claudekit-cli 3.7.1 → 3.8.0

package/dist/index.js

@@ -6324,6 +6324,7 @@ var init_types2 = __esm(() => {
     beta: exports_external.boolean().default(false),
     dryRun: exports_external.boolean().default(false),
     forceOverwrite: exports_external.boolean().default(false),
+    forceOverwriteSettings: exports_external.boolean().default(false),
     skipSetup: exports_external.boolean().default(false),
     refresh: exports_external.boolean().default(false),
     docsDir: exports_external.string().optional(),
@@ -13157,7 +13158,7 @@ async function installSkillsDependencies(skillsDir) {
   }
   try {
     const { existsSync: existsSync6 } = await import("node:fs");
-    const { readFile: readFile11 } = await import("node:fs/promises");
+    const { readFile: readFile12 } = await import("node:fs/promises");
     const clack = await Promise.resolve().then(() => (init_dist2(), exports_dist));
     const platform9 = process.platform;
     const scriptName = platform9 === "win32" ? "install.ps1" : "install.sh";
@@ -13193,7 +13194,7 @@ async function installSkillsDependencies(skillsDir) {
     logger.info(`  Platform: ${platform9 === "win32" ? "Windows (PowerShell)" : "Unix (bash)"}`);
     logger.info("");
     try {
-      const scriptContent = await readFile11(scriptPath, "utf-8");
+      const scriptContent = await readFile12(scriptPath, "utf-8");
       const previewLines = scriptContent.split(`
 `).slice(0, 20);
       logger.info("Script preview (first 20 lines):");
@@ -14925,7 +14926,7 @@ var cac = (name = "") => new CAC(name);
 // package.json
 var package_default = {
   name: "claudekit-cli",
-  version: "3.7.1",
+  version: "3.8.0",
   description: "CLI tool for bootstrapping and updating ClaudeKit projects",
   type: "module",
   repository: {
@@ -18765,7 +18766,7 @@ async function doctorCommand(options = {}) {
 }
 
 // src/commands/init.ts
-var import_fs_extra17 = __toESM(require_lib(), 1);
+var import_fs_extra18 = __toESM(require_lib(), 1);
 import { join as join29, resolve as resolve5 } from "node:path";
 
 // src/lib/commands-prefix.ts
@@ -28492,7 +28493,7 @@ async function transformPathsForGlobalInstall(directory, options = {}) {
 
 // src/lib/merge.ts
 init_dist2();
-var import_fs_extra6 = __toESM(require_lib(), 1);
+var import_fs_extra7 = __toESM(require_lib(), 1);
 var import_ignore2 = __toESM(require_ignore(), 1);
 import { dirname as dirname4, join as join15, relative as relative4 } from "node:path";
 
@@ -29934,11 +29935,168 @@ minimatch.unescape = unescape;
 init_types2();
 init_logger();
 
