnpm-pkg", "user")).toBe(packagePath);
+		});
+
+		it("should ignore malformed legacy pnpm global package lists", () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["pnpm"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			vi.spyOn(packageManager as any, "runCommandSync").mockReturnValue("not json");
+
+			expect(packageManager.getInstalledPath("npm:pnpm-pkg", "user")).toBeUndefined();
+		});
+	});
+
+	describe("source parsing", () => {
+		it("should emit progress events on install attempt", async () => {
+			const events: ProgressEvent[] = [];
+			packageManager.setProgressCallback((event) => events.push(event));
+
+			// Use public install method which emits progress events
+			try {
+				await packageManager.install("npm:nonexistent-package@1.0.0");
+			} catch {
+				// Expected to fail - package doesn't exist
+			}
+
+			// Should have emitted start event before failure
+			expect(events.some((e) => e.type === "start" && e.action === "install")).toBe(true);
+			// Should have emitted error event
+			expect(events.some((e) => e.type === "error")).toBe(true);
+		});
+
+		it("should recognize github URLs without git: prefix", async () => {
+			const events: ProgressEvent[] = [];
+			packageManager.setProgressCallback((event) => events.push(event));
+			const previousGitTerminalPrompt = process.env.GIT_TERMINAL_PROMPT;
+			process.env.GIT_TERMINAL_PROMPT = "0";
+
+			try {
+				// This should be parsed as a git source, not throw "unsupported"
+				try {
+					await packageManager.install("https://github.com/nonexistent/repo");
+				} catch {
+					// Expected to fail - repo doesn't exist
+				}
+			} finally {
+				if (previousGitTerminalPrompt === undefined) {
+					delete process.env.GIT_TERMINAL_PROMPT;
+				} else {
+					process.env.GIT_TERMINAL_PROMPT = previousGitTerminalPrompt;
+				}
+			}
+
+			// Should have attempted clone, not thrown unsupported error
+			expect(events.some((e) => e.type === "start" && e.action === "install")).toBe(true);
+		});
+
+		it("should parse package source types from docs examples", () => {
+			const parseNpm = (source: string) => {
+				const parsed = (packageManager as any).parseSource(source);
+				if (parsed.type !== "npm") {
+					throw new Error(`Expected npm source: ${source}`);
+				}
+				return parsed;
+			};
+
+			expect(parseNpm("npm:@scope/pkg@1.2.3").pinned).toBe(true);
+			expect(parseNpm("npm:@scope/pkg@^1.2.3").pinned).toBe(false);
+			expect(parseNpm("npm:pkg").pinned).toBe(false);
+
+			expect((packageManager as any).parseSource("git:github.com/user/repo@v1").type).toBe("git");
+			expect((packageManager as any).parseSource("https://github.com/user/repo@v1").type).toBe("git");
+			expect((packageManager as any).parseSource("git:git@github.com:user/repo@v1").type).toBe("git");
+			expect((packageManager as any).parseSource("ssh://git@github.com/user/repo@v1").type).toBe("git");
+
+			expect((packageManager as any).parseSource("/absolute/path/to/package").type).toBe("local");
+			expect((packageManager as any).parseSource("./relative/path/to/package").type).toBe("local");
+			expect((packageManager as any).parseSource("../relative/path/to/package").type).toBe("local");
+		});
+
+		it("should never parse dot-relative paths as git", () => {
+			const dotSlash = (packageManager as any).parseSource("./packages/agent-timers");
+			expect(dotSlash.type).toBe("local");
+			expect(dotSlash.path).toBe("./packages/agent-timers");
+
+			const dotDotSlash = (packageManager as any).parseSource("../packages/agent-timers");
+			expect(dotDotSlash.type).toBe("local");
+			expect(dotDotSlash.path).toBe("../packages/agent-timers");
+		});
+	});
+
+	describe("git install paths", () => {
+		it("should reject paths outside git install roots", () => {
+			const managerWithInternals = packageManager as unknown as PackageManagerInternals;
+			const traversalSource = {
+				type: "git" as const,
+				repo: "git@evil.example:../../victim/repo",
+				host: "evil.example",
+				path: "../../victim/repo",
+				pinned: false,
+			};
+
+			for (const scope of ["user", "project", "temporary"] as const) {
+				expect(() => managerWithInternals.getGitInstallPath(traversalSource, scope)).toThrow(
+					"outside package install root",
+				);
+			}
+		});
+	});
+
+	describe("temporary install paths", () => {
+		it("should place temporary npm packages under the agent temp extension folder", () => {
+			const managerWithInternals = packageManager as unknown as PackageManagerInternals;
+			const source = managerWithInternals.parseSource("npm:left-pad");
+			if (source.type !== "npm") {
+				throw new Error("Expected npm source");
+			}
+
+			const installPath = managerWithInternals.getNpmInstallPath(source, "temporary");
+			const tempRoot = join(agentDir, "tmp", "extensions");
+
+			expect(pathEndsWith(installPath, "node_modules/left-pad")).toBe(true);
+			expect(relative(tempRoot, installPath).startsWith("..")).toBe(false);
+			expect(installPath.startsWith(join(tmpdir(), "pi-extensions"))).toBe(false);
+			if (process.platform !== "win32") {
+				expect(statSync(tempRoot).mode & 0o777).toBe(0o700);
+			}
+		});
+	});
+
+	describe("settings source normalization", () => {
+		it("should store global local packages relative to agent settings base", () => {
+			const pkgDir = join(tempDir, "packages", "local-global-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "index.ts"), "export default function() {}");
+
+			const added = packageManager.addSourceToSettings("./packages/local-global-pkg");
+			expect(added).toBe(true);
+
+			const settings = settingsManager.getGlobalSettings();
+			const rel = relative(agentDir, pkgDir);
+			const expected = rel.startsWith(".") ? rel : `./${rel}`;
+			expect(settings.packages?.[0]).toBe(expected);
+		});
+
+		it("should store project local packages relative to .pi settings base", () => {
+			const projectPkgDir = join(tempDir, "project-local-pkg");
+			mkdirSync(join(projectPkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(projectPkgDir, "extensions", "index.ts"), "export default function() {}");
+
+			const added = packageManager.addSourceToSettings("./project-local-pkg", { local: true });
+			expect(added).toBe(true);
+
+			const settings = settingsManager.getProjectSettings();
+			const rel = relative(join(tempDir, ".pi"), projectPkgDir);
+			const expected = rel.startsWith(".") ? rel : `./${rel}`;
+			expect(settings.packages?.[0]).toBe(expected);
+		});
+
+		it("should remove local package entries using equivalent path forms", () => {
+			const pkgDir = join(tempDir, "remove-local-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "index.ts"), "export default function() {}");
+
+			packageManager.addSourceToSettings("./remove-local-pkg");
+			const removed = packageManager.removeSourceFromSettings(`${pkgDir}/`);
+			expect(removed).toBe(true);
+			expect(settingsManager.getGlobalSettings().packages ?? []).toHaveLength(0);
+		});
+
+		it("should return false when adding the same git source with the same ref", () => {
+			const first = packageManager.addSourceToSettings("git:github.com/user/repo@v1");
+			expect(first).toBe(true);
+
+			const second = packageManager.addSourceToSettings("git:github.com/user/repo@v1");
+			expect(second).toBe(false);
+			expect(settingsManager.getGlobalSettings().packages).toEqual(["git:github.com/user/repo@v1"]);
+		});
+
