claudekit-cli 3.35.0-dev.23 → 3.35.0-dev.25

package/dist/index.js

@@ -42500,14 +42500,11 @@ function normalizeCommand(cmd) {
   if (!cmd)
     return "";
   let normalized = cmd;
-  normalized = normalized.replace(/"\$HOME"/g, "$HOME");
-  normalized = normalized.replace(/"\$CLAUDE_PROJECT_DIR"/g, "$HOME");
-  normalized = normalized.replace(/"\$\{HOME\}"/g, "$HOME");
+  normalized = normalized.replace(/"/g, "");
+  normalized = normalized.replace(/~\//g, "$HOME/");
   normalized = normalized.replace(/\$CLAUDE_PROJECT_DIR/g, "$HOME");
   normalized = normalized.replace(/\$\{HOME\}/g, "$HOME");
-  normalized = normalized.replace(/"%USERPROFILE%"/g, "$HOME");
   normalized = normalized.replace(/%USERPROFILE%/g, "$HOME");
-  normalized = normalized.replace(/"%CLAUDE_PROJECT_DIR%"/g, "$HOME");
   normalized = normalized.replace(/%CLAUDE_PROJECT_DIR%/g, "$HOME");
   normalized = normalized.replace(/\\/g, "/");
   normalized = normalized.replace(/\s+/g, " ").trim();
@@ -50915,11 +50912,17 @@ function registerMigrationRoutes(app) {
       const registry = await readPortableRegistry();
       const targetStates = new Map;
       for (const entry of registry.installations) {
+        if (entry.type === "skill")
+          continue;
         const exists = existsSync20(entry.path);
         const state = { path: entry.path, exists };
         if (exists) {
-          const content = await readFile15(entry.path, "utf-8");
-          state.currentChecksum = computeContentChecksum(content);
+          try {
+            const content = await readFile15(entry.path, "utf-8");
+            state.currentChecksum = computeContentChecksum(content);
+          } catch (error) {
+            warnReadFailure("registry-target", entry.path, error);
+          }
         }
         targetStates.set(entry.path, state);
       }
@@ -52836,6 +52839,27 @@ var init_skill_routes = __esm(() => {
 });
 
 // src/domains/github/npm-registry.ts
+function redactRegistryUrlForLog(url) {
+  if (!url)
+    return url;
+  try {
+    const parsed = new URL(url);
+    if (parsed.username) {
+      parsed.username = REDACTED_VALUE;
+    }
+    if (parsed.password) {
+      parsed.password = REDACTED_VALUE;
+    }
+    for (const key of parsed.searchParams.keys()) {
+      if (/(token|auth|password|secret|key)/i.test(key)) {
+        parsed.searchParams.set(key, REDACTED_VALUE);
+      }
+    }
+    return parsed.toString();
+  } catch {
+    return url.replace(/\/\/([^/@\s]+)@/, `//${REDACTED_VALUE}@`);
+  }
+}
 async function fetchWithTimeout(url, options2 = {}, timeout2 = REQUEST_TIMEOUT) {
   const controller = new AbortController;
   const timeoutId = setTimeout(() => controller.abort(), timeout2);
@@ -52857,7 +52881,7 @@ class NpmRegistryClient {
     }
     const registry = registryUrl || DEFAULT_REGISTRY_URL;
     const url = `${registry}/${encodeURIComponent(packageName)}`;
-    logger.debug(`Fetching package info from: ${url}`);
+    logger.debug(`Fetching package info from: ${redactRegistryUrlForLog(url)}`);
     try {
       const response = await fetchWithTimeout(url, {
         headers: {
@@ -52920,18 +52944,12 @@ class NpmRegistryClient {
     }
   }
   static async versionExists(packageName, version, registryUrl) {
-    try {
-      const info = await NpmRegistryClient.getPackageInfo(packageName, registryUrl);
-      if (!info)
-        return false;
-      const exists = version in (info.versions || {});
-      logger.debug(`Version ${version} exists for ${packageName}: ${exists}`);
-      return exists;
-    } catch (error) {
-      const message = error instanceof Error ? error.message : "Unknown error";
-      logger.debug(`Failed to check version ${version} for ${packageName}: ${message}`);
+    const info = await NpmRegistryClient.getPackageInfo(packageName, registryUrl);
+    if (!info)
       return false;
-    }
+    const exists = version in (info.versions || {});
+    logger.debug(`Version ${version} exists for ${packageName}: ${exists}`);
+    return exists;
   }
   static async getVersionInfo(packageName, version, registryUrl) {