+// src/lib/settings-merger.ts
+init_logger();
+var import_fs_extra6 = __toESM(require_lib(), 1);
+
+class SettingsMerger {
+  static merge(source, destination) {
+    const result = {
+      merged: { ...destination },
+      hooksAdded: 0,
+      hooksPreserved: 0,
+      mcpServersPreserved: 0,
+      conflictsDetected: []
+    };
+    if (source.hooks) {
+      result.merged.hooks = SettingsMerger.mergeHooks(source.hooks, destination.hooks || {}, result);
+    }
+    if (source.mcp) {
+      result.merged.mcp = SettingsMerger.mergeMcp(source.mcp, destination.mcp || {}, result);
+    }
+    for (const key of Object.keys(source)) {
+      if (key !== "hooks" && key !== "mcp" && !(key in destination)) {
+        result.merged[key] = source[key];
+      }
+    }
+    return result;
+  }
+  static mergeHooks(sourceHooks, destHooks, result) {
+    const merged = { ...destHooks };
+    for (const [eventName, sourceEntries] of Object.entries(sourceHooks)) {
+      const destEntries = destHooks[eventName] || [];
+      merged[eventName] = SettingsMerger.mergeHookEntries(sourceEntries, destEntries, eventName, result);
+    }
+    return merged;
+  }
+  static mergeHookEntries(sourceEntries, destEntries, eventName, result) {
+    const existingCommands = new Set;
+    SettingsMerger.extractCommands(destEntries, existingCommands);
+    if (destEntries.length > 0) {
+      result.hooksPreserved += destEntries.length;
+    }
+    const merged = [...destEntries];
+    for (const entry of sourceEntries) {
+      const commands = SettingsMerger.getEntryCommands(entry);
+      const isFullyDuplicated = commands.length > 0 && commands.every((cmd) => existingCommands.has(cmd));
+      const duplicateCommands = commands.filter((cmd) => existingCommands.has(cmd));
+      if (duplicateCommands.length > 0) {
+        const summary = duplicateCommands.length === 1 ? `"${SettingsMerger.truncateCommand(duplicateCommands[0])}"` : `${duplicateCommands.length} commands`;
+        result.conflictsDetected.push(`${eventName}: duplicate ${summary}`);
+      }
+      if (!isFullyDuplicated) {
+        merged.push(entry);
+        result.hooksAdded++;
+        for (const cmd of commands) {
+          existingCommands.add(cmd);
+        }
+      }
+    }
+    return merged;
+  }
+  static extractCommands(entries, commands) {
+    for (const entry of entries) {
+      if ("command" in entry && entry.command) {
+        commands.add(entry.command);
+      }
+      if ("hooks" in entry && entry.hooks) {
+        for (const hook of entry.hooks) {
+          if (hook.command) {
+            commands.add(hook.command);
+          }
+        }
+      }
+    }
+  }
+  static getEntryCommands(entry) {
+    const commands = [];
+    if ("command" in entry && entry.command) {
+      commands.push(entry.command);
+    }
+    if ("hooks" in entry && entry.hooks) {
+      for (const hook of entry.hooks) {
+        if (hook.command) {
+          commands.push(hook.command);
+        }
+      }
+    }
+    return commands;
+  }
+  static truncateCommand(cmd, maxLen = 50) {
+    if (cmd.length <= maxLen)
+      return cmd;
+    return `${cmd.slice(0, maxLen - 3)}...`;
+  }
+  static mergeMcp(sourceMcp, destMcp, result) {
+    if (!sourceMcp)
+      return destMcp;
+    if (!destMcp)
+      return sourceMcp;
+    const merged = { ...destMcp };
+    if (sourceMcp.servers) {
+      const destServers = destMcp.servers || {};
+      merged.servers = { ...destServers };
+      for (const [serverName, serverConfig] of Object.entries(sourceMcp.servers)) {
+        if (serverName in destServers) {
+          result.mcpServersPreserved++;
+          logger.debug(`Preserved user MCP server: ${serverName}`);
+        } else {
+          merged.servers[serverName] = serverConfig;
+          logger.debug(`Added ClaudeKit MCP server: ${serverName}`);
+        }
+      }
+    }
+    for (const key of Object.keys(sourceMcp)) {
+      if (key !== "servers" && !(key in merged)) {
+        merged[key] = sourceMcp[key];
+      }
+    }
+    return merged;
+  }
+  static async readSettingsFile(filePath) {
+    try {
+      if (!await import_fs_extra6.pathExists(filePath)) {
+        return null;
+      }
+      const content = await import_fs_extra6.readFile(filePath, "utf-8");
+      const parsed = JSON.parse(content);
+      if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
+        logger.warning(`Invalid settings file format (expected object): ${filePath}`);
+        return null;
+      }
+      return parsed;
+    } catch (error) {
+      logger.warning(`Failed to parse settings file: ${filePath} - ${error}`);
+      return null;
+    }
+  }
+  static async writeSettingsFile(filePath, settings) {
+    const content = JSON.stringify(settings, null, "\t");
+    await import_fs_extra6.writeFile(filePath, content, "utf-8");
+  }
+  static async createBackup(filePath) {
+    try {
+      if (!await import_fs_extra6.pathExists(filePath)) {
+        return null;
+      }
+      const backupPath = `${filePath}.backup`;
+      const content = await import_fs_extra6.readFile(filePath, "utf-8");
+      await import_fs_extra6.writeFile(backupPath, content, "utf-8");
+      return backupPath;
+    } catch (error) {
+      logger.warning(`Failed to create backup: ${error}`);
+      return null;
+    }
+  }
+}
+
+// src/lib/merge.ts
 class FileMerger {
   neverCopyChecker = import_ignore2.default().add(NEVER_COPY_PATTERNS);
   userConfigChecker = import_ignore2.default().add(USER_CONFIG_PATTERNS);
   includePatterns = [];
   isGlobal = false;
+  forceOverwriteSettings = false;
   installedFiles = new Set;
   installedDirectories = new Set;
   setIncludePatterns(patterns) {
@@ -29947,6 +30105,9 @@ class FileMerger {
   setGlobalFlag(isGlobal) {
     this.isGlobal = isGlobal;
   }
+  setForceOverwriteSettings(force) {
+    this.forceOverwriteSettings = force;
+  }
   async merge(sourceDir, destDir, skipConfirmation = false) {
     const conflicts = await this.detectConflicts(sourceDir, destDir);