+		it("should update the ref when adding the same git source with a different ref", () => {
+			packageManager.addSourceToSettings("git:github.com/user/repo@v1");
+
+			const updated = packageManager.addSourceToSettings("git:github.com/user/repo@v2");
+			expect(updated).toBe(true);
+			expect(settingsManager.getGlobalSettings().packages).toEqual(["git:github.com/user/repo@v2"]);
+		});
+
+		it("should preserve package filters when replacing a package source ref", () => {
+			settingsManager.setPackages([
+				{
+					source: "git:github.com/user/repo@v1",
+					extensions: ["extensions/main.ts"],
+					skills: [],
+					prompts: ["prompts/review.md"],
+					themes: ["themes/dark.json"],
+				},
+			]);
+
+			const updated = packageManager.addSourceToSettings("git:github.com/user/repo@v2");
+			expect(updated).toBe(true);
+			expect(settingsManager.getGlobalSettings().packages).toEqual([
+				{
+					source: "git:github.com/user/repo@v2",
+					extensions: ["extensions/main.ts"],
+					skills: [],
+					prompts: ["prompts/review.md"],
+					themes: ["themes/dark.json"],
+				},
+			]);
+		});
+	});
+
+	describe("HTTPS git URL parsing (old behavior)", () => {
+		it("should parse HTTPS GitHub URLs correctly", async () => {
+			const parsed = (packageManager as any).parseSource("https://github.com/user/repo");
+			expect(parsed.type).toBe("git");
+			expect(parsed.host).toBe("github.com");
+			expect(parsed.path).toBe("user/repo");
+			expect(parsed.pinned).toBe(false);
+		});
+
+		it("should parse HTTPS URLs with git: prefix", async () => {
+			const parsed = (packageManager as any).parseSource("git:https://github.com/user/repo");
+			expect(parsed.type).toBe("git");
+			expect(parsed.host).toBe("github.com");
+			expect(parsed.path).toBe("user/repo");
+		});
+
+		it("should parse HTTPS URLs with ref", async () => {
+			const parsed = (packageManager as any).parseSource("https://github.com/user/repo@v1.2.3");
+			expect(parsed.type).toBe("git");
+			expect(parsed.host).toBe("github.com");
+			expect(parsed.path).toBe("user/repo");
+			expect(parsed.ref).toBe("v1.2.3");
+			expect(parsed.pinned).toBe(true);
+		});
+
+		it("should parse host/path shorthand only with git: prefix", async () => {
+			const parsed = (packageManager as any).parseSource("git:github.com/user/repo");
+			expect(parsed.type).toBe("git");
+			expect(parsed.host).toBe("github.com");
+			expect(parsed.path).toBe("user/repo");
+		});
+
+		it("should treat host/path shorthand as local without git: prefix", async () => {
+			const parsed = (packageManager as any).parseSource("github.com/user/repo");
+			expect(parsed.type).toBe("local");
+		});
+
+		it("should parse HTTPS URLs with .git suffix", async () => {
+			const parsed = (packageManager as any).parseSource("https://github.com/user/repo.git");
+			expect(parsed.type).toBe("git");
+			expect(parsed.host).toBe("github.com");
+			expect(parsed.path).toBe("user/repo");
+		});
+
+		it("should parse GitLab HTTPS URLs", async () => {
+			const parsed = (packageManager as any).parseSource("https://gitlab.com/user/repo");
+			expect(parsed.type).toBe("git");
+			expect(parsed.host).toBe("gitlab.com");
+			expect(parsed.path).toBe("user/repo");
+		});
+
+		it("should parse Bitbucket HTTPS URLs", async () => {
+			const parsed = (packageManager as any).parseSource("https://bitbucket.org/user/repo");
+			expect(parsed.type).toBe("git");
+			expect(parsed.host).toBe("bitbucket.org");
+			expect(parsed.path).toBe("user/repo");
+		});
+
+		it("should parse Codeberg HTTPS URLs", async () => {
+			const parsed = (packageManager as any).parseSource("https://codeberg.org/user/repo");
+			expect(parsed.type).toBe("git");
+			expect(parsed.host).toBe("codeberg.org");
+			expect(parsed.path).toBe("user/repo");
+		});
+
+		it("should generate correct package identity for protocol and git:-prefixed URLs", async () => {
+			const identity1 = (packageManager as any).getPackageIdentity("https://github.com/user/repo");
+			const identity2 = (packageManager as any).getPackageIdentity("https://github.com/user/repo@v1.0.0");
+			const identity3 = (packageManager as any).getPackageIdentity("git:github.com/user/repo");
+			const identity4 = (packageManager as any).getPackageIdentity("https://github.com/user/repo.git");
+
+			// All should have the same identity (normalized)
+			expect(identity1).toBe("git:github.com/user/repo");
+			expect(identity2).toBe("git:github.com/user/repo");
+			expect(identity3).toBe("git:github.com/user/repo");
+			expect(identity4).toBe("git:github.com/user/repo");
+		});
+
+		it("should deduplicate git URLs with different supported formats", async () => {
+			const pkgDir = join(tempDir, "https-dedup-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "test.ts"), "export default function() {}");
+
+			// Mock the package as if it were cloned from different URL formats
+			// In reality, these would all point to the same local dir after install
+			settingsManager.setPackages([
+				"https://github.com/user/repo",
+				"git:github.com/user/repo",
+				"https://github.com/user/repo.git",
+			]);
+
+			// Since these URLs don't actually exist and we can't clone them,
+			// we verify they produce the same identity
+			const id1 = (packageManager as any).getPackageIdentity("https://github.com/user/repo");
+			const id2 = (packageManager as any).getPackageIdentity("git:github.com/user/repo");
+			const id3 = (packageManager as any).getPackageIdentity("https://github.com/user/repo.git");
+
+			expect(id1).toBe(id2);
+			expect(id2).toBe(id3);
+		});
+
+		it("should handle HTTPS URLs with refs in resolve", async () => {
+			// This tests that the ref is properly extracted and stored
+			const parsed = (packageManager as any).parseSource("https://github.com/user/repo@main");
+			expect(parsed.ref).toBe("main");
+			expect(parsed.pinned).toBe(true);
+
+			const parsed2 = (packageManager as any).parseSource("https://github.com/user/repo@feature/branch");
+			expect(parsed2.ref).toBe("feature/branch");
+		});
+	});
+
+	describe("pattern filtering in top-level arrays", () => {
+		it("should exclude extensions with ! pattern", async () => {
+			const extDir = join(agentDir, "extensions");
+			mkdirSync(extDir, { recursive: true });
+			writeFileSync(join(extDir, "keep.ts"), "export default function() {}");
+			writeFileSync(join(extDir, "remove.ts"), "export default function() {}");
+
+			settingsManager.setExtensionPaths(["extensions", "!**/remove.ts"]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => isEnabled(r, "keep.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isDisabled(r, "remove.ts"))).toBe(true);
+		});
+
+		it("should filter themes with glob patterns", async () => {
+			const themesDir = join(agentDir, "themes");
+			mkdirSync(themesDir, { recursive: true });
+			writeFileSync(join(themesDir, "dark.json"), "{}");
+			writeFileSync(join(themesDir, "light.json"), "{}");
+			writeFileSync(join(themesDir, "funky.json"), "{}");
+
+			settingsManager.setThemePaths(["themes", "!funky.json"]);
+
+			const result = await packageManager.resolve();
+			expect(result.themes.some((r) => isEnabled(r, "dark.json"))).toBe(true);
+			expect(result.themes.some((r) => isEnabled(r, "light.json"))).toBe(true);
+			expect(result.themes.some((r) => isDisabled(r, "funky.json"))).toBe(true);
+		});
+
+		it("should filter prompts with exclusion pattern", async () => {