     try {
@@ -52969,7 +52987,7 @@ class NpmRegistryClient {
     }
   }
 }
-var DEFAULT_REGISTRY_URL = "https://registry.npmjs.org", REQUEST_TIMEOUT = 5000;
+var DEFAULT_REGISTRY_URL = "https://registry.npmjs.org", REQUEST_TIMEOUT = 5000, REDACTED_VALUE = "***";
 var init_npm_registry = __esm(() => {
   init_logger();
 });
@@ -53006,9 +53024,9 @@ function getNpmQuery() {
     checkFn: (stdout) => {
       try {
         const data = JSON.parse(stdout);
-        return !!(data.dependencies?.[CLAUDEKIT_CLI_NPM_PACKAGE_NAME] || stdout.includes(CLAUDEKIT_CLI_NPM_PACKAGE_NAME));
+        return !!data.dependencies?.["claudekit-cli"];
       } catch {
-        return stdout.includes(CLAUDEKIT_CLI_NPM_PACKAGE_NAME);
+        return /"claudekit-cli"\s*:/.test(stdout) || /(?:^|[^a-z0-9-])claudekit-cli@/m.test(stdout);
       }
     }
   };
@@ -53026,7 +53044,36 @@ async function getNpmVersion() {
     return null;
   }
 }
-function getNpmUpdateCommand(packageName, version) {
+function normalizeNpmRegistryUrl(rawValue) {
+  const value = rawValue.trim();
+  if (!value) {
+    return null;
+  }
+  if (!/^https?:\/\//i.test(value)) {
+    return null;
+  }
+  try {
+    const parsed = new URL(value);
+    const protocol = parsed.protocol.toLowerCase();
+    if (protocol !== "http:" && protocol !== "https:") {
+      return null;
+    }
+    const normalizedPath = parsed.pathname.replace(/\/+$/, "");
+    return `${parsed.protocol}//${parsed.host}${normalizedPath}${parsed.search}${parsed.hash}`;
+  } catch {
+    return null;
+  }
+}
+async function getNpmRegistryUrl() {
+  try {
+    const cmd = isWindows() ? "npm.cmd config get registry" : "npm config get registry";
+    const { stdout } = await execAsync(cmd, { timeout: 3000 });
+    return normalizeNpmRegistryUrl(stdout);
+  } catch {
+    return null;
+  }
+}
+function getNpmUpdateCommand(packageName, version, registryUrl) {
   if (!isValidPackageName(packageName)) {
     throw new Error(`Invalid package name: ${packageName}`);
   }
@@ -53034,7 +53081,8 @@ function getNpmUpdateCommand(packageName, version) {
     throw new Error(`Invalid version: ${version}`);
   }
   const versionSuffix = version ? `@${version}` : "@latest";
-  return isWindows() ? `npm.cmd install -g ${packageName}${versionSuffix}` : `npm install -g ${packageName}${versionSuffix}`;
+  const registryFlag = registryUrl ? ` --registry ${registryUrl}` : "";
+  return isWindows() ? `npm.cmd install -g ${packageName}${versionSuffix}${registryFlag}` : `npm install -g ${packageName}${versionSuffix}${registryFlag}`;
 }
 var init_npm_detector = __esm(() => {
   init_claudekit_constants();
@@ -53048,7 +53096,7 @@ function getBunQuery() {
   return {
     pm: "bun",
     cmd: "bun pm ls -g",
-    checkFn: (stdout) => stdout.includes(CLAUDEKIT_CLI_NPM_PACKAGE_NAME)
+    checkFn: (stdout) => /(?:^|[^a-z0-9-])claudekit-cli@/m.test(stdout)
   };
 }
 function getBunVersionCommand() {
@@ -53064,7 +53112,7 @@ async function getBunVersion() {
     return null;
   }
 }
-function getBunUpdateCommand(packageName, version) {
+function getBunUpdateCommand(packageName, version, registryUrl) {
   if (!isValidPackageName(packageName)) {
     throw new Error(`Invalid package name: ${packageName}`);
   }
@@ -53072,10 +53120,10 @@ function getBunUpdateCommand(packageName, version) {
     throw new Error(`Invalid version: ${version}`);
   }
   const versionSuffix = version ? `@${version}` : "@latest";
-  return `bun add -g ${packageName}${versionSuffix}`;
+  const registryFlag = registryUrl ? ` --registry ${registryUrl}` : "";
+  return `bun add -g ${packageName}${versionSuffix}${registryFlag}`;
 }
 var init_bun_detector = __esm(() => {
-  init_claudekit_constants();
   init_constants();
   init_detector_base();
 });
@@ -53084,8 +53132,8 @@ var init_bun_detector = __esm(() => {
 function getYarnQuery() {
   return {
     pm: "yarn",
-    cmd: isWindows() ? `yarn.cmd global list --pattern ${CLAUDEKIT_CLI_NPM_PACKAGE_NAME}` : `yarn global list --pattern ${CLAUDEKIT_CLI_NPM_PACKAGE_NAME}`,