     if (conflicts.length > 0 && !skipConfirmation) {
@@ -29971,7 +30132,7 @@ class FileMerger {
       const relativePath = relative4(sourceDir, file);
       const normalizedRelativePath = relativePath.replace(/\\/g, "/");
       const destPath = join15(destDir, relativePath);
-      if (await import_fs_extra6.pathExists(destPath)) {
+      if (await import_fs_extra7.pathExists(destPath)) {
         if (this.neverCopyChecker.ignores(normalizedRelativePath)) {
           logger.debug(`Security-sensitive file exists but won't be overwritten: ${normalizedRelativePath}`);
           continue;
@@ -29999,7 +30160,7 @@ class FileMerger {
         continue;
       }
       if (this.userConfigChecker.ignores(normalizedRelativePath)) {
-        const fileExists = await import_fs_extra6.pathExists(destPath);
+        const fileExists = await import_fs_extra7.pathExists(destPath);
         if (fileExists) {
           logger.debug(`Skipping existing user config file: ${normalizedRelativePath}`);
           skippedCount++;
@@ -30013,7 +30174,7 @@ class FileMerger {
         copiedCount++;
         continue;
       }
-      await import_fs_extra6.copy(file, destPath, { overwrite: true });
+      await import_fs_extra7.copy(file, destPath, { overwrite: true });
       this.trackInstalledFile(normalizedRelativePath);
       copiedCount++;
     }
@@ -30021,27 +30182,69 @@ class FileMerger {
   }
   async processSettingsJson(sourceFile, destFile) {
     try {
-      const content = await import_fs_extra6.readFile(sourceFile, "utf-8");
+      const sourceContent = await import_fs_extra7.readFile(sourceFile, "utf-8");
       const isWindows5 = process.platform === "win32";
-      let processedContent = content;
+      let transformedSource = sourceContent;
       if (this.isGlobal) {
         const homeVar = isWindows5 ? '"%USERPROFILE%"' : '"$HOME"';
-        processedContent = this.transformClaudePaths(content, homeVar);
-        if (processedContent !== content) {
+        transformedSource = this.transformClaudePaths(sourceContent, homeVar);
+        if (transformedSource !== sourceContent) {
           logger.debug(`Transformed .claude/ paths to ${homeVar}/.claude/ in settings.json for global installation`);
         }
       } else {
         const projectDirVar = isWindows5 ? '"%CLAUDE_PROJECT_DIR%"' : '"$CLAUDE_PROJECT_DIR"';
-        processedContent = this.transformClaudePaths(content, projectDirVar);
-        if (processedContent !== content) {
+        transformedSource = this.transformClaudePaths(sourceContent, projectDirVar);
+        if (transformedSource !== sourceContent) {
           logger.debug(`Transformed .claude/ paths to ${projectDirVar}/.claude/ in settings.json for local installation`);
         }
       }
-      await import_fs_extra6.writeFile(destFile, processedContent, "utf-8");
+      const destExists = await import_fs_extra7.pathExists(destFile);
+      if (destExists && !this.forceOverwriteSettings) {
+        await this.selectiveMergeSettings(transformedSource, destFile);
+      } else {
+        await import_fs_extra7.writeFile(destFile, transformedSource, "utf-8");
+        if (this.forceOverwriteSettings && destExists) {
+          logger.debug("Force overwrite enabled, replaced settings.json completely");
+        }
+      }
     } catch (error) {
       logger.error(`Failed to process settings.json: ${error}`);
-      await import_fs_extra6.copy(sourceFile, destFile, { overwrite: true });
+      await import_fs_extra7.copy(sourceFile, destFile, { overwrite: true });
+    }
+  }
+  async selectiveMergeSettings(transformedSourceContent, destFile) {
+    let sourceSettings;
+    try {
+      sourceSettings = JSON.parse(transformedSourceContent);
+    } catch {
+      logger.warning("Failed to parse source settings.json, falling back to overwrite");
+      await import_fs_extra7.writeFile(destFile, transformedSourceContent, "utf-8");
+      return;
+    }
+    const destSettings = await SettingsMerger.readSettingsFile(destFile);
+    if (!destSettings) {
+      await import_fs_extra7.writeFile(destFile, transformedSourceContent, "utf-8");
+      return;
+    }
+    const backupPath = await SettingsMerger.createBackup(destFile);
+    if (backupPath) {
+      logger.debug(`Created settings backup: ${backupPath}`);
+    }
+    const mergeResult = SettingsMerger.merge(sourceSettings, destSettings);
+    if (mergeResult.hooksAdded > 0) {
+      logger.debug(`Added ${mergeResult.hooksAdded} new hook(s)`);
     }
+    if (mergeResult.hooksPreserved > 0) {
+      logger.debug(`Preserved ${mergeResult.hooksPreserved} existing hook(s)`);
+    }
+    if (mergeResult.mcpServersPreserved > 0) {
+      logger.debug(`Preserved ${mergeResult.mcpServersPreserved} MCP server(s)`);
+    }
+    if (mergeResult.conflictsDetected.length > 0) {
+      logger.warning(`Duplicate hooks detected (skipped): ${mergeResult.conflictsDetected.join(", ")}`);
+    }
+    await SettingsMerger.writeSettingsFile(destFile, mergeResult.merged);
+    logger.success("Merged settings.json (user customizations preserved)");
   }
   transformClaudePaths(content, prefix) {
     if (/\.claude\/[^\s"']*[;`$&|><]/.test(content)) {
@@ -30060,12 +30263,12 @@ class FileMerger {
   }
   async getFiles(dir, baseDir = dir) {
     const files = [];
-    const entries = await import_fs_extra6.readdir(dir, { encoding: "utf8" });
+    const entries = await import_fs_extra7.readdir(dir, { encoding: "utf8" });
     for (const entry of entries) {
       const fullPath = join15(dir, entry);
       const relativePath = relative4(baseDir, fullPath);
       const normalizedRelativePath = relativePath.replace(/\\/g, "/");
-      const stats = await import_fs_extra6.lstat(fullPath);
+      const stats = await import_fs_extra7.lstat(fullPath);
       if (stats.isSymbolicLink()) {
         logger.warning(`Skipping symbolic link: ${normalizedRelativePath}`);
         continue;
@@ -30123,14 +30326,14 @@ class FileMerger {
 