+			const promptsDir = join(agentDir, "prompts");
+			mkdirSync(promptsDir, { recursive: true });
+			writeFileSync(join(promptsDir, "review.md"), "Review code");
+			writeFileSync(join(promptsDir, "explain.md"), "Explain code");
+
+			settingsManager.setPromptTemplatePaths(["prompts", "!explain.md"]);
+
+			const result = await packageManager.resolve();
+			expect(result.prompts.some((r) => isEnabled(r, "review.md"))).toBe(true);
+			expect(result.prompts.some((r) => isDisabled(r, "explain.md"))).toBe(true);
+		});
+
+		it("should filter skills with exclusion pattern", async () => {
+			const skillsDir = join(agentDir, "skills");
+			mkdirSync(join(skillsDir, "good-skill"), { recursive: true });
+			mkdirSync(join(skillsDir, "bad-skill"), { recursive: true });
+			writeFileSync(
+				join(skillsDir, "good-skill", "SKILL.md"),
+				"---\nname: good-skill\ndescription: Good\n---\nContent",
+			);
+			writeFileSync(
+				join(skillsDir, "bad-skill", "SKILL.md"),
+				"---\nname: bad-skill\ndescription: Bad\n---\nContent",
+			);
+
+			settingsManager.setSkillPaths(["skills", "!**/bad-skill"]);
+
+			const result = await packageManager.resolve();
+			expect(result.skills.some((r) => isEnabled(r, "good-skill", "includes"))).toBe(true);
+			expect(result.skills.some((r) => isDisabled(r, "bad-skill", "includes"))).toBe(true);
+		});
+
+		it("should work without patterns (backward compatible)", async () => {
+			const extDir = join(agentDir, "extensions");
+			mkdirSync(extDir, { recursive: true });
+			const extPath = join(extDir, "my-ext.ts");
+			writeFileSync(extPath, "export default function() {}");
+
+			settingsManager.setExtensionPaths(["extensions/my-ext.ts"]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => r.path === extPath && r.enabled)).toBe(true);
+		});
+	});
+
+	describe("pattern filtering in pi manifest", () => {
+		it("should support glob patterns in manifest extensions", async () => {
+			const pkgDir = join(tempDir, "manifest-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			mkdirSync(join(pkgDir, "node_modules/dep/extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "local.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "node_modules/dep/extensions", "remote.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "node_modules/dep/extensions", "skip.ts"), "export default function() {}");
+			writeFileSync(
+				join(pkgDir, "package.json"),
+				JSON.stringify({
+					name: "manifest-pkg",
+					pi: {
+						extensions: ["extensions", "node_modules/dep/extensions", "!**/skip.ts"],
+					},
+				}),
+			);
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+			expect(result.extensions.some((r) => isEnabled(r, "local.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isEnabled(r, "remote.ts"))).toBe(true);
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "skip.ts"))).toBe(false);
+		});
+
+		it("should support glob patterns in manifest skills", async () => {
+			const pkgDir = join(tempDir, "skill-manifest-pkg");
+			mkdirSync(join(pkgDir, "skills/good-skill"), { recursive: true });
+			mkdirSync(join(pkgDir, "skills/bad-skill"), { recursive: true });
+			writeFileSync(
+				join(pkgDir, "skills/good-skill", "SKILL.md"),
+				"---\nname: good-skill\ndescription: Good\n---\nContent",
+			);
+			writeFileSync(
+				join(pkgDir, "skills/bad-skill", "SKILL.md"),
+				"---\nname: bad-skill\ndescription: Bad\n---\nContent",
+			);
+			writeFileSync(
+				join(pkgDir, "package.json"),
+				JSON.stringify({
+					name: "skill-manifest-pkg",
+					pi: {
+						skills: ["skills", "!**/bad-skill"],
+					},
+				}),
+			);
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+			expect(result.skills.some((r) => isEnabled(r, "good-skill", "includes"))).toBe(true);
+			expect(result.skills.some((r) => r.path.includes("bad-skill"))).toBe(false);
+		});
+
+		it("should expand positive glob manifest entries before collecting skills", async () => {
+			const pkgDir = join(tempDir, "skill-manifest-glob-pkg");
+			mkdirSync(join(pkgDir, "plugins/pdf-to-markdown/skills/pdf-to-markdown"), { recursive: true });
+			mkdirSync(join(pkgDir, "plugins/nutrient-dws/skills/document-processor-api"), { recursive: true });
+			writeFileSync(
+				join(pkgDir, "plugins/pdf-to-markdown/skills/pdf-to-markdown", "SKILL.md"),
+				"---\nname: pdf-to-markdown\ndescription: PDF to Markdown\n---\nContent",
+			);
+			writeFileSync(
+				join(pkgDir, "plugins/nutrient-dws/skills/document-processor-api", "SKILL.md"),
+				"---\nname: document-processor-api\ndescription: DWS\n---\nContent",
+			);
+			writeFileSync(
+				join(pkgDir, "package.json"),
+				JSON.stringify({
+					name: "skill-manifest-glob-pkg",
+					pi: {
+						skills: ["./plugins/*/skills"],
+					},
+				}),
+			);
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+			expect(result.skills.some((r) => isEnabled(r, "pdf-to-markdown", "includes"))).toBe(true);
+			expect(result.skills.some((r) => isEnabled(r, "document-processor-api", "includes"))).toBe(true);
+		});
+	});
+
+	describe("pattern filtering in package filters", () => {
+		it("should apply user filters on top of manifest filters (not replace)", async () => {
+			// Manifest excludes baz.ts, user excludes bar.ts
+			// Result should exclude BOTH
+			const pkgDir = join(tempDir, "layered-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "foo.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "bar.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "baz.ts"), "export default function() {}");
+			writeFileSync(
+				join(pkgDir, "package.json"),
+				JSON.stringify({
+					name: "layered-pkg",
+					pi: {
+						extensions: ["extensions", "!**/baz.ts"],
+					},
+				}),
+			);
+
+			// User filter adds exclusion for bar.ts
+			settingsManager.setPackages([
+				{
+					source: pkgDir,
+					extensions: ["!**/bar.ts"],
+					skills: [],
+					prompts: [],
+					themes: [],
+				},
+			]);
+
+			const result = await packageManager.resolve();
+			// foo.ts should be included (not excluded by anyone)
+			expect(result.extensions.some((r) => isEnabled(r, "foo.ts"))).toBe(true);
+			// bar.ts should be excluded (by user)
+			expect(result.extensions.some((r) => isDisabled(r, "bar.ts"))).toBe(true);
+			// baz.ts should be excluded (by manifest)
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "baz.ts"))).toBe(false);
+		});
+
+		it("should exclude extensions from package with ! pattern", async () => {
+			const pkgDir = join(tempDir, "pattern-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "foo.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "bar.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "baz.ts"), "export default function() {}");
+
+			settingsManager.setPackages([
+				{
+					source: pkgDir,
+					extensions: ["!**/baz.ts"],
+					skills: [],
+					prompts: [],
+					themes: [],
+				},
+			]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => isEnabled(r, "foo.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isEnabled(r, "bar.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isDisabled(r, "baz.ts"))).toBe(true);
+		});
+
+		it("should filter themes from package", async () => {
+			const pkgDir = join(tempDir, "theme-pkg");
+			mkdirSync(join(pkgDir, "themes"), { recursive: true });
+			writeFileSync(join(pkgDir, "themes", "nice.json"), "{}");
+			writeFileSync(join(pkgDir, "themes", "ugly.json"), "{}");
+