-    checkFn: (stdout) => stdout.includes(CLAUDEKIT_CLI_NPM_PACKAGE_NAME)
+    cmd: isWindows() ? "yarn.cmd global list --pattern claudekit-cli" : "yarn global list --pattern claudekit-cli",
+    checkFn: (stdout) => /(?:^|[^a-z0-9-])claudekit-cli@/m.test(stdout)
   };
 }
 function getYarnVersionCommand() {
@@ -53101,7 +53149,7 @@ async function getYarnVersion() {
     return null;
   }
 }
-function getYarnUpdateCommand(packageName, version) {
+function getYarnUpdateCommand(packageName, version, registryUrl) {
   if (!isValidPackageName(packageName)) {
     throw new Error(`Invalid package name: ${packageName}`);
   }
@@ -53109,10 +53157,10 @@ function getYarnUpdateCommand(packageName, version) {
     throw new Error(`Invalid version: ${version}`);
   }
   const versionSuffix = version ? `@${version}` : "@latest";
-  return isWindows() ? `yarn.cmd global add ${packageName}${versionSuffix}` : `yarn global add ${packageName}${versionSuffix}`;
+  const registryFlag = registryUrl ? ` --registry ${registryUrl}` : "";
+  return isWindows() ? `yarn.cmd global add ${packageName}${versionSuffix}${registryFlag}` : `yarn global add ${packageName}${versionSuffix}${registryFlag}`;
 }
 var init_yarn_detector = __esm(() => {
-  init_claudekit_constants();
   init_environment();
   init_constants();
   init_detector_base();
@@ -53122,8 +53170,8 @@ var init_yarn_detector = __esm(() => {
 function getPnpmQuery() {
   return {
     pm: "pnpm",
-    cmd: isWindows() ? `pnpm.cmd ls -g ${CLAUDEKIT_CLI_NPM_PACKAGE_NAME}` : `pnpm ls -g ${CLAUDEKIT_CLI_NPM_PACKAGE_NAME}`,
-    checkFn: (stdout) => stdout.includes(CLAUDEKIT_CLI_NPM_PACKAGE_NAME)
+    cmd: isWindows() ? "pnpm.cmd ls -g claudekit-cli" : "pnpm ls -g claudekit-cli",
+    checkFn: (stdout) => /(?:^|[^a-z0-9-])claudekit-cli(?:@|\s+\d)/m.test(stdout)
   };
 }
 function getPnpmVersionCommand() {
@@ -53139,7 +53187,7 @@ async function getPnpmVersion() {
     return null;
   }
 }
-function getPnpmUpdateCommand(packageName, version) {
+function getPnpmUpdateCommand(packageName, version, registryUrl) {
   if (!isValidPackageName(packageName)) {
     throw new Error(`Invalid package name: ${packageName}`);
   }
@@ -53147,10 +53195,10 @@ function getPnpmUpdateCommand(packageName, version) {
     throw new Error(`Invalid version: ${version}`);
   }
   const versionSuffix = version ? `@${version}` : "@latest";
-  return isWindows() ? `pnpm.cmd add -g ${packageName}${versionSuffix}` : `pnpm add -g ${packageName}${versionSuffix}`;
+  const registryFlag = registryUrl ? ` --registry ${registryUrl}` : "";
+  return isWindows() ? `pnpm.cmd add -g ${packageName}${versionSuffix}${registryFlag}` : `pnpm add -g ${packageName}${versionSuffix}${registryFlag}`;
 }
 var init_pnpm_detector = __esm(() => {
-  init_claudekit_constants();
   init_environment();
   init_constants();
   init_detector_base();
@@ -53423,24 +53471,25 @@ var init_package_manager_detector = __esm(() => {
           return "echo unknown";
       }
     }
-    static getUpdateCommand(pm, packageName, version) {
+    static getNpmRegistryUrl = getNpmRegistryUrl;
+    static getUpdateCommand(pm, packageName, version, registryUrl) {
       if (!isValidPackageName(packageName))
         throw new Error(`Invalid package name: ${packageName}`);
       if (version && !isValidVersion(version))
         throw new Error(`Invalid version: ${version}`);
       switch (pm) {
         case "bun":
-          return getBunUpdateCommand(packageName, version);
+          return getBunUpdateCommand(packageName, version, registryUrl);
         case "yarn":
-          return getYarnUpdateCommand(packageName, version);
+          return getYarnUpdateCommand(packageName, version, registryUrl);
         case "pnpm":
-          return getPnpmUpdateCommand(packageName, version);
+          return getPnpmUpdateCommand(packageName, version, registryUrl);
         default:
-          return getNpmUpdateCommand(packageName, version);
+          return getNpmUpdateCommand(packageName, version, registryUrl);
       }
     }
-    static getInstallCommand(pm, packageName, version) {
