fix: kit uninstall, HOME directory handling, and legacy migration improvements

src/__tests__/domains/migration/metadata-migration.test.ts

@@ -405,6 +405,18 @@ describe("metadata-migration", () => {
 			expect(result).toEqual(["marketing"]);
 		});
 
+		it("detects BOTH kits from legacy name containing both", () => {
+			const metadata: Metadata = {
+				name: "ClaudeKit Engineer + Marketing Bundle",
+				version: "v1.0.0",
+			};
+
+			const result = getInstalledKits(metadata);
+			expect(result).toContain("engineer");
+			expect(result).toContain("marketing");
+			expect(result.length).toBe(2);
+		});
+
 		it("defaults to engineer for unnamed legacy", () => {
 			const metadata: Metadata = {
 				version: "v1.0.0",

src/commands/init/phases/conflict-handler.ts

@@ -3,7 +3,7 @@
  * Detects and resolves conflicts when using global mode with existing local installation
  */
 
-import { join, resolve } from "node:path";
+import { join } from "node:path";
 import { logger } from "@/shared/logger.js";
 import { PathResolver } from "@/shared/path-resolver.js";
 import { pathExists, remove } from "fs-extra";
@@ -19,14 +19,14 @@ export async function handleConflicts(ctx: InitContext): Promise<InitContext> {
 	// Only check in global mode
 	if (!ctx.options.global) return ctx;
 
-	// Skip local detection if cwd is the global kit directory itself
-	const globalKitDir = PathResolver.getGlobalKitDir();
-	const cwdResolved = resolve(process.cwd());
-	const isInGlobalDir = cwdResolved === globalKitDir || cwdResolved === resolve(globalKitDir, "..");
+	// Skip if at HOME directory (local === global, no conflict possible)
+	if (PathResolver.isLocalSameAsGlobal()) {
+		return ctx;
+	}
 
 	const localSettingsPath = join(process.cwd(), ".claude", "settings.json");
 
-	if (isInGlobalDir || !(await pathExists(localSettingsPath))) {
+	if (!(await pathExists(localSettingsPath))) {
 		return ctx;
 	}
 

src/commands/init/phases/selection-handler.ts

@@ -202,6 +202,35 @@ export async function handleSelection(ctx: InitContext): Promise<InitContext> {
 	const resolvedDir = resolve(targetDir);
 	logger.info(`Target directory: ${resolvedDir}`);
 
+	// HOME directory detection: warn if installing to HOME without --global flag
+	// Installing to HOME's .claude/ is effectively a global installation
+	if (!ctx.options.global && PathResolver.isLocalSameAsGlobal(resolvedDir)) {
+		logger.warning("You're at HOME directory. Installing here modifies your GLOBAL ClaudeKit.");
+
+		if (!ctx.isNonInteractive) {
+			// Interactive mode: offer choices
+			const choice = await ctx.prompts.selectScope();
+			if (choice === "cancel") {
+				return { ...ctx, cancelled: true };
+			}
+			if (choice === "global") {
+				// User confirmed global installation - continue with same resolved directory
+				logger.info("Proceeding with global installation");
+			}
+			// "different" choice would require re-prompting for directory, but for simplicity
+			// we just cancel and ask them to run from a different directory
+			if (choice === "different") {
+				logger.info("Please run 'ck init' from a project directory instead.");
+				return { ...ctx, cancelled: true };
+			}
+		} else {
+			// Non-interactive: fail with clear message
+			logger.error("Cannot use local installation at HOME directory.");
+			logger.info("Use -g/--global flag or run from a project directory.");
+			return { ...ctx, cancelled: true };
+		}
+	}
+
 	// Check if directory exists (create if global mode)
 	if (!(await pathExists(resolvedDir))) {
 		if (ctx.options.global) {

src/commands/new/phases/directory-setup.ts

@@ -9,6 +9,7 @@ import { ConfigManager } from "@/domains/config/config-manager.js";
 import { detectAccessibleKits } from "@/domains/github/kit-access-checker.js";
 import type { PromptsManager } from "@/domains/ui/prompts.js";
 import { logger } from "@/shared/logger.js";
+import { PathResolver } from "@/shared/path-resolver.js";
 import { AVAILABLE_KITS, type KitType, type NewCommandOptions, isValidKitType } from "@/types";
 import { pathExists, readdir } from "fs-extra";
 import type { DirectorySetupResult, NewContext } from "../types.js";
@@ -123,6 +124,28 @@ export async function directorySetup(
 	const resolvedDir = resolve(targetDir);
 	logger.info(`Target directory: ${resolvedDir}`);
 