+			settingsManager.setPackages([
+				{
+					source: pkgDir,
+					extensions: [],
+					skills: [],
+					prompts: [],
+					themes: ["!ugly.json"],
+				},
+			]);
+
+			const result = await packageManager.resolve();
+			expect(result.themes.some((r) => isEnabled(r, "nice.json"))).toBe(true);
+			expect(result.themes.some((r) => isDisabled(r, "ugly.json"))).toBe(true);
+		});
+
+		it("should combine include and exclude patterns", async () => {
+			const pkgDir = join(tempDir, "combo-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "alpha.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "beta.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "gamma.ts"), "export default function() {}");
+
+			settingsManager.setPackages([
+				{
+					source: pkgDir,
+					extensions: ["**/alpha.ts", "**/beta.ts", "!**/beta.ts"],
+					skills: [],
+					prompts: [],
+					themes: [],
+				},
+			]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => isEnabled(r, "alpha.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isDisabled(r, "beta.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isDisabled(r, "gamma.ts"))).toBe(true);
+		});
+
+		it("should work with direct paths (no patterns)", async () => {
+			const pkgDir = join(tempDir, "direct-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "one.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "two.ts"), "export default function() {}");
+
+			settingsManager.setPackages([
+				{
+					source: pkgDir,
+					extensions: ["extensions/one.ts"],
+					skills: [],
+					prompts: [],
+					themes: [],
+				},
+			]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => isEnabled(r, "one.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isDisabled(r, "two.ts"))).toBe(true);
+		});
+
+		it("should resolve autoload-disabled project package entries as deltas over global packages", async () => {
+			const pkgDir = join(agentDir, "npm", "node_modules", "pi-tools");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "package.json"), JSON.stringify({ name: "pi-tools", version: "1.0.0" }));
+			writeFileSync(join(pkgDir, "extensions", "foo.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "bar.ts"), "export default function() {}");
+			settingsManager.setPackages(["npm:pi-tools"]);
+			settingsManager.setProjectPackages([
+				{ source: "npm:pi-tools", autoload: false, extensions: ["-extensions/foo.ts"] },
+			]);
+			const runCommandSpy = vi
+				.spyOn(packageManager as unknown as PackageManagerInternals, "runCommand")
+				.mockRejectedValue(new Error("unexpected install"));
+
+			const result = await packageManager.resolve();
+			const states = Object.fromEntries(
+				result.extensions.map((resource) => [
+					resource.path,
+					{ enabled: resource.enabled, scope: resource.metadata.scope },
+				]),
+			);
+			expect(runCommandSpy).not.toHaveBeenCalled();
+			expect(states[join(pkgDir, "extensions", "foo.ts")]).toEqual({ enabled: false, scope: "project" });
+			expect(states[join(pkgDir, "extensions", "bar.ts")]).toEqual({ enabled: true, scope: "user" });
+		});
+
+		it("should resolve autoload-disabled package entries as positive-only without a global package", async () => {
+			const pkgDir = join(tempDir, "positive-only-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			mkdirSync(join(pkgDir, "skills", "foo"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "foo.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "bar.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "skills", "foo", "SKILL.md"), "# Foo\n");
+			settingsManager.setProjectPackages([
+				{ source: relative(join(tempDir, ".pi"), pkgDir), autoload: false, extensions: ["+extensions/foo.ts"] },
+			]);
+
+			const result = await packageManager.resolve();
+
+			expect(result.extensions.map((resource) => resource.path)).toEqual([join(pkgDir, "extensions", "foo.ts")]);
+			expect(result.skills).toEqual([]);
+		});
+	});
+
+	describe("force-include patterns", () => {
+		it("should force-include extensions with + pattern after exclusion", async () => {
+			const extDir = join(agentDir, "extensions");
+			mkdirSync(extDir, { recursive: true });
+			writeFileSync(join(extDir, "keep.ts"), "export default function() {}");
+			writeFileSync(join(extDir, "excluded.ts"), "export default function() {}");
+			writeFileSync(join(extDir, "force-back.ts"), "export default function() {}");
+
+			// Exclude all, then force-include one back
+			settingsManager.setExtensionPaths(["extensions", "!extensions/*.ts", "+extensions/force-back.ts"]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => isDisabled(r, "keep.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isDisabled(r, "excluded.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isEnabled(r, "force-back.ts"))).toBe(true);
+		});
+
+		it("should force-include overrides exclude in package filters", async () => {
+			const pkgDir = join(tempDir, "force-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "alpha.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "beta.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "gamma.ts"), "export default function() {}");
+
+			settingsManager.setPackages([
+				{
+					source: pkgDir,
+					extensions: ["!**/*.ts", "+extensions/beta.ts"],
+					skills: [],
+					prompts: [],
+					themes: [],
+				},
+			]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => isDisabled(r, "alpha.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isEnabled(r, "beta.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isDisabled(r, "gamma.ts"))).toBe(true);
+		});
+
+		it("should force-include multiple resources", async () => {
+			const pkgDir = join(tempDir, "multi-force-pkg");
+			mkdirSync(join(pkgDir, "skills/skill-a"), { recursive: true });
+			mkdirSync(join(pkgDir, "skills/skill-b"), { recursive: true });
+			mkdirSync(join(pkgDir, "skills/skill-c"), { recursive: true });
+			writeFileSync(join(pkgDir, "skills/skill-a", "SKILL.md"), "---\nname: skill-a\ndescription: A\n---\nContent");
+			writeFileSync(join(pkgDir, "skills/skill-b", "SKILL.md"), "---\nname: skill-b\ndescription: B\n---\nContent");
+			writeFileSync(join(pkgDir, "skills/skill-c", "SKILL.md"), "---\nname: skill-c\ndescription: C\n---\nContent");
+
+			settingsManager.setPackages([
+				{
+					source: pkgDir,
+					extensions: [],
+					skills: ["!**/*", "+skills/skill-a", "+skills/skill-c"],
+					prompts: [],
+					themes: [],
+				},
+			]);
+
+			const result = await packageManager.resolve();
+			expect(result.skills.some((r) => isEnabled(r, "skill-a", "includes"))).toBe(true);
+			expect(result.skills.some((r) => isDisabled(r, "skill-b", "includes"))).toBe(true);
+			expect(result.skills.some((r) => isEnabled(r, "skill-c", "includes"))).toBe(true);
+		});
+
+		it("should force-include after specific exclusion", async () => {
+			const extDir = join(agentDir, "extensions");
+			mkdirSync(extDir, { recursive: true });
+			writeFileSync(join(extDir, "a.ts"), "export default function() {}");
+			writeFileSync(join(extDir, "b.ts"), "export default function() {}");
+
+			// Specifically exclude b.ts, then force it back
+			settingsManager.setExtensionPaths(["extensions", "!extensions/b.ts", "+extensions/b.ts"]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => isEnabled(r, "a.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isEnabled(r, "b.ts"))).toBe(true);
+		});
+