-      return PackageManagerDetector.getUpdateCommand(pm, packageName, version);
+    static getInstallCommand(pm, packageName, version, registryUrl) {
+      return PackageManagerDetector.getUpdateCommand(pm, packageName, version, registryUrl);
     }
     static getDisplayName(pm) {
       switch (pm) {
@@ -53869,7 +53918,7 @@ var package_default;
 var init_package = __esm(() => {
   package_default = {
     name: "claudekit-cli",
-    version: "3.35.0-dev.23",
+    version: "3.35.0-dev.25",
     description: "CLI tool for bootstrapping and updating ClaudeKit projects",
     type: "module",
     repository: {
@@ -53980,6 +54029,12 @@ var init_package = __esm(() => {
 import { exec as exec2 } from "node:child_process";
 import { join as join37 } from "node:path";
 import { promisify as promisify8 } from "node:util";
+function redactCommandForLog(command) {
+  if (!command)
+    return command;
+  const redactedRegistryFlags = command.replace(/(--registry(?:=|\s+))(['"]?)(\S+?)(\2)(?=\s|$)/g, (_match, prefix, quote, url) => `${prefix}${quote}${redactRegistryUrlForLog(url)}${quote}`);
+  return redactedRegistryFlags.replace(/https?:\/\/[^\s"']+/g, (url) => redactRegistryUrlForLog(url));
+}
 function buildInitCommand(isGlobal, kit, beta) {
   const parts = ["ck init"];
   if (isGlobal)
@@ -54109,31 +54164,50 @@ async function updateCliCommand(options2) {
     const pmVersion = await PackageManagerDetector.getVersion(pm);
     s.stop(`Using ${PackageManagerDetector.getDisplayName(pm)}${pmVersion ? ` v${pmVersion}` : ""}`);
     logger.verbose(`Detected package manager: ${pm}`);
+    let registryUrl = opts.registry;
+    if (!registryUrl && pm === "npm") {
+      const userRegistry = await PackageManagerDetector.getNpmRegistryUrl();
+      if (userRegistry) {
+        registryUrl = userRegistry;
+        logger.verbose(`Using npm configured registry: ${redactRegistryUrlForLog(registryUrl)}`);
+      }
+    }
     s.start("Checking for updates...");
     let targetVersion = null;
     if (opts.release && opts.release !== "latest") {
-      const exists = await NpmRegistryClient.versionExists(CLAUDEKIT_CLI_NPM_PACKAGE_NAME, opts.release, opts.registry);
-      if (!exists) {
-        s.stop("Version not found");
-        throw new CliUpdateError(`Version ${opts.release} does not exist on npm registry. Run 'ck versions' to see available versions.`);
+      try {
+        const exists = await NpmRegistryClient.versionExists(CLAUDEKIT_CLI_NPM_PACKAGE_NAME, opts.release, registryUrl);
+        if (!exists) {
+          s.stop("Version not found");
+          throw new CliUpdateError(`Version ${opts.release} does not exist on npm registry. Run 'ck versions' to see available versions.`);
+        }
+      } catch (error) {
+        if (error instanceof CliUpdateError) {
+          throw error;
+        }
+        s.stop("Version check failed");
+        const message = error instanceof Error ? error.message : "Unknown error";
+        logger.verbose(`Release check failed for ${opts.release}: ${message}`);
+        const registryHint = registryUrl ? ` (${redactRegistryUrlForLog(registryUrl)})` : " (default registry)";
+        throw new CliUpdateError(`Failed to verify version ${opts.release} on npm registry${registryHint}. Check registry settings/network connectivity and try again.`);
       }
       targetVersion = opts.release;
       s.stop(`Target version: ${targetVersion}`);
     } else if (opts.dev || opts.beta) {
-      targetVersion = await NpmRegistryClient.getDevVersion(CLAUDEKIT_CLI_NPM_PACKAGE_NAME, opts.registry);
+      targetVersion = await NpmRegistryClient.getDevVersion(CLAUDEKIT_CLI_NPM_PACKAGE_NAME, registryUrl);
       if (!targetVersion) {
         s.stop("No dev version available");
         logger.warning("No dev version found. Using latest stable version instead.");
-        targetVersion = await NpmRegistryClient.getLatestVersion(CLAUDEKIT_CLI_NPM_PACKAGE_NAME, opts.registry);
+        targetVersion = await NpmRegistryClient.getLatestVersion(CLAUDEKIT_CLI_NPM_PACKAGE_NAME, registryUrl);