 // src/lib/migration/legacy-migration.ts
 init_logger();
-var import_fs_extra8 = __toESM(require_lib(), 1);
+var import_fs_extra9 = __toESM(require_lib(), 1);
 import { readdir as readdir7, stat as stat3 } from "node:fs/promises";
 import { join as join17, relative as relative5 } from "node:path";
 
 // src/lib/migration/release-manifest.ts
 init_zod();
 init_logger();
-var import_fs_extra7 = __toESM(require_lib(), 1);
+var import_fs_extra8 = __toESM(require_lib(), 1);
 import { join as join16 } from "node:path";
 var ReleaseManifestFileSchema = exports_external.object({
   path: exports_external.string(),
@@ -30147,7 +30350,7 @@ class ReleaseManifestLoader {
   static async load(extractDir) {
     const manifestPath = join16(extractDir, "release-manifest.json");
     try {
-      const content = await import_fs_extra7.readFile(manifestPath, "utf-8");
+      const content = await import_fs_extra8.readFile(manifestPath, "utf-8");
       const parsed = JSON.parse(content);
       return ReleaseManifestSchema.parse(parsed);
     } catch (error) {
@@ -30315,7 +30518,7 @@ User-created files (sample):`);
       files: trackedFiles
     };
     const metadataPath = join17(claudeDir, "metadata.json");
-    await import_fs_extra8.writeFile(metadataPath, JSON.stringify(updatedMetadata, null, 2));
+    await import_fs_extra9.writeFile(metadataPath, JSON.stringify(updatedMetadata, null, 2));
     logger.success(`Migration complete: tracked ${trackedFiles.length} files`);
     return true;
   }
@@ -30894,11 +31097,11 @@ class PromptsManager {
 // src/lib/setup-wizard.ts
 init_dist2();
 init_logger();
-var import_fs_extra10 = __toESM(require_lib(), 1);
+var import_fs_extra11 = __toESM(require_lib(), 1);
 import { join as join21 } from "node:path";
 