+		it("should handle force-include in manifest patterns", async () => {
+			const pkgDir = join(tempDir, "manifest-force-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "one.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "two.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "three.ts"), "export default function() {}");
+			writeFileSync(
+				join(pkgDir, "package.json"),
+				JSON.stringify({
+					name: "manifest-force-pkg",
+					pi: {
+						extensions: ["extensions", "!**/two.ts", "+extensions/two.ts"],
+					},
+				}),
+			);
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+			expect(result.extensions.some((r) => isEnabled(r, "one.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isEnabled(r, "two.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isEnabled(r, "three.ts"))).toBe(true);
+		});
+
+		it("should force-include themes", async () => {
+			const themesDir = join(agentDir, "themes");
+			mkdirSync(themesDir, { recursive: true });
+			writeFileSync(join(themesDir, "dark.json"), "{}");
+			writeFileSync(join(themesDir, "light.json"), "{}");
+			writeFileSync(join(themesDir, "special.json"), "{}");
+
+			settingsManager.setThemePaths(["themes", "!themes/*.json", "+themes/special.json"]);
+
+			const result = await packageManager.resolve();
+			expect(result.themes.some((r) => isDisabled(r, "dark.json"))).toBe(true);
+			expect(result.themes.some((r) => isDisabled(r, "light.json"))).toBe(true);
+			expect(result.themes.some((r) => isEnabled(r, "special.json"))).toBe(true);
+		});
+
+		it("should force-include prompts", async () => {
+			const promptsDir = join(agentDir, "prompts");
+			mkdirSync(promptsDir, { recursive: true });
+			writeFileSync(join(promptsDir, "review.md"), "Review");
+			writeFileSync(join(promptsDir, "explain.md"), "Explain");
+			writeFileSync(join(promptsDir, "debug.md"), "Debug");
+
+			settingsManager.setPromptTemplatePaths(["prompts", "!prompts/*.md", "+prompts/debug.md"]);
+
+			const result = await packageManager.resolve();
+			expect(result.prompts.some((r) => isDisabled(r, "review.md"))).toBe(true);
+			expect(result.prompts.some((r) => isDisabled(r, "explain.md"))).toBe(true);
+			expect(result.prompts.some((r) => isEnabled(r, "debug.md"))).toBe(true);
+		});
+	});
+
+	describe("force-exclude patterns", () => {
+		it("should force-exclude top-level resources", async () => {
+			const extDir = join(agentDir, "extensions");
+			mkdirSync(extDir, { recursive: true });
+			writeFileSync(join(extDir, "alpha.ts"), "export default function() {}");
+			writeFileSync(join(extDir, "beta.ts"), "export default function() {}");
+
+			settingsManager.setExtensionPaths(["extensions", "+extensions/alpha.ts", "-extensions/alpha.ts"]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => isDisabled(r, "alpha.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isEnabled(r, "beta.ts"))).toBe(true);
+		});
+
+		it("should force-exclude in package filters", async () => {
+			const pkgDir = join(tempDir, "force-exclude-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "alpha.ts"), "export default function() {}");
+			writeFileSync(join(pkgDir, "extensions", "beta.ts"), "export default function() {}");
+
+			settingsManager.setPackages([
+				{
+					source: pkgDir,
+					extensions: ["extensions/*.ts", "+extensions/alpha.ts", "-extensions/alpha.ts"],
+					skills: [],
+					prompts: [],
+					themes: [],
+				},
+			]);
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => isDisabled(r, "alpha.ts"))).toBe(true);
+			expect(result.extensions.some((r) => isEnabled(r, "beta.ts"))).toBe(true);
+		});
+	});
+
+	describe("package deduplication", () => {
+		it("should dedupe same local package in global and project (project wins)", async () => {
+			const pkgDir = join(tempDir, "shared-pkg");
+			mkdirSync(join(pkgDir, "extensions"), { recursive: true });
+			writeFileSync(join(pkgDir, "extensions", "shared.ts"), "export default function() {}");
+
+			// Same package in both global and project
+			settingsManager.setPackages([pkgDir]); // global
+			settingsManager.setProjectPackages([pkgDir]); // project
+
+			// Debug: verify settings are stored correctly
+			const globalSettings = settingsManager.getGlobalSettings();
+			const projectSettings = settingsManager.getProjectSettings();
+			expect(globalSettings.packages).toEqual([pkgDir]);
+			expect(projectSettings.packages).toEqual([pkgDir]);
+
+			const result = await packageManager.resolve();
+			// Should only appear once (deduped), with project scope
+			const sharedPaths = result.extensions.filter((r) => r.path.includes("shared-pkg"));
+			expect(sharedPaths.length).toBe(1);
+			expect(sharedPaths[0].metadata.scope).toBe("project");
+		});
+
+		it("should keep both if different packages", async () => {
+			const pkg1Dir = join(tempDir, "pkg1");
+			const pkg2Dir = join(tempDir, "pkg2");
+			mkdirSync(join(pkg1Dir, "extensions"), { recursive: true });
+			mkdirSync(join(pkg2Dir, "extensions"), { recursive: true });
+			writeFileSync(join(pkg1Dir, "extensions", "from-pkg1.ts"), "export default function() {}");
+			writeFileSync(join(pkg2Dir, "extensions", "from-pkg2.ts"), "export default function() {}");
+
+			settingsManager.setPackages([pkg1Dir]); // global
+			settingsManager.setProjectPackages([pkg2Dir]); // project
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => r.path.includes("pkg1"))).toBe(true);
+			expect(result.extensions.some((r) => r.path.includes("pkg2"))).toBe(true);
+		});
+
+		it("should dedupe SSH and HTTPS URLs for same repo", async () => {
+			// Same repository, different URL formats
+			const httpsUrl = "https://github.com/user/repo";
+			const sshUrl = "git:git@github.com:user/repo";
+
+			const httpsIdentity = (packageManager as any).getPackageIdentity(httpsUrl);
+			const sshIdentity = (packageManager as any).getPackageIdentity(sshUrl);
+
+			// Both should resolve to the same identity
+			expect(httpsIdentity).toBe("git:github.com/user/repo");
+			expect(sshIdentity).toBe("git:github.com/user/repo");
+			expect(httpsIdentity).toBe(sshIdentity);
+		});
+
+		it("should dedupe SSH and HTTPS with refs", async () => {
+			const httpsUrl = "https://github.com/user/repo@v1.0.0";
+			const sshUrl = "git:git@github.com:user/repo@v1.0.0";
+
+			const httpsIdentity = (packageManager as any).getPackageIdentity(httpsUrl);
+			const sshIdentity = (packageManager as any).getPackageIdentity(sshUrl);
+
+			// Identity should ignore ref (version)
+			expect(httpsIdentity).toBe("git:github.com/user/repo");
+			expect(sshIdentity).toBe("git:github.com/user/repo");
+			expect(httpsIdentity).toBe(sshIdentity);
+		});
+
+		it("should dedupe SSH URL with ssh:// protocol and git@ format", async () => {
+			const sshProtocol = "ssh://git@github.com/user/repo";
+			const gitAt = "git:git@github.com:user/repo";
+
+			const sshProtocolIdentity = (packageManager as any).getPackageIdentity(sshProtocol);
+			const gitAtIdentity = (packageManager as any).getPackageIdentity(gitAt);
+
+			// Both SSH formats should resolve to same identity
+			expect(sshProtocolIdentity).toBe("git:github.com/user/repo");
+			expect(gitAtIdentity).toBe("git:github.com/user/repo");
+			expect(sshProtocolIdentity).toBe(gitAtIdentity);
+		});
+
+		it("should dedupe all supported URL formats for same repo", async () => {
+			const urls = [
+				"https://github.com/user/repo",
+				"https://github.com/user/repo.git",