+	// HOME directory detection: warn if creating project at HOME
+	// Creating a project at HOME modifies global ~/.claude/
+	if (PathResolver.isLocalSameAsGlobal(resolvedDir)) {
+		logger.warning("You're creating a project at HOME directory.");
+		logger.warning("This will install to your GLOBAL ~/.claude/ directory.");
+
+		if (!isNonInteractive) {
+			const choice = await prompts.selectScope();
+			if (choice === "cancel" || choice === "different") {
+				logger.info("Please run 'ck new' from or specify a different directory.");
+				return null;
+			}
+			// choice === "global": user confirmed, continue
+			logger.info("Proceeding with global installation");
+		} else {
+			// Non-interactive: fail with clear message
+			logger.error("Cannot create project at HOME directory in non-interactive mode.");
+			logger.info("Specify a different directory with --dir flag.");
+			return null;
+		}
+	}
+
 	// Check if directory exists and is not empty
 	if (await pathExists(resolvedDir)) {
 		const files = await readdir(resolvedDir);

src/commands/uninstall/installation-detector.ts

@@ -2,9 +2,11 @@
  * Installation Detector
  *
  * Detects ClaudeKit installations (local and global).
+ * Handles HOME directory edge case where local === global.
  */
 
 import { getClaudeKitSetup } from "@/services/file-operations/claudekit-scanner.js";
+import { PathResolver } from "@/shared/path-resolver.js";
 import { pathExists } from "fs-extra";
 
 export interface Installation {
@@ -15,15 +17,20 @@ export interface Installation {
 
 /**
  * Detect both local and global ClaudeKit installations
+ * Deduplicates when at HOME directory (local path === global path)
  */
 export async function detectInstallations(): Promise<Installation[]> {
 	const installations: Installation[] = [];
 
 	// Detect both local and global installations
 	const setup = await getClaudeKitSetup(process.cwd());
 
+	// Check if local and global point to same path (HOME directory edge case)
+	const isLocalSameAsGlobal = PathResolver.isLocalSameAsGlobal();
+
 	// Add local installation if found (must have metadata to be valid ClaudeKit installation)
-	if (setup.project.path && setup.project.metadata) {
+	// Skip if local === global to avoid duplicates
+	if (setup.project.path && setup.project.metadata && !isLocalSameAsGlobal) {
 		installations.push({
 			type: "local",
 			path: setup.project.path,

src/commands/uninstall/uninstall-command.ts

@@ -8,6 +8,7 @@ import { getInstalledKits } from "@/domains/migration/metadata-migration.js";
 import { PromptsManager } from "@/domains/ui/prompts.js";
 import { ManifestWriter } from "@/services/file-operations/manifest-writer.js";
 import { logger } from "@/shared/logger.js";
+import { PathResolver } from "@/shared/path-resolver.js";
 import { confirm, isCancel, log, select } from "@/shared/safe-prompts.js";
 import { type UninstallCommandOptions, UninstallCommandOptionsSchema } from "@/types";
 import pc from "picocolors";
@@ -111,14 +112,28 @@ export async function uninstallCommand(options: UninstallCommandOptions): Promis
 			}
 		}
 
-		// 5. Determine scope (from flags or interactive prompt)
+		// 5. Check if running at HOME directory (local === global)
+		const isAtHome = PathResolver.isLocalSameAsGlobal();
+
+		// 6. Handle --local flag at HOME directory (invalid scenario)
+		if (validOptions.local && !validOptions.global && isAtHome) {
+			log.warn(pc.yellow("Cannot use --local at HOME directory (local path equals global path)."));
+			log.info("Use -g/--global or run from a project directory.");
+			return;
+		}
+
+		// 7. Determine scope (from flags or interactive prompt)
 		let scope: UninstallScope;
 		if (validOptions.all || (validOptions.local && validOptions.global)) {
 			scope = "all";
 		} else if (validOptions.local) {
 			scope = "local";
 		} else if (validOptions.global) {
 			scope = "global";
+		} else if (isAtHome) {
+			// At HOME directory: skip scope prompt, auto-select global
+			log.info(pc.cyan("Running at HOME directory - targeting global installation"));
+			scope = "global";
 		} else {
 			// Interactive: prompt user to choose scope
 			const promptedScope = await promptScope(allInstallations);
@@ -129,7 +144,7 @@ export async function uninstallCommand(options: UninstallCommandOptions): Promis
 			scope = promptedScope;
 		}
 