       } else {
         s.stop(`Latest dev version: ${targetVersion}`);
       }
     } else {
-      targetVersion = await NpmRegistryClient.getLatestVersion(CLAUDEKIT_CLI_NPM_PACKAGE_NAME, opts.registry);
+      targetVersion = await NpmRegistryClient.getLatestVersion(CLAUDEKIT_CLI_NPM_PACKAGE_NAME, registryUrl);
       s.stop(`Latest version: ${targetVersion || "unknown"}`);
     }
     if (!targetVersion) {
-      throw new CliUpdateError(`Failed to fetch version information from npm registry. Check your internet connection and try again. Manual update: ${PackageManagerDetector.getUpdateCommand(pm, CLAUDEKIT_CLI_NPM_PACKAGE_NAME)}`);
+      throw new CliUpdateError(`Failed to fetch version information from npm registry. Check your internet connection and try again. Manual update: ${PackageManagerDetector.getUpdateCommand(pm, CLAUDEKIT_CLI_NPM_PACKAGE_NAME, undefined, registryUrl)}`);
     }
     const comparison = import_compare_versions.compareVersions(currentVersion, targetVersion);
     if (comparison === 0) {
@@ -54166,8 +54240,8 @@ Run 'ck update' to install`, "Update Check");
         return;
       }
     }
-    const updateCmd = PackageManagerDetector.getUpdateCommand(pm, CLAUDEKIT_CLI_NPM_PACKAGE_NAME, targetVersion);
-    logger.info(`Running: ${updateCmd}`);
+    const updateCmd = PackageManagerDetector.getUpdateCommand(pm, CLAUDEKIT_CLI_NPM_PACKAGE_NAME, targetVersion, registryUrl);
+    logger.info(`Running: ${redactCommandForLog(updateCmd)}`);
     s.start("Updating CLI...");
     try {
       await execAsync2(updateCmd, {
@@ -54194,7 +54268,7 @@ Or fix npm permissions: https://docs.npmjs.com/resolving-eacces-permissions-erro
         throw new CliUpdateError(`Permission denied. Try: ${elevationHint}${permHint}`);
       }
       logger.error(`Update failed: ${errorMessage}`);
-      logger.info(`Try running: ${updateCmd}`);
+      logger.info(`Try running: ${redactCommandForLog(updateCmd)}`);
       throw new CliUpdateError(`Update failed: ${errorMessage}
 
 Manual update: ${updateCmd}`);
@@ -54214,7 +54288,6 @@ Manual update: ${updateCmd}`);
     }
   } catch (error) {
     if (error instanceof CliUpdateError) {
-      logger.error(error.message);
       throw error;
     }
     const errorMessage = error instanceof Error ? error.message : "Unknown error";
@@ -64243,7 +64316,7 @@ var init_init_command_help = __esm(() => {
           },
           {
             flags: "--fresh",
-            description: "Remove ClaudeKit directories (commands/, agents/, skills/, rules/, hooks/) and reinstall"
+            description: "Full reset: remove CK files, replace settings.json and CLAUDE.md, reinstall from scratch"
           }
         ]
       },
@@ -84784,7 +84857,6 @@ class InstalledSettingsTracker {
 
 // src/domains/installation/merger/settings-processor.ts
 init_settings_merger();
-init_environment();
 init_logger();
 var import_fs_extra11 = __toESM(require_lib3(), 1);
 var import_semver3 = __toESM(require_semver2(), 1);
@@ -84825,13 +84897,13 @@ class SettingsProcessor {
       const sourceContent = await import_fs_extra11.readFile(sourceFile, "utf-8");
       let transformedSource = sourceContent;
       if (this.isGlobal) {
-        const homeVar = isWindows() ? '"%USERPROFILE%"' : '"$HOME"';
+        const homeVar = '"$HOME"';
         transformedSource = this.transformClaudePaths(sourceContent, homeVar);
         if (transformedSource !== sourceContent) {
           logger.debug(`Transformed .claude/ paths to ${homeVar}/.claude/ in settings.json for global installation`);
         }
       } else {
-        const projectDirVar = isWindows() ? '"%CLAUDE_PROJECT_DIR%"' : '"$CLAUDE_PROJECT_DIR"';
+        const projectDirVar = '"$CLAUDE_PROJECT_DIR"';
         transformedSource = this.transformClaudePaths(sourceContent, projectDirVar);
         if (transformedSource !== sourceContent) {
           logger.debug(`Transformed .claude/ paths to ${projectDirVar}/.claude/ in settings.json for local installation`);
@@ -84841,20 +84913,26 @@ class SettingsProcessor {