 // src/lib/config-generator.ts
-var import_fs_extra9 = __toESM(require_lib(), 1);
+var import_fs_extra10 = __toESM(require_lib(), 1);
 import { join as join20 } from "node:path";
 async function generateEnvFile(targetDir, values) {
   const lines = [
@@ -30912,7 +31115,7 @@ async function generateEnvFile(targetDir, values) {
     }
   }
   const envPath = join20(targetDir, ".env");
-  await import_fs_extra9.writeFile(envPath, `${lines.join(`
+  await import_fs_extra10.writeFile(envPath, `${lines.join(`
 `)}
 `, { mode: 384 });
 }
@@ -30956,7 +31159,7 @@ var ESSENTIAL_CONFIGS = [
 ];
 async function parseEnvFile(path9) {
   try {
-    const content = await import_fs_extra10.readFile(path9, "utf-8");
+    const content = await import_fs_extra11.readFile(path9, "utf-8");
     const env2 = {};
     for (const line of content.split(`
 `)) {
@@ -30983,7 +31186,7 @@ async function parseEnvFile(path9) {
 }
 async function checkGlobalConfig() {
   const globalEnvPath = join21(PathResolver.getGlobalKitDir(), ".env");
-  if (!await import_fs_extra10.pathExists(globalEnvPath))
+  if (!await import_fs_extra11.pathExists(globalEnvPath))
     return false;
   const env2 = await parseEnvFile(globalEnvPath);
   return Object.keys(env2).length > 0;
@@ -30999,7 +31202,7 @@ async function runSetupWizard(options) {
   const hasGlobalConfig = !isGlobal && await checkGlobalConfig();
   if (!isGlobal) {
     const globalEnvPath = join21(PathResolver.getGlobalKitDir(), ".env");
-    if (await import_fs_extra10.pathExists(globalEnvPath)) {
+    if (await import_fs_extra11.pathExists(globalEnvPath)) {
       globalEnv = await parseEnvFile(globalEnvPath);
     }
   }
@@ -31057,16 +31260,16 @@ async function runSetupWizard(options) {
 
 // src/lib/skills-detector.ts
 init_logger();
-var import_fs_extra12 = __toESM(require_lib(), 1);
+var import_fs_extra13 = __toESM(require_lib(), 1);
 import { readdir as readdir9 } from "node:fs/promises";
 import { join as join23 } from "node:path";
 
 // src/lib/skills-manifest.ts
 init_types2();
 init_logger();
-var import_fs_extra11 = __toESM(require_lib(), 1);
+var import_fs_extra12 = __toESM(require_lib(), 1);
 import { createHash as createHash2 } from "node:crypto";
-import { readFile as readFile12, readdir as readdir8, writeFile as writeFile11 } from "node:fs/promises";
+import { readFile as readFile13, readdir as readdir8, writeFile as writeFile12 } from "node:fs/promises";
 import { join as join22, relative as relative6 } from "node:path";
 
 class SkillsManifestManager {
@@ -31074,7 +31277,7 @@ class SkillsManifestManager {
   static MANIFEST_VERSION = "1.0.0";
   static async generateManifest(skillsDir) {
     logger.debug(`Generating manifest for: ${skillsDir}`);
-    if (!await import_fs_extra11.pathExists(skillsDir)) {
+    if (!await import_fs_extra12.pathExists(skillsDir)) {
       throw new SkillsMigrationError(`Skills directory does not exist: ${skillsDir}`);
     }
     const structure = await SkillsManifestManager.detectStructure(skillsDir);
@@ -31090,17 +31293,17 @@ class SkillsManifestManager {
   }
   static async writeManifest(skillsDir, manifest) {
     const manifestPath = join22(skillsDir, SkillsManifestManager.MANIFEST_FILENAME);
-    await writeFile11(manifestPath, JSON.stringify(manifest, null, 2), "utf-8");
+    await writeFile12(manifestPath, JSON.stringify(manifest, null, 2), "utf-8");
     logger.debug(`Wrote manifest to: ${manifestPath}`);
   }
   static async readManifest(skillsDir) {
     const manifestPath = join22(skillsDir, SkillsManifestManager.MANIFEST_FILENAME);
-    if (!await import_fs_extra11.pathExists(manifestPath)) {
+    if (!await import_fs_extra12.pathExists(manifestPath)) {
       logger.debug(`No manifest found at: ${manifestPath}`);
       return null;
     }
     try {
-      const content = await readFile12(manifestPath, "utf-8");
+      const content = await readFile13(manifestPath, "utf-8");
       const data = JSON.parse(content);
       const manifest = SkillsManifestSchema.parse(data);
       logger.debug(`Read manifest from: ${manifestPath}`);
@@ -31172,7 +31375,7 @@ class SkillsManifestManager {
     files.sort();
     for (const file of files) {
       const relativePath = relative6(dirPath, file);
-      const content = await readFile12(file);
+      const content = await readFile13(file);
       hash.update(relativePath);
       hash.update(content);
     }
@@ -31302,8 +31505,8 @@ function getPathMapping(skillName, oldBasePath, newBasePath) {
 class SkillsMigrationDetector {
   static async detectMigration(oldSkillsDir, currentSkillsDir) {
     logger.debug("Detecting skills migration need...");
-    const oldExists = await import_fs_extra12.pathExists(oldSkillsDir);
-    const currentExists = await import_fs_extra12.pathExists(currentSkillsDir);
+    const oldExists = await import_fs_extra13.pathExists(oldSkillsDir);
+    const currentExists = await import_fs_extra13.pathExists(currentSkillsDir);
     if (!oldExists && !currentExists) {
       logger.debug("No skills directories found, migration not needed");
       return {
@@ -31414,7 +31617,7 @@ class SkillsMigrationDetector {
     };
   }
   static async scanDirectory(skillsDir) {
-    if (!await import_fs_extra12.pathExists(skillsDir)) {
+    if (!await import_fs_extra13.pathExists(skillsDir)) {
       return ["flat", []];
     }
     const entries = await readdir9(skillsDir, { withFileTypes: true });
@@ -31467,14 +31670,14 @@ class SkillsMigrationDetector {
 // src/lib/skills-migrator.ts
 init_types2();
 init_logger();
-var import_fs_extra15 = __toESM(require_lib(), 1);
+var import_fs_extra16 = __toESM(require_lib(), 1);
 import { copyFile as copyFile2, mkdir as mkdir8, readdir as readdir12, rm as rm2 } from "node:fs/promises";
 import { join as join26 } from "node:path";
 