-		// 6. Filter installations by scope
+		// 8. Filter installations by scope
 		const installations = allInstallations.filter((i) => {
 			if (scope === "all") return true;
 			return i.type === scope;
@@ -141,13 +156,13 @@ export async function uninstallCommand(options: UninstallCommandOptions): Promis
 			return;
 		}
 
-		// 7. Display found installations
+		// 9. Display found installations
 		displayInstallations(installations, scope);
 		if (validOptions.kit) {
 			log.info(pc.cyan(`Kit-scoped uninstall: ${validOptions.kit} kit only`));
 		}
 
-		// 8. Dry-run mode - skip confirmation
+		// 10. Dry-run mode - skip confirmation
 		if (validOptions.dryRun) {
 			log.info(pc.yellow("DRY RUN MODE - No files will be deleted"));
 			await removeInstallations(installations, {
@@ -159,14 +174,14 @@ export async function uninstallCommand(options: UninstallCommandOptions): Promis
 			return;
 		}
 
-		// 9. Force-overwrite warning
+		// 11. Force-overwrite warning
 		if (validOptions.forceOverwrite) {
 			log.warn(
 				`${pc.yellow(pc.bold("FORCE MODE ENABLED"))}\n${pc.yellow("User modifications will be permanently deleted!")}`,
 			);
 		}
 
-		// 10. Confirm deletion
+		// 12. Confirm deletion
 		if (!validOptions.yes) {
 			const kitLabel = validOptions.kit ? ` (${validOptions.kit} kit only)` : "";
 			const confirmed = await confirmUninstall(scope, kitLabel);
@@ -176,14 +191,14 @@ export async function uninstallCommand(options: UninstallCommandOptions): Promis
 			}
 		}
 
-		// 11. Remove files using manifest
+		// 13. Remove files using manifest
 		await removeInstallations(installations, {
 			dryRun: false,
 			forceOverwrite: validOptions.forceOverwrite,
 			kit: validOptions.kit,
 		});
 
-		// 12. Success message
+		// 14. Success message
 		const kitMsg = validOptions.kit ? ` (${validOptions.kit} kit)` : "";
 		prompts.outro(`ClaudeKit${kitMsg} uninstalled successfully!`);
 	} catch (error) {

src/domains/migration/legacy-migration.ts

@@ -4,6 +4,7 @@ import { ManifestWriter } from "@/services/file-operations/manifest-writer.js";
 import { OwnershipChecker } from "@/services/file-operations/ownership-checker.js";
 import { mapWithLimit } from "@/shared/concurrent-file-ops.js";
 import { logger } from "@/shared/logger.js";
+import { SKIP_DIRS_ALL } from "@/shared/skip-directories.js";
 import type { Metadata, TrackedFile } from "@/types";
 import { writeFile } from "fs-extra";
 import { type ReleaseManifest, ReleaseManifestLoader } from "./release-manifest.js";
@@ -68,6 +69,8 @@ export class LegacyMigration {
 		for (const entry of entries) {
 			// Skip metadata.json itself
 			if (entry === "metadata.json") continue;
+			// Skip build artifacts, venvs, and Claude Code internal dirs
+			if (SKIP_DIRS_ALL.includes(entry)) continue;
 
 			const fullPath = join(dir, entry);
 			let stats;

src/domains/migration/metadata-migration.ts

@@ -227,22 +227,30 @@ export function getAllTrackedFiles(metadata: Metadata): TrackedFile[] {
 
 /**
  * Get installed kits from metadata
+ * Returns ALL matching kits (not just first match) for legacy format
  */
 export function getInstalledKits(metadata: Metadata): KitType[] {
 	if (metadata.kits) {
 		return Object.keys(metadata.kits) as KitType[];
 	}
 