       if (destExists && !this.forceOverwriteSettings) {
         await this.selectiveMergeSettings(transformedSource, destFile);
       } else {
-        const formattedContent = this.formatJsonContent(transformedSource);
-        await import_fs_extra11.writeFile(destFile, formattedContent, "utf-8");
-        let parsedSettings;
         try {
-          parsedSettings = JSON.parse(formattedContent);
-          if (this.forceOverwriteSettings && destExists) {
-            logger.debug("Force overwrite enabled, replaced settings.json completely");
-            if (this.tracker) {
-              await this.tracker.clearTracking();
+          const parsedSettings = JSON.parse(transformedSource);
+          this.fixHookCommandPaths(parsedSettings);
+          await SettingsMerger.writeSettingsFile(destFile, parsedSettings);
+          try {
+            if (this.forceOverwriteSettings && destExists) {
+              logger.debug("Force overwrite enabled, replaced settings.json completely");
+              if (this.tracker) {
+                await this.tracker.clearTracking();
+              }
             }
+            await this.trackInstalledSettings(parsedSettings);
+          } catch {
+            logger.debug("Settings tracking failed (non-fatal)");
           }
-          await this.trackInstalledSettings(parsedSettings);
-        } catch {}
-        await this.injectTeamHooksIfSupported(destFile, parsedSettings);
+        } catch {
+          const formattedContent = this.formatJsonContent(transformedSource);
+          await import_fs_extra11.writeFile(destFile, formattedContent, "utf-8");
+        }
+        await this.injectTeamHooksIfSupported(destFile);
       }
     } catch (error) {
       logger.error(`Failed to process settings.json: ${error}`);
@@ -84914,6 +84992,10 @@ class SettingsProcessor {
       }
       await this.tracker.saveInstalledSettings(installedSettings);
     }
+    const pathsFixed = this.fixHookCommandPaths(mergeResult.merged);
+    if (pathsFixed) {
+      logger.info("Fixed hook command paths to canonical quoted format");
+    }
     await SettingsMerger.writeSettingsFile(destFile, mergeResult.merged);
     logger.success("Merged settings.json (user customizations preserved)");
     await this.injectTeamHooksIfSupported(destFile, mergeResult.merged);
@@ -84999,12 +85081,14 @@ class SettingsProcessor {
       const content = await import_fs_extra11.readFile(destFile, "utf-8");
       if (!content.trim())
         return null;
-      const homeVar = isWindows() ? "%USERPROFILE%" : "$HOME";
+      const homeVar = "$HOME";
       let normalized = content;
       normalized = normalized.replace(/"\$CLAUDE_PROJECT_DIR"/g, `"${homeVar}"`);
       normalized = normalized.replace(/\$CLAUDE_PROJECT_DIR/g, homeVar);
       normalized = normalized.replace(/"%CLAUDE_PROJECT_DIR%"/g, `"${homeVar}"`);
       normalized = normalized.replace(/%CLAUDE_PROJECT_DIR%/g, homeVar);
+      normalized = normalized.replace(/"%USERPROFILE%"/g, `"${homeVar}"`);
+      normalized = normalized.replace(/%USERPROFILE%/g, homeVar);
       if (normalized !== content) {
         logger.debug("Normalized $CLAUDE_PROJECT_DIR paths to $HOME in existing global settings");
       }
@@ -85019,15 +85103,85 @@ class SettingsProcessor {
       throw new Error("Settings file contains potentially unsafe path characters");
     }
     let transformed = content;
-    const jsonSafePrefix = prefix.includes('"') ? prefix.replace(/"/g, "\\\"") : prefix;
     const rawPrefix = prefix.replace(/"/g, "");
-    transformed = transformed.replace(/(node\s+)(?:\.\/)?\.claude\//g, `$1${jsonSafePrefix}/.claude/`);
+    transformed = transformed.replace(/(node\s+)(?:\.\/)?(\.claude\/[^\s"\\]+)/g, `$1\\"${rawPrefix}/$2\\"`);
     if (rawPrefix.includes("HOME") || rawPrefix.includes("USERPROFILE")) {
       transformed = transformed.replace(/\$CLAUDE_PROJECT_DIR/g, rawPrefix);
       transformed = transformed.replace(/%CLAUDE_PROJECT_DIR%/g, rawPrefix);
     }
     return transformed;
   }
+  fixHookCommandPaths(settings) {