+				"ssh://git@github.com/user/repo",
+				"git:https://github.com/user/repo",
+				"git:github.com/user/repo",
+				"git:git@github.com:user/repo",
+				"git:git@github.com:user/repo.git",
+			];
+
+			const identities = urls.map((url) => (packageManager as any).getPackageIdentity(url));
+
+			// All should produce the same identity
+			const uniqueIdentities = [...new Set(identities)];
+			expect(uniqueIdentities.length).toBe(1);
+			expect(uniqueIdentities[0]).toBe("git:github.com/user/repo");
+		});
+
+		it("should keep different repos separate (HTTPS vs SSH)", async () => {
+			const repo1Https = "https://github.com/user/repo1";
+			const repo2Ssh = "git:git@github.com:user/repo2";
+
+			const id1 = (packageManager as any).getPackageIdentity(repo1Https);
+			const id2 = (packageManager as any).getPackageIdentity(repo2Ssh);
+
+			// Different repos should have different identities
+			expect(id1).toBe("git:github.com/user/repo1");
+			expect(id2).toBe("git:github.com/user/repo2");
+			expect(id1).not.toBe(id2);
+		});
+	});
+
+	describe("multi-file extension discovery (issue #1102)", () => {
+		it("should only load index.ts from subdirectories, not helper modules", async () => {
+			// Regression test: packages with multi-file extensions in subdirectories
+			// should only load the index.ts entry point, not helper modules like agents.ts
+			const pkgDir = join(tempDir, "multifile-pkg");
+			mkdirSync(join(pkgDir, "extensions", "subagent"), { recursive: true });
+
+			// Main entry point
+			writeFileSync(
+				join(pkgDir, "extensions", "subagent", "index.ts"),
+				`import { helper } from "./agents.ts";
+export default function(api) { api.registerTool({ name: "test", description: "test", execute: async () => helper() }); }`,
+			);
+			// Helper module (should NOT be loaded as standalone extension)
+			writeFileSync(
+				join(pkgDir, "extensions", "subagent", "agents.ts"),
+				`export function helper() { return "helper"; }`,
+			);
+			// Top-level extension file (should be loaded)
+			writeFileSync(join(pkgDir, "extensions", "standalone.ts"), "export default function(api) {}");
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+
+			// Should find the index.ts and standalone.ts
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "subagent/index.ts") && r.enabled)).toBe(true);
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "standalone.ts") && r.enabled)).toBe(true);
+
+			// Should NOT find agents.ts as a standalone extension
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "agents.ts"))).toBe(false);
+		});
+
+		it("should respect package.json pi.extensions manifest in subdirectories", async () => {
+			const pkgDir = join(tempDir, "manifest-subdir-pkg");
+			mkdirSync(join(pkgDir, "extensions", "custom"), { recursive: true });
+
+			// Subdirectory with its own manifest
+			writeFileSync(
+				join(pkgDir, "extensions", "custom", "package.json"),
+				JSON.stringify({
+					pi: {
+						extensions: ["./main.ts"],
+					},
+				}),
+			);
+			writeFileSync(join(pkgDir, "extensions", "custom", "main.ts"), "export default function(api) {}");
+			writeFileSync(join(pkgDir, "extensions", "custom", "utils.ts"), "export const util = 1;");
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+
+			// Should find main.ts declared in manifest
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "custom/main.ts") && r.enabled)).toBe(true);
+
+			// Should NOT find utils.ts (not declared in manifest)
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "utils.ts"))).toBe(false);
+		});
+
+		it("should handle mixed top-level files and subdirectories", async () => {
+			const pkgDir = join(tempDir, "mixed-pkg");
+			mkdirSync(join(pkgDir, "extensions", "complex"), { recursive: true });
+
+			// Top-level extension
+			writeFileSync(join(pkgDir, "extensions", "simple.ts"), "export default function(api) {}");
+
+			// Subdirectory with index.ts + helpers
+			writeFileSync(
+				join(pkgDir, "extensions", "complex", "index.ts"),
+				"import { a } from './a.ts'; export default function(api) {}",
+			);
+			writeFileSync(join(pkgDir, "extensions", "complex", "a.ts"), "export const a = 1;");
+			writeFileSync(join(pkgDir, "extensions", "complex", "b.ts"), "export const b = 2;");
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+
+			// Should find simple.ts and complex/index.ts
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "simple.ts") && r.enabled)).toBe(true);
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "complex/index.ts") && r.enabled)).toBe(true);
+
+			// Should NOT find helper modules
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "complex/a.ts"))).toBe(false);
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "complex/b.ts"))).toBe(false);
+
+			// Total should be exactly 2
+			expect(result.extensions.filter((r) => r.enabled).length).toBe(2);
+		});
+
+		it("should skip subdirectories without index.ts or manifest", async () => {
+			const pkgDir = join(tempDir, "no-entry-pkg");
+			mkdirSync(join(pkgDir, "extensions", "broken"), { recursive: true });
+
+			// Subdirectory with no index.ts and no manifest
+			writeFileSync(join(pkgDir, "extensions", "broken", "helper.ts"), "export const x = 1;");
+			writeFileSync(join(pkgDir, "extensions", "broken", "another.ts"), "export const y = 2;");
+
+			// Valid top-level extension
+			writeFileSync(join(pkgDir, "extensions", "valid.ts"), "export default function(api) {}");
+
+			const result = await packageManager.resolveExtensionSources([pkgDir]);
+
+			// Should only find the valid top-level extension
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "valid.ts") && r.enabled)).toBe(true);
+			expect(result.extensions.filter((r) => r.enabled).length).toBe(1);
+		});
+	});
+
+	describe("offline mode and network timeouts", () => {
+		it("should update npm range packages using the configured spec", async () => {
+			const installedPath = join(tempDir, ".pi", "npm", "node_modules", "example");
+			mkdirSync(installedPath, { recursive: true });
+			writeFileSync(join(installedPath, "package.json"), JSON.stringify({ name: "example", version: "1.0.0" }));
+			settingsManager.setProjectPackages(["npm:example@^1.0.0"]);
+
+			const runCommandCaptureSpy = vi
+				.spyOn(packageManager as any, "runCommandCapture")
+				.mockResolvedValue('["1.0.0","1.2.0"]');
+			const runCommandSpy = vi.spyOn(packageManager as any, "runCommand").mockResolvedValue(undefined);
+
+			await packageManager.update("npm:example");
+
+			expect(runCommandCaptureSpy).toHaveBeenCalledWith(
+				"npm",
+				["view", "example@^1.0.0", "version", "--json"],
+				expect.objectContaining({ cwd: tempDir, timeoutMs: expect.any(Number) }),
+			);
+			expect(runCommandSpy).toHaveBeenCalledWith(
+				"npm",
+				["install", "example@^1.0.0", "--prefix", join(tempDir, ".pi", "npm"), "--legacy-peer-deps"],
+				undefined,
+			);
+		});
+
+		it("should skip project npm update when installed version matches latest", async () => {
+			const installedPath = join(tempDir, ".pi", "npm", "node_modules", "example");
+			mkdirSync(installedPath, { recursive: true });
+			writeFileSync(join(installedPath, "package.json"), JSON.stringify({ name: "example", version: "1.3.1" }));
+			settingsManager.setProjectPackages(["npm:example@^1.0.0"]);
+
+			const runCommandCaptureSpy = vi
+				.spyOn(packageManager as any, "runCommandCapture")