 // src/lib/skills-backup-manager.ts
 init_types2();
 init_logger();
-var import_fs_extra13 = __toESM(require_lib(), 1);
+var import_fs_extra14 = __toESM(require_lib(), 1);
 import { copyFile, mkdir as mkdir7, readdir as readdir10, rm, stat as stat4 } from "node:fs/promises";
 import { basename as basename2, join as join24, normalize as normalize4 } from "node:path";
 function validatePath2(path9, paramName) {
@@ -31496,7 +31699,7 @@ class SkillsBackupManager {
     if (parentDir) {
       validatePath2(parentDir, "parentDir");
     }
-    if (!await import_fs_extra13.pathExists(skillsDir)) {
+    if (!await import_fs_extra14.pathExists(skillsDir)) {
       throw new SkillsMigrationError(`Cannot create backup: Skills directory does not exist: ${skillsDir}`);
     }
     const timestamp = Date.now();
@@ -31519,12 +31722,12 @@ class SkillsBackupManager {
   static async restoreBackup(backupDir, targetDir) {
     validatePath2(backupDir, "backupDir");
     validatePath2(targetDir, "targetDir");
-    if (!await import_fs_extra13.pathExists(backupDir)) {
+    if (!await import_fs_extra14.pathExists(backupDir)) {
       throw new SkillsMigrationError(`Cannot restore: Backup directory does not exist: ${backupDir}`);
     }
     logger.info(`Restoring from backup: ${backupDir}`);
     try {
-      if (await import_fs_extra13.pathExists(targetDir)) {
+      if (await import_fs_extra14.pathExists(targetDir)) {
         await rm(targetDir, { recursive: true, force: true });
       }
       await mkdir7(targetDir, { recursive: true });
@@ -31535,7 +31738,7 @@ class SkillsBackupManager {
     }
   }
   static async deleteBackup(backupDir) {
-    if (!await import_fs_extra13.pathExists(backupDir)) {
+    if (!await import_fs_extra14.pathExists(backupDir)) {
       logger.warning(`Backup directory does not exist: ${backupDir}`);
       return;
     }
@@ -31548,7 +31751,7 @@ class SkillsBackupManager {
     }
   }
   static async listBackups(parentDir) {
-    if (!await import_fs_extra13.pathExists(parentDir)) {
+    if (!await import_fs_extra14.pathExists(parentDir)) {
       return [];
     }
     try {
@@ -31573,7 +31776,7 @@ class SkillsBackupManager {
     }
   }
   static async getBackupSize(backupDir) {
-    if (!await import_fs_extra13.pathExists(backupDir)) {
+    if (!await import_fs_extra14.pathExists(backupDir)) {
       return 0;
     }
     return await SkillsBackupManager.getDirectorySize(backupDir);
@@ -31625,10 +31828,10 @@ class SkillsBackupManager {
 // src/lib/skills-customization-scanner.ts
 init_types2();
 init_logger();
-var import_fs_extra14 = __toESM(require_lib(), 1);
+var import_fs_extra15 = __toESM(require_lib(), 1);
 import { createHash as createHash3 } from "node:crypto";
 import { createReadStream as createReadStream2 } from "node:fs";
-import { readFile as readFile13, readdir as readdir11 } from "node:fs/promises";
+import { readFile as readFile14, readdir as readdir11 } from "node:fs/promises";
 import { join as join25, normalize as normalize5, relative as relative7 } from "node:path";
 function validatePath3(path9, paramName) {
   if (!path9 || typeof path9 !== "string") {
@@ -31708,7 +31911,7 @@ class SkillsCustomizationScanner {
   static async detectFileChanges(currentSkillPath, baselineSkillPath) {
     const changes = [];
     const currentFiles = await SkillsCustomizationScanner.getAllFiles(currentSkillPath);
-    const baselineFiles = await import_fs_extra14.pathExists(baselineSkillPath) ? await SkillsCustomizationScanner.getAllFiles(baselineSkillPath) : [];
+    const baselineFiles = await import_fs_extra15.pathExists(baselineSkillPath) ? await SkillsCustomizationScanner.getAllFiles(baselineSkillPath) : [];
     const currentFileMap = new Map(await Promise.all(currentFiles.map(async (f3) => {
       const relPath = relative7(currentSkillPath, f3);
       const hash = await SkillsCustomizationScanner.hashFile(f3);
@@ -31768,7 +31971,7 @@ class SkillsCustomizationScanner {
     return false;
   }
   static async scanSkillsDirectory(skillsDir) {
-    if (!await import_fs_extra14.pathExists(skillsDir)) {
+    if (!await import_fs_extra15.pathExists(skillsDir)) {
       return ["flat", []];
     }
     const entries = await readdir11(skillsDir, { withFileTypes: true });
@@ -31803,7 +32006,7 @@ class SkillsCustomizationScanner {
   }
   static async findSkillPath(skillsDir, skillName) {
     const flatPath = join25(skillsDir, skillName);
-    if (await import_fs_extra14.pathExists(flatPath)) {
+    if (await import_fs_extra15.pathExists(flatPath)) {
       return { path: flatPath, category: undefined };
     }
     const entries = await readdir11(skillsDir, { withFileTypes: true });
@@ -31813,7 +32016,7 @@ class SkillsCustomizationScanner {
       }
       const categoryPath = join25(skillsDir, entry.name);
       const skillPath = join25(categoryPath, skillName);
-      if (await import_fs_extra14.pathExists(skillPath)) {
+      if (await import_fs_extra15.pathExists(skillPath)) {
         return { path: skillPath, category: entry.name };
       }
     }
@@ -31856,7 +32059,7 @@ class SkillsCustomizationScanner {
     files.sort();
     for (const file of files) {
       const relativePath = relative7(dirPath, file);
-      const content = await readFile13(file);
+      const content = await readFile14(file);
       hash.update(relativePath);
       hash.update(content);
     }
@@ -32125,7 +32328,7 @@ class SkillsMigrator {
         try {
           const skillName = mapping.skillName;
           const currentSkillPath = mapping.oldPath;
-          if (!await import_fs_extra15.pathExists(currentSkillPath)) {
+          if (!await import_fs_extra16.pathExists(currentSkillPath)) {
             logger.warning(`Skill not found, skipping: ${skillName}`);
             continue;
           }
@@ -32196,7 +32399,7 @@ init_types2();
 init_types2();
 init_logger();
 import { existsSync as existsSync6 } from "node:fs";
-import { mkdir as mkdir9, readFile as readFile14, rename as rename2, rm as rm3, writeFile as writeFile12 } from "node:fs/promises";
+import { mkdir as mkdir9, readFile as readFile15, rename as rename2, rm as rm3, writeFile as writeFile13 } from "node:fs/promises";
 import { chmod as chmod2 } from "node:fs/promises";
 import { platform as platform9 } from "node:os";
 import { join as join27 } from "node:path";
@@ -32222,7 +32425,7 @@ class ConfigManager {
     const configFile = PathResolver.getConfigFile(ConfigManager.globalFlag);
     try {
       if (existsSync6(configFile)) {
-        const content = await readFile14(configFile, "utf-8");
+        const content = await readFile15(configFile, "utf-8");
         const data = JSON.parse(content);
         ConfigManager.config = ConfigSchema.parse(data);
         logger.debug(`Config loaded from ${configFile}`);
@@ -32245,7 +32448,7 @@ class ConfigManager {
           await chmod2(configDir, 448);
         }
       }
-      await writeFile12(configFile, JSON.stringify(validConfig, null, 2), "utf-8");
+      await writeFile13(configFile, JSON.stringify(validConfig, null, 2), "utf-8");
       if (platform9() !== "win32") {
         await chmod2(configFile, 384);
       }
@@ -32276,7 +32479,7 @@ class ConfigManager {
     const configPath = join27(configDir, PROJECT_CONFIG_FILE);
     try {
       if (existsSync6(configPath)) {
-        const content = await readFile14(configPath, "utf-8");
+        const content = await readFile15(configPath, "utf-8");
         const data = JSON.parse(content);
         const folders = FoldersConfigSchema.parse(data.paths || data);
         logger.debug(`Project config loaded from ${configPath}`);
@@ -32295,7 +32498,7 @@ class ConfigManager {
         await mkdir9(configDir, { recursive: true });
       }
       const validFolders = FoldersConfigSchema.parse(folders);
-      await writeFile12(configPath, JSON.stringify({ paths: validFolders }, null, 2), "utf-8");
+      await writeFile13(configPath, JSON.stringify({ paths: validFolders }, null, 2), "utf-8");
       logger.debug(`Project config saved to ${configPath}`);
     } catch (error) {
       throw new Error(`Failed to save project config: ${error instanceof Error ? error.message : "Unknown error"}`);
@@ -32357,7 +32560,7 @@ init_environment();
 