+    let fixed = false;
+    if (settings.hooks) {
+      for (const entries of Object.values(settings.hooks)) {
+        for (const entry of entries) {
+          if ("command" in entry && entry.command) {
+            const result = this.fixSingleCommandPath(entry.command);
+            if (result !== entry.command) {
+              entry.command = result;
+              fixed = true;
+            }
+          }
+          if ("hooks" in entry && entry.hooks) {
+            for (const hook of entry.hooks) {
+              if (hook.command) {
+                const result = this.fixSingleCommandPath(hook.command);
+                if (result !== hook.command) {
+                  hook.command = result;
+                  fixed = true;
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+    const statusLine = settings.statusLine;
+    if (statusLine?.command) {
+      const result = this.fixSingleCommandPath(statusLine.command);
+      if (result !== statusLine.command) {
+        statusLine.command = result;
+        fixed = true;
+      }
+    }
+    return fixed;
+  }
+  fixSingleCommandPath(cmd) {
+    if (!cmd.includes(".claude/") && !cmd.includes(".claude\\"))
+      return cmd;
+    const varOnlyQuotingRe = /^(node\s+)"(\$HOME|\$CLAUDE_PROJECT_DIR|%USERPROFILE%|%CLAUDE_PROJECT_DIR%)"[/\\](.+)$/;
+    const varOnlyMatch = cmd.match(varOnlyQuotingRe);
+    if (varOnlyMatch) {
+      const [, nodePrefix, capturedVar, restPath] = varOnlyMatch;
+      const canonicalVar = this.canonicalizePathVar(capturedVar);
+      return `${nodePrefix}"${canonicalVar}/${restPath.replace(/\\/g, "/")}"`;
+    }
+    const tildeRe = /^(node\s+)~[/\\](.+)$/;
+    const tildeMatch = cmd.match(tildeRe);
+    if (tildeMatch) {
+      const [, nodePrefix, restPath] = tildeMatch;
+      return `${nodePrefix}"$HOME/${restPath.replace(/\\/g, "/")}"`;
+    }
+    const unquotedRe = /^(node\s+)(\$HOME|\$CLAUDE_PROJECT_DIR|%USERPROFILE%|%CLAUDE_PROJECT_DIR%)[/\\](.+)$/;
+    const unquotedMatch = cmd.match(unquotedRe);
+    if (unquotedMatch) {
+      const [, nodePrefix, capturedVar, restPath] = unquotedMatch;
+      const canonicalVar = this.canonicalizePathVar(capturedVar);
+      return `${nodePrefix}"${canonicalVar}/${restPath.replace(/\\/g, "/")}"`;
+    }
+    return cmd;
+  }
+  canonicalizePathVar(capturedVar) {
+    switch (capturedVar) {
+      case "%USERPROFILE%":
+        return "$HOME";
+      case "%CLAUDE_PROJECT_DIR%":
+        return "$CLAUDE_PROJECT_DIR";
+      default:
+        return capturedVar;
+    }
+  }
   detectClaudeCodeVersion() {
     if (this.cachedVersion !== undefined)
       return this.cachedVersion;
@@ -85066,7 +85220,7 @@ class SettingsProcessor {
       logger.warning("Failed to read settings file for team hooks injection");
       return;
     }
-    const prefix = this.isGlobal ? isWindows() ? "%USERPROFILE%" : "$HOME" : isWindows() ? "%CLAUDE_PROJECT_DIR%" : "$CLAUDE_PROJECT_DIR";
+    const prefix = this.isGlobal ? "$HOME" : "$CLAUDE_PROJECT_DIR";
     if (!settings.hooks) {
       settings.hooks = {};
     }
@@ -85077,7 +85231,7 @@ class SettingsProcessor {
       { event: "TeammateIdle", handler: "teammate-idle-handler.cjs" }
     ];
     for (const { event, handler } of teamHooks) {
-      const hookCommand = `node ${prefix}/.claude/hooks/${handler}`;
+      const hookCommand = `node "${prefix}/.claude/hooks/${handler}"`;
       const eventHooks = settings.hooks[event];
       if (eventHooks && eventHooks.length > 0)
         continue;
@@ -88056,6 +88210,10 @@ Please use only one download method.`);
   if (validOptions.useGit && validOptions.beta) {
     logger.warning("--beta flag is ignored when using --use-git (version already specified via --release)");
   }
+  if (validOptions.fresh && !validOptions.forceOverwriteSettings) {
+    validOptions.forceOverwriteSettings = true;
+    logger.debug("--fresh: auto-enabling settings.json full replace");
+  }
   if (validOptions.fresh && validOptions.sync) {
     throw new Error(`--fresh and --sync are mutually exclusive.