+				.mockResolvedValue('["1.0.0","1.3.1","1.0.2"]');
+			const runCommandSpy = vi.spyOn(packageManager as any, "runCommand").mockResolvedValue(undefined);
+
+			await packageManager.update("npm:example");
+
+			expect(runCommandCaptureSpy).toHaveBeenCalledWith(
+				"npm",
+				["view", "example@^1.0.0", "version", "--json"],
+				expect.objectContaining({ cwd: tempDir, timeoutMs: expect.any(Number) }),
+			);
+			expect(runCommandSpy).not.toHaveBeenCalled();
+		});
+
+		it("should migrate legacy user npm installs into the managed npm root during update", async () => {
+			const legacyRoot = join(tempDir, "legacy-global", "node_modules");
+			const legacyPath = join(legacyRoot, "legacy-pkg");
+			const managedPath = join(agentDir, "npm", "node_modules", "legacy-pkg");
+			mkdirSync(legacyPath, { recursive: true });
+			writeFileSync(join(legacyPath, "package.json"), JSON.stringify({ name: "legacy-pkg", version: "1.0.0" }));
+			settingsManager.setPackages(["npm:legacy-pkg"]);
+
+			vi.spyOn(packageManager as any, "getGlobalNpmRoot").mockReturnValue(legacyRoot);
+			const runCommandCaptureSpy = vi.spyOn(packageManager as any, "runCommandCapture").mockResolvedValue('"1.0.0"');
+			const runCommandSpy = vi
+				.spyOn(packageManager as any, "runCommand")
+				.mockImplementation(async (...callArgs: unknown[]) => {
+					const [command, args] = callArgs as [string, string[]];
+					expect(command).toBe("npm");
+					expect(args).toEqual([
+						"install",
+						"legacy-pkg@latest",
+						"--prefix",
+						join(agentDir, "npm"),
+						"--legacy-peer-deps",
+					]);
+					mkdirSync(managedPath, { recursive: true });
+					writeFileSync(
+						join(managedPath, "package.json"),
+						JSON.stringify({ name: "legacy-pkg", version: "1.0.0" }),
+					);
+				});
+
+			expect(packageManager.getInstalledPath("npm:legacy-pkg", "user")).toBe(legacyPath);
+
+			await packageManager.update("npm:legacy-pkg");
+
+			expect(runCommandCaptureSpy).not.toHaveBeenCalled();
+			expect(runCommandSpy).toHaveBeenCalledTimes(1);
+			expect(packageManager.getInstalledPath("npm:legacy-pkg", "user")).toBe(managedPath);
+		});
+
+		it("should batch npm updates per scope and run git updates in parallel while skipping pinned npm and current packages", async () => {
+			const userOldPath = join(agentDir, "npm", "node_modules", "user-old");
+			const userCurrentPath = join(agentDir, "npm", "node_modules", "user-current");
+			const userUnknownPath = join(agentDir, "npm", "node_modules", "user-unknown");
+			const projectOldPath = join(tempDir, ".pi", "npm", "node_modules", "project-old");
+			const projectCurrentPath = join(tempDir, ".pi", "npm", "node_modules", "project-current");
+			const installPaths = [userOldPath, userCurrentPath, userUnknownPath, projectOldPath, projectCurrentPath];
+			for (const installPath of installPaths) {
+				mkdirSync(installPath, { recursive: true });
+			}
+			writeFileSync(join(userOldPath, "package.json"), JSON.stringify({ name: "user-old", version: "1.0.0" }));
+			writeFileSync(
+				join(userCurrentPath, "package.json"),
+				JSON.stringify({ name: "user-current", version: "1.0.0" }),
+			);
+			writeFileSync(
+				join(userUnknownPath, "package.json"),
+				JSON.stringify({ name: "user-unknown", version: "1.0.0" }),
+			);
+			writeFileSync(join(projectOldPath, "package.json"), JSON.stringify({ name: "project-old", version: "1.0.0" }));
+			writeFileSync(
+				join(projectCurrentPath, "package.json"),
+				JSON.stringify({ name: "project-current", version: "1.0.0" }),
+			);
+
+			settingsManager.setPackages([
+				"npm:user-old",
+				"npm:user-current",
+				"npm:user-unknown",
+				"npm:user-pinned@1.0.0",
+				"git:github.com/example/user-repo-a",
+				"git:github.com/example/user-repo-b",
+				"git:github.com/example/user-repo-pinned@v1",
+			]);
+			settingsManager.setProjectPackages([
+				"npm:project-old",
+				"npm:project-current",
+				"npm:project-missing",
+				"git:github.com/example/project-repo-a",
+			]);
+
+			const runCommandCaptureSpy = vi
+				.spyOn(packageManager as any, "runCommandCapture")
+				.mockImplementation(async (...callArgs: unknown[]) => {
+					const [_command, args] = callArgs as [string, string[]];
+					if (args[0] !== "view") {
+						throw new Error(`Unexpected runCommandCapture args: ${args.join(" ")}`);
+					}
+					switch (args[1]) {
+						case "user-old":
+						case "project-old":
+							return '"2.0.0"';
+						case "user-current":
+						case "project-current":
+							return '"1.0.0"';
+						case "user-unknown":
+							throw new Error("registry unavailable");
+						default:
+							throw new Error(`Unexpected package lookup: ${args[1]}`);
+					}
+				});
+
+			let activeNpmUpdates = 0;
+			let maxConcurrentNpmUpdates = 0;
+			const runCommandSpy = vi
+				.spyOn(packageManager as any, "runCommand")
+				.mockImplementation(async (...callArgs: unknown[]) => {
+					const [command, args] = callArgs as [string, string[]];
+					if (command !== "npm") {
+						throw new Error(`Unexpected runCommand call: ${command} ${args.join(" ")}`);
+					}
+					activeNpmUpdates += 1;
+					maxConcurrentNpmUpdates = Math.max(maxConcurrentNpmUpdates, activeNpmUpdates);
+					await new Promise((resolve) => setTimeout(resolve, 20));
+					activeNpmUpdates -= 1;
+				});
+
+			let activeGitUpdates = 0;
+			let maxConcurrentGitUpdates = 0;
+			const updateGitSpy = vi.spyOn(packageManager as any, "updateGit").mockImplementation(async () => {
+				activeGitUpdates += 1;
+				maxConcurrentGitUpdates = Math.max(maxConcurrentGitUpdates, activeGitUpdates);
+				await new Promise((resolve) => setTimeout(resolve, 20));
+				activeGitUpdates -= 1;
+			});
+
+			await packageManager.update();
+
+			expect(runCommandCaptureSpy).toHaveBeenCalledTimes(5);
+			expect(runCommandSpy).toHaveBeenCalledTimes(2);
+			expect(runCommandSpy).toHaveBeenNthCalledWith(
+				1,
+				"npm",
+				[
+					"install",
+					"user-old@latest",
+					"user-unknown@latest",
+					"--prefix",
+					join(agentDir, "npm"),
+					"--legacy-peer-deps",
+				],
+				undefined,
+			);
+			expect(runCommandSpy).toHaveBeenNthCalledWith(
+				2,
+				"npm",
+				[
+					"install",
+					"project-old@latest",
+					"project-missing@latest",
+					"--prefix",
+					join(tempDir, ".pi", "npm"),
+					"--legacy-peer-deps",
+				],
+				undefined,
+			);
+			expect(updateGitSpy).toHaveBeenCalledTimes(4);
+			expect(maxConcurrentNpmUpdates).toBeGreaterThan(1);
+			expect(maxConcurrentGitUpdates).toBeGreaterThan(1);
+		});
+
+		it("should suggest npm source prefixes for update lookups", async () => {
+			settingsManager.setProjectPackages(["npm:example"]);
+
+			await expect(packageManager.update("example")).rejects.toThrow(
+				"No matching package found for example. Did you mean npm:example?",
+			);
+		});
+
+		it("should suggest git source prefixes for update lookups", async () => {
+			settingsManager.setProjectPackages(["git:github.com/example/repo"]);
+
+			await expect(packageManager.update("github.com/example/repo")).rejects.toThrow(
+				"No matching package found for github.com/example/repo. Did you mean git:github.com/example/repo?",
+			);
+		});
+
+		it("should skip installing missing package sources when offline", async () => {
+			process.env.PI_OFFLINE = "1";
+			settingsManager.setProjectPackages(["npm:missing-package", "git:github.com/example/missing-repo"]);