-	// Legacy format - detect from name using word boundaries to avoid false matches
+	// Legacy format - detect ALL kits from name using word boundaries
 	const nameToCheck = metadata.name || "";
+	const kits: KitType[] = [];
+
 	if (/\bengineer\b/i.test(nameToCheck)) {
-		return ["engineer"];
+		kits.push("engineer");
 	}
 	if (/\bmarketing\b/i.test(nameToCheck)) {
-		return ["marketing"];
+		kits.push("marketing");
+	}
+
+	// If kits found, return them
+	if (kits.length > 0) {
+		return kits;
 	}
 
-	// Default to engineer for legacy
+	// Default to engineer for legacy installs with version but no identifiable name
 	if (metadata.version) {
 		return ["engineer"];
 	}

src/domains/skills/customization/hash-calculator.ts

@@ -2,6 +2,7 @@ import { createHash } from "node:crypto";
 import { createReadStream } from "node:fs";
 import { readFile, readdir } from "node:fs/promises";
 import { join, relative } from "node:path";
+import { BUILD_ARTIFACT_DIRS } from "@/shared/skip-directories.js";
 
 /**
  * Get all files in a directory recursively
@@ -16,8 +17,12 @@ export async function getAllFiles(dirPath: string): Promise<string[]> {
 	for (const entry of entries) {
 		const fullPath = join(dirPath, entry.name);
 
-		// Skip hidden files, node_modules, and symlinks
-		if (entry.name.startsWith(".") || entry.name === "node_modules" || entry.isSymbolicLink()) {
+		// Skip hidden files, build artifacts (node_modules, .venv, etc.), and symlinks
+		if (
+			entry.name.startsWith(".") ||
+			BUILD_ARTIFACT_DIRS.includes(entry.name) ||
+			entry.isSymbolicLink()
+		) {
 			continue;
 		}
 

src/domains/skills/skills-manifest.ts

@@ -2,6 +2,7 @@ import { createHash } from "node:crypto";
 import { readFile, readdir, writeFile } from "node:fs/promises";
 import { join, relative } from "node:path";
 import { logger } from "@/shared/logger.js";
+import { BUILD_ARTIFACT_DIRS } from "@/shared/skip-directories.js";
 import type { SkillsManifest } from "@/types";
 import { SkillsManifestSchema, SkillsMigrationError } from "@/types";
 import { pathExists } from "fs-extra";
@@ -93,10 +94,12 @@ export class SkillsManifestManager {
 	private static async detectStructure(skillsDir: string): Promise<"flat" | "categorized"> {
 		const entries = await readdir(skillsDir, { withFileTypes: true });
 
-		// Filter out manifest and common files
+		// Filter out manifest and build artifact directories
 		const dirs = entries.filter(
 			(entry) =>
-				entry.isDirectory() && entry.name !== "node_modules" && !entry.name.startsWith("."),
+				entry.isDirectory() &&
+				!BUILD_ARTIFACT_DIRS.includes(entry.name) &&
+				!entry.name.startsWith("."),
 		);
 
 		if (dirs.length === 0) {
@@ -145,7 +148,11 @@ export class SkillsManifestManager {
 			// Flat structure: skills are direct subdirectories
 			const entries = await readdir(skillsDir, { withFileTypes: true });
 			for (const entry of entries) {
-				if (entry.isDirectory() && entry.name !== "node_modules" && !entry.name.startsWith(".")) {
+				if (
+					entry.isDirectory() &&
+					!BUILD_ARTIFACT_DIRS.includes(entry.name) &&
+					!entry.name.startsWith(".")
+				) {
 					const skillPath = join(skillsDir, entry.name);
 					const hash = await SkillsManifestManager.hashDirectory(skillPath);
 					skills.push({
@@ -160,7 +167,7 @@ export class SkillsManifestManager {
 			for (const category of categories) {
 				if (
 					category.isDirectory() &&
-					category.name !== "node_modules" &&
+					!BUILD_ARTIFACT_DIRS.includes(category.name) &&
 					!category.name.startsWith(".")
 				) {
 					const categoryPath = join(skillsDir, category.name);
@@ -223,8 +230,8 @@ export class SkillsManifestManager {
 		for (const entry of entries) {
 			const fullPath = join(dirPath, entry.name);
 
-			// Skip hidden files and node_modules
-			if (entry.name.startsWith(".") || entry.name === "node_modules") {
+			// Skip hidden files and build artifacts (node_modules, .venv, etc.)
+			if (entry.name.startsWith(".") || BUILD_ARTIFACT_DIRS.includes(entry.name)) {
 				continue;
 			}