 // src/utils/file-scanner.ts
 init_logger();
-var import_fs_extra16 = __toESM(require_lib(), 1);
+var import_fs_extra17 = __toESM(require_lib(), 1);
 import { join as join28, relative as relative8, resolve as resolve4 } from "node:path";
 var SKIP_DIRS2 = [
   "node_modules",
@@ -32383,11 +32586,11 @@ class FileScanner {
   static async getFiles(dirPath, relativeTo) {
     const basePath = relativeTo || dirPath;
     const files = [];
-    if (!await import_fs_extra16.pathExists(dirPath)) {
+    if (!await import_fs_extra17.pathExists(dirPath)) {
       return files;
     }
     try {
-      const entries = await import_fs_extra16.readdir(dirPath, { encoding: "utf8" });
+      const entries = await import_fs_extra17.readdir(dirPath, { encoding: "utf8" });
       for (const entry of entries) {
         if (SKIP_DIRS2.includes(entry)) {
           logger.debug(`Skipping directory: ${entry}`);
@@ -32400,7 +32603,7 @@ class FileScanner {
         }
         let stats;
         try {
-          stats = await import_fs_extra16.lstat(fullPath);
+          stats = await import_fs_extra17.lstat(fullPath);
         } catch (error) {
           if (error instanceof Error && "code" in error && (error.code === "EACCES" || error.code === "EPERM")) {
             logger.warning(`Skipping inaccessible path: ${entry}`);
@@ -32439,7 +32642,7 @@ class FileScanner {
     const sourceFiles = await FileScanner.getFiles(sourceSubDir, sourceDir);
     logger.debug(`findCustomFiles - destFiles count: ${destFiles.length}`);
     logger.debug(`findCustomFiles - sourceFiles count: ${sourceFiles.length}`);
-    const sourceExists = await import_fs_extra16.pathExists(sourceSubDir);
+    const sourceExists = await import_fs_extra17.pathExists(sourceSubDir);
     if (sourceExists && sourceFiles.length === 0 && destFiles.length > 100) {
       logger.warning(`Source directory exists but is empty while destination has ${destFiles.length} files. This may indicate an extraction issue. Skipping custom file detection.`);
       return [];
@@ -32487,7 +32690,7 @@ async function initCommand(options) {
       const cwdResolved = resolve5(process.cwd());
       const isInGlobalDir = cwdResolved === globalKitDir || cwdResolved === resolve5(globalKitDir, "..");
       const localSettingsPath = join29(process.cwd(), ".claude", "settings.json");
-      if (!isInGlobalDir && await import_fs_extra17.pathExists(localSettingsPath)) {
+      if (!isInGlobalDir && await import_fs_extra18.pathExists(localSettingsPath)) {
         if (isNonInteractive2) {
           logger.warning("Local .claude/settings.json detected. Local settings take precedence over global.");
           logger.warning("Consider removing local installation: rm -rf .claude");
@@ -32500,7 +32703,7 @@ async function initCommand(options) {
           if (choice === "remove") {
             const localClaudeDir = join29(process.cwd(), ".claude");
             try {
-              await import_fs_extra17.remove(localClaudeDir);
+              await import_fs_extra18.remove(localClaudeDir);
               logger.success("Removed local .claude/ directory");
             } catch (error) {
               logger.error(`Failed to remove local installation: ${error instanceof Error ? error.message : "Unknown error"}`);
@@ -32544,7 +32747,7 @@ async function initCommand(options) {
     }
     const resolvedDir = resolve5(targetDir);
     logger.info(`Target directory: ${resolvedDir}`);
-    if (!await import_fs_extra17.pathExists(resolvedDir)) {
+    if (!await import_fs_extra18.pathExists(resolvedDir)) {
       if (validOptions.global) {
         const { mkdir: mkdir10 } = await import("node:fs/promises");
         await mkdir10(resolvedDir, { recursive: true });
@@ -32696,7 +32899,7 @@ async function initCommand(options) {
     if (!validOptions.fresh) {
       const newSkillsDir = join29(extractDir, ".claude", "skills");
       const currentSkillsDir = PathResolver.buildSkillsPath(resolvedDir, validOptions.global);
-      if (await import_fs_extra17.pathExists(newSkillsDir) && await import_fs_extra17.pathExists(currentSkillsDir)) {
+      if (await import_fs_extra18.pathExists(newSkillsDir) && await import_fs_extra18.pathExists(currentSkillsDir)) {
         logger.info("Checking for skills directory migration...");
         const migrationDetection = await SkillsMigrationDetector.detectMigration(newSkillsDir, currentSkillsDir);
         if (migrationDetection.status === "recommended" || migrationDetection.status === "required") {
@@ -32748,9 +32951,10 @@ async function initCommand(options) {
       merger.addIgnorePatterns(validOptions.exclude);
     }
     merger.setGlobalFlag(validOptions.global);
+    merger.setForceOverwriteSettings(validOptions.forceOverwriteSettings);
     const claudeDir = validOptions.global ? resolvedDir : join29(resolvedDir, ".claude");
     const releaseManifest = await ReleaseManifestLoader.load(extractDir);
-    if (!validOptions.fresh && await import_fs_extra17.pathExists(claudeDir)) {
+    if (!validOptions.fresh && await import_fs_extra18.pathExists(claudeDir)) {
       const legacyDetection = await LegacyMigration.detectLegacy(claudeDir);
       if (legacyDetection.isLegacy && releaseManifest) {
         logger.info("Legacy installation detected - migrating to ownership tracking...");
@@ -32802,9 +33006,9 @@ async function initCommand(options) {
     if (validOptions.global) {
       const claudeMdSource = join29(extractDir, "CLAUDE.md");
       const claudeMdDest = join29(resolvedDir, "CLAUDE.md");
-      if (await import_fs_extra17.pathExists(claudeMdSource)) {
-        if (!await import_fs_extra17.pathExists(claudeMdDest)) {
-          await import_fs_extra17.copy(claudeMdSource, claudeMdDest);
+      if (await import_fs_extra18.pathExists(claudeMdSource)) {
+        if (!await import_fs_extra18.pathExists(claudeMdDest)) {
+          await import_fs_extra18.copy(claudeMdSource, claudeMdDest);
           logger.success("Copied CLAUDE.md to global directory");
         } else {
           logger.debug("CLAUDE.md already exists in global directory (preserved)");
@@ -32822,7 +33026,7 @@ async function initCommand(options) {
     }
     if (!validOptions.skipSetup && !isNonInteractive2) {
       const envPath = join29(claudeDir, ".env");
-      if (!await import_fs_extra17.pathExists(envPath)) {
+      if (!await import_fs_extra18.pathExists(envPath)) {
         const shouldSetup = await prompts.confirm("Set up API keys now? (Gemini API key for ai-multimodal skill, optional webhooks)");
         if (shouldSetup) {
           await runSetupWizard({
@@ -32852,7 +33056,7 @@ Protected files (.env, etc.) were not modified.`;
 }
 