+
+			const installParsedSourceSpy = vi.spyOn(packageManager as any, "installParsedSource");
+
+			const result = await packageManager.resolve();
+			const allResources = [...result.extensions, ...result.skills, ...result.prompts, ...result.themes];
+			expect(allResources.some((r) => r.metadata.origin === "package")).toBe(false);
+			expect(installParsedSourceSpy).not.toHaveBeenCalled();
+		});
+
+		it("should skip refreshing temporary git sources when offline", async () => {
+			process.env.PI_OFFLINE = "1";
+			const gitSource = "git:github.com/example/repo";
+			const parsedGitSource = (packageManager as any).parseSource(gitSource);
+			const installedPath = (packageManager as any).getGitInstallPath(parsedGitSource, "temporary") as string;
+
+			mkdirSync(join(installedPath, "extensions"), { recursive: true });
+			writeFileSync(join(installedPath, "extensions", "index.ts"), "export default function() {};");
+
+			const refreshTemporaryGitSourceSpy = vi.spyOn(packageManager as any, "refreshTemporaryGitSource");
+
+			const result = await packageManager.resolveExtensionSources([gitSource], { temporary: true });
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "extensions/index.ts") && r.enabled)).toBe(true);
+			expect(refreshTemporaryGitSourceSpy).not.toHaveBeenCalled();
+		});
+
+		it("should not run npm view during resolve for installed unpinned packages", async () => {
+			process.env.PI_OFFLINE = "1";
+			const installedPath = join(tempDir, ".pi", "npm", "node_modules", "example");
+			mkdirSync(join(installedPath, "extensions"), { recursive: true });
+			writeFileSync(join(installedPath, "package.json"), JSON.stringify({ name: "example", version: "1.0.0" }));
+			writeFileSync(join(installedPath, "extensions", "index.ts"), "export default function() {};");
+			settingsManager.setProjectPackages(["npm:example@^1.0.0"]);
+
+			const runCommandCaptureSpy = vi.spyOn(packageManager as any, "runCommandCapture");
+
+			const result = await packageManager.resolve();
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "extensions/index.ts") && r.enabled)).toBe(true);
+			expect(runCommandCaptureSpy).not.toHaveBeenCalled();
+		});
+
+		it("should reinstall pinned npm packages when installed version does not match", async () => {
+			const installedPath = join(tempDir, ".pi", "npm", "node_modules", "example");
+			mkdirSync(installedPath, { recursive: true });
+			writeFileSync(join(installedPath, "package.json"), JSON.stringify({ name: "example", version: "1.0.0" }));
+			settingsManager.setProjectPackages(["npm:example@2.0.0"]);
+
+			const installParsedSourceSpy = vi
+				.spyOn(packageManager as any, "installParsedSource")
+				.mockResolvedValue(undefined);
+
+			await packageManager.resolve();
+			expect(installParsedSourceSpy).toHaveBeenCalledTimes(1);
+		});
+
+		it("should not check package updates when offline", async () => {
+			process.env.PI_OFFLINE = "1";
+			const runCommandCaptureSpy = vi.spyOn(packageManager as any, "runCommandCapture");
+
+			const updates = await packageManager.checkForAvailableUpdates();
+			expect(updates).toEqual([]);
+			expect(runCommandCaptureSpy).not.toHaveBeenCalled();
+		});
+
+		it("should report updates for installed unpinned npm packages", async () => {
+			const installedPath = join(tempDir, ".pi", "npm", "node_modules", "example");
+			mkdirSync(installedPath, { recursive: true });
+			writeFileSync(join(installedPath, "package.json"), JSON.stringify({ name: "example", version: "1.0.0" }));
+			settingsManager.setProjectPackages(["npm:example"]);
+
+			vi.spyOn(packageManager as any, "runCommandCapture").mockResolvedValue('"1.2.3"');
+
+			const updates = await packageManager.checkForAvailableUpdates();
+			expect(updates).toEqual([
+				{
+					source: "npm:example",
+					displayName: "example",
+					type: "npm",
+					scope: "project",
+				},
+			]);
+		});
+
+		it("should skip pinned packages when checking for updates", async () => {
+			const installedNpmPath = join(tempDir, ".pi", "npm", "node_modules", "example");
+			mkdirSync(installedNpmPath, { recursive: true });
+			writeFileSync(join(installedNpmPath, "package.json"), JSON.stringify({ name: "example", version: "1.0.0" }));
+			const parsedGitSource = (packageManager as any).parseSource("git:github.com/example/repo@v1");
+			const installedGitPath = (packageManager as any).getGitInstallPath(parsedGitSource, "project") as string;
+			mkdirSync(installedGitPath, { recursive: true });
+
+			settingsManager.setProjectPackages(["npm:example@1.0.0", "git:github.com/example/repo@v1"]);
+
+			const runCommandCaptureSpy = vi.spyOn(packageManager as any, "runCommandCapture");
+			const gitUpdateSpy = vi.spyOn(packageManager as any, "gitHasAvailableUpdate");
+
+			const updates = await packageManager.checkForAvailableUpdates();
+			expect(updates).toEqual([]);
+			expect(runCommandCaptureSpy).not.toHaveBeenCalled();
+			expect(gitUpdateSpy).not.toHaveBeenCalled();
+		});
+
+		it("should use npm view to fetch latest version", async () => {
+			const runCommandCaptureSpy = vi.spyOn(packageManager as any, "runCommandCapture").mockResolvedValue('"1.2.3"');
+
+			const latest = await (packageManager as any).getLatestNpmVersion("example");
+			expect(latest).toBe("1.2.3");
+			expect(runCommandCaptureSpy).toHaveBeenCalledTimes(1);
+			expect(runCommandCaptureSpy).toHaveBeenCalledWith(
+				"npm",
+				["view", "example", "version", "--json"],
+				expect.objectContaining({ cwd: tempDir, timeoutMs: expect.any(Number) }),
+			);
+		});
+
+		it("should use npmCommand argv for npm update checks", async () => {
+			settingsManager = SettingsManager.inMemory({
+				npmCommand: ["mise", "exec", "node@20", "--", "npm"],
+			});
+			packageManager = new DefaultPackageManager({
+				cwd: tempDir,
+				agentDir,
+				settingsManager,
+			});
+
+			const runCommandCaptureSpy = vi.spyOn(packageManager as any, "runCommandCapture").mockResolvedValue('"1.2.3"');
+
+			const latest = await (packageManager as any).getLatestNpmVersion("@scope/pkg");
+			expect(latest).toBe("1.2.3");
+			expect(runCommandCaptureSpy).toHaveBeenCalledWith(
+				"mise",
+				["exec", "node@20", "--", "npm", "view", "@scope/pkg", "version", "--json"],
+				expect.objectContaining({ cwd: tempDir }),
+			);
+		});
+
+		it("should wait for close before resolving captured stdout", async () => {
+			const managerWithInternals = packageManager as unknown as {
+				spawnCaptureCommand(
+					command: string,
+					args: string[],
+					options?: { cwd?: string; env?: Record<string, string> },
+				): MockSpawnedProcess;
+				runCommandCapture(
+					command: string,
+					args: string[],
+					options?: { cwd?: string; timeoutMs?: number; env?: Record<string, string> },
+				): Promise<string>;
+			};
+			const child = new MockSpawnedProcess();
+			vi.spyOn(managerWithInternals, "spawnCaptureCommand").mockReturnValue(child);
+
+			let settled = false;
+			const capturePromise = managerWithInternals.runCommandCapture("git", ["rev-parse", "HEAD"]).then((value) => {
+				settled = true;
+				return value;
+			});
+
+			child.emit("exit", 0, null);
+			await Promise.resolve();
+			expect(settled).toBe(false);
+
+			child.stdout.write("abc123\n");
+			child.stdout.end();
+			child.emit("close", 0, null);
+
+			await expect(capturePromise).resolves.toBe("abc123");
+		});
+	});
+});