 // src/commands/new.ts
-var import_fs_extra18 = __toESM(require_lib(), 1);
+var import_fs_extra19 = __toESM(require_lib(), 1);
 import { join as join30, resolve as resolve6 } from "node:path";
 init_types2();
 init_environment();
@@ -32884,8 +33088,8 @@ async function newCommand(options) {
     }
     const resolvedDir = resolve6(targetDir);
     logger.info(`Target directory: ${resolvedDir}`);
-    if (await import_fs_extra18.pathExists(resolvedDir)) {
-      const files = await import_fs_extra18.readdir(resolvedDir);
+    if (await import_fs_extra19.pathExists(resolvedDir)) {
+      const files = await import_fs_extra19.readdir(resolvedDir);
       const isEmpty = files.length === 0;
       if (!isEmpty) {
         if (isNonInteractive2) {
@@ -33085,7 +33289,7 @@ async function newCommand(options) {
 }
 
 // src/commands/uninstall.ts
-var import_fs_extra19 = __toESM(require_lib(), 1);
+var import_fs_extra20 = __toESM(require_lib(), 1);
 var import_picocolors10 = __toESM(require_picocolors(), 1);
 import { readdirSync, rmSync } from "node:fs";
 import { dirname as dirname5, join as join31 } from "node:path";
@@ -33098,14 +33302,14 @@ async function detectInstallations() {
     installations.push({
       type: "local",
       path: setup.project.path,
-      exists: await import_fs_extra19.pathExists(setup.project.path)
+      exists: await import_fs_extra20.pathExists(setup.project.path)
     });
   }
   if (setup.global.path && setup.global.metadata) {
     installations.push({
       type: "global",
       path: setup.global.path,
-      exists: await import_fs_extra19.pathExists(setup.global.path)
+      exists: await import_fs_extra20.pathExists(setup.global.path)
     });
   }
   return installations.filter((i) => i.exists);
@@ -33238,8 +33442,8 @@ async function removeInstallations(installations, options) {
       let cleanedDirs = 0;
       for (const item of analysis.toDelete) {
         const filePath = join31(installation.path, item.path);
-        if (await import_fs_extra19.pathExists(filePath)) {
-          await import_fs_extra19.remove(filePath);
+        if (await import_fs_extra20.pathExists(filePath)) {
+          await import_fs_extra20.remove(filePath);
           removedCount++;
           logger.debug(`Removed: ${item.path}`);
           cleanedDirs += await cleanupEmptyDirectories(filePath, installation.path);
@@ -33338,7 +33542,7 @@ import { promisify as promisify6 } from "node:util";
 // package.json
 var package_default2 = {
   name: "claudekit-cli",
-  version: "3.7.1",
+  version: "3.8.0",
   description: "CLI tool for bootstrapping and updating ClaudeKit projects",
   type: "module",
   repository: {
@@ -33784,7 +33988,7 @@ var import_picocolors12 = __toESM(require_picocolors(), 1);
 // src/lib/version-cache.ts
 init_logger();
 import { existsSync as existsSync7 } from "node:fs";
-import { mkdir as mkdir10, readFile as readFile15, writeFile as writeFile13 } from "node:fs/promises";
+import { mkdir as mkdir10, readFile as readFile16, writeFile as writeFile14 } from "node:fs/promises";
 import { join as join32 } from "node:path";
 class VersionCacheManager {
   static CACHE_FILENAME = "version-check.json";
@@ -33800,7 +34004,7 @@ class VersionCacheManager {
         logger.debug("Version check cache not found");
         return null;
       }
-      const content = await readFile15(cacheFile, "utf-8");
+      const content = await readFile16(cacheFile, "utf-8");
       const cache2 = JSON.parse(content);
       if (!cache2.lastCheck || !cache2.currentVersion || !cache2.latestVersion) {
         logger.debug("Invalid cache structure, ignoring");
@@ -33820,7 +34024,7 @@ class VersionCacheManager {
       if (!existsSync7(cacheDir)) {
         await mkdir10(cacheDir, { recursive: true, mode: 448 });
       }
-      await writeFile13(cacheFile, JSON.stringify(cache2, null, 2), "utf-8");
+      await writeFile14(cacheFile, JSON.stringify(cache2, null, 2), "utf-8");
       logger.debug(`Version check cache saved to ${cacheFile}`);
     } catch (error) {
       logger.debug(`Failed to save version check cache: ${error}`);
@@ -34064,6 +34268,7 @@ var UpdateCommandOptionsSchema2 = exports_external.object({
   beta: exports_external.boolean().default(false),
   dryRun: exports_external.boolean().default(false),
   forceOverwrite: exports_external.boolean().default(false),
+  forceOverwriteSettings: exports_external.boolean().default(false),
   skipSetup: exports_external.boolean().default(false),
   refresh: exports_external.boolean().default(false),
   docsDir: exports_external.string().optional(),
@@ -34447,7 +34652,7 @@ cli.command("new", "Bootstrap a new ClaudeKit project (with interactive version
   }
   await newCommand(options);
 });
-cli.command("init", "Initialize or update ClaudeKit project (with interactive version selection)").option("--dir <dir>", "Target directory (default: .)").option("--kit <kit>", "Kit to use (engineer, marketing)").option("-r, --release <version>", "Skip version selection, use specific version (e.g., latest, v1.0.0)").option("--exclude <pattern>", "Exclude files matching glob pattern (can be used multiple times)").option("--only <pattern>", "Include only files matching glob pattern (can be used multiple times)").option("-g, --global", "Use platform-specific user configuration directory").option("--fresh", "Completely remove .claude directory before downloading (requires confirmation)").option("--install-skills", "Install skills dependencies (non-interactive mode)").option("--prefix", "Add /ck: prefix to all slash commands by moving them to commands/ck/ subdirectory").option("--beta", "Show beta versions in selection prompt").option("--refresh", "Bypass release cache to fetch latest versions from GitHub").option("--dry-run", "Preview changes without applying them (requires --prefix)").option("--force-overwrite", "Override ownership protections and delete user-modified files (requires --prefix)").option("--skip-setup", "Skip interactive configuration wizard").option("--docs-dir <name>", "Custom docs folder name (default: docs)").option("--plans-dir <name>", "Custom plans folder name (default: plans)").option("-y, --yes", "Non-interactive mode with sensible defaults (skip all prompts)").action(async (options) => {
+cli.command("init", "Initialize or update ClaudeKit project (with interactive version selection)").option("--dir <dir>", "Target directory (default: .)").option("--kit <kit>", "Kit to use (engineer, marketing)").option("-r, --release <version>", "Skip version selection, use specific version (e.g., latest, v1.0.0)").option("--exclude <pattern>", "Exclude files matching glob pattern (can be used multiple times)").option("--only <pattern>", "Include only files matching glob pattern (can be used multiple times)").option("-g, --global", "Use platform-specific user configuration directory").option("--fresh", "Completely remove .claude directory before downloading (requires confirmation)").option("--install-skills", "Install skills dependencies (non-interactive mode)").option("--prefix", "Add /ck: prefix to all slash commands by moving them to commands/ck/ subdirectory").option("--beta", "Show beta versions in selection prompt").option("--refresh", "Bypass release cache to fetch latest versions from GitHub").option("--dry-run", "Preview changes without applying them (requires --prefix)").option("--force-overwrite", "Override ownership protections and delete user-modified files (requires --prefix)").option("--force-overwrite-settings", "Fully replace settings.json instead of selective merge (destroys user customizations)").option("--skip-setup", "Skip interactive configuration wizard").option("--docs-dir <name>", "Custom docs folder name (default: docs)").option("--plans-dir <name>", "Custom plans folder name (default: plans)").option("-y, --yes", "Non-interactive mode with sensible defaults (skip all prompts)").action(async (options) => {
   if (options.exclude && !Array.isArray(options.exclude)) {
     options.exclude = [options.exclude];
   }

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "claudekit-cli",
-	"version": "3.7.1",
+	"version": "3.8.0",
 	"description": "CLI tool for bootstrapping and updating ClaudeKit projects",
 	"type": "module",
 	"repository": {