 
@@ -88086,7 +88244,16 @@ async function handlePostInstall(ctx) {
     return ctx;
   }
   if (ctx.options.global) {
-    await handleGlobalClaudeMd(ctx);
+    const claudeMdSource = join100(ctx.extractDir, "CLAUDE.md");
+    const claudeMdDest = join100(ctx.resolvedDir, "CLAUDE.md");
+    if (await import_fs_extra30.pathExists(claudeMdSource)) {
+      if (ctx.options.fresh || !await import_fs_extra30.pathExists(claudeMdDest)) {
+        await import_fs_extra30.copy(claudeMdSource, claudeMdDest);
+        logger.success(ctx.options.fresh ? "Replaced CLAUDE.md in global directory (fresh install)" : "Copied CLAUDE.md to global directory");
+      } else {
+        logger.debug("CLAUDE.md already exists in global directory (preserved)");
+      }
+    }
   }
   let installSkills = ctx.options.installSkills;
   if (!ctx.isNonInteractive && !installSkills) {
@@ -88146,49 +88313,6 @@ async function handlePostInstall(ctx) {
     installSkills
   };
 }
-function normalizeLineEndings(content) {
-  return content.replace(/\r\n/g, `
-`);
-}
-async function handleGlobalClaudeMd(ctx) {
-  if (!ctx.extractDir || !ctx.resolvedDir)
-    return;
-  const claudeMdSource = join100(ctx.extractDir, "CLAUDE.md");
-  const claudeMdDest = join100(ctx.resolvedDir, "CLAUDE.md");
-  if (!await import_fs_extra30.pathExists(claudeMdSource))
-    return;
-  const destExists = await import_fs_extra30.pathExists(claudeMdDest);
-  if (!destExists) {
-    await import_fs_extra30.copy(claudeMdSource, claudeMdDest);
-    logger.success("Copied CLAUDE.md to global directory");
-    return;
-  }
-  if (ctx.options.fresh || ctx.options.forceOverwrite) {
-    await import_fs_extra30.copy(claudeMdSource, claudeMdDest);
-    logger.success("Updated CLAUDE.md in global directory");
-    return;
-  }
-  const [srcContent, destContent] = await Promise.all([
-    import_fs_extra30.readFile(claudeMdSource, "utf-8"),
-    import_fs_extra30.readFile(claudeMdDest, "utf-8")
-  ]);
-  if (normalizeLineEndings(srcContent) === normalizeLineEndings(destContent)) {
-    logger.debug("CLAUDE.md already up to date");
-    return;
-  }
-  if (!ctx.isNonInteractive) {
-    const shouldOverwrite = await ctx.prompts.confirm(`CLAUDE.md has changed in the new version. Update it?
-  (Your customizations will be replaced)`);
-    if (!shouldOverwrite) {
-      logger.info("CLAUDE.md preserved (user chose to keep existing)");
-      return;
-    }
-  } else {
-    logger.warning("Updating CLAUDE.md (content differs from new version)");
-  }
-  await import_fs_extra30.copy(claudeMdSource, claudeMdDest);
-  logger.success("Updated CLAUDE.md (new version detected)");
-}
 // src/commands/init/phases/selection-handler.ts
 init_config_manager();
 init_github_client();
@@ -88850,7 +88974,7 @@ async function handleSelection(ctx) {
   };
 }
 // src/commands/init/phases/sync-handler.ts
-import { copyFile as copyFile7, mkdir as mkdir30, open as open4, readFile as readFile49, rename as rename5, stat as stat17, unlink as unlink11, writeFile as writeFile29 } from "node:fs/promises";
+import { copyFile as copyFile7, mkdir as mkdir30, open as open4, readFile as readFile48, rename as rename5, stat as stat17, unlink as unlink11, writeFile as writeFile29 } from "node:fs/promises";
 import { dirname as dirname22, join as join103, resolve as resolve21 } from "node:path";
 init_logger();
 init_path_resolver();
@@ -89018,7 +89142,7 @@ async function executeSyncMerge(ctx) {
     try {
       const sourceMetadataPath = join103(upstreamDir, "metadata.json");
       if (await import_fs_extra33.pathExists(sourceMetadataPath)) {
-        const content = await readFile49(sourceMetadataPath, "utf-8");
+        const content = await readFile48(sourceMetadataPath, "utf-8");
         const sourceMetadata = JSON.parse(content);
         deletions = sourceMetadata.deletions || [];
       }
@@ -89316,7 +89440,7 @@ async function renameFolders(dirsToRename, extractDir, options2) {
 // src/services/transformers/folder-transform/path-replacer.ts
 init_logger();
 init_types3();
-import { readFile as readFile50, readdir as readdir32, writeFile as writeFile30 } from "node:fs/promises";
+import { readFile as readFile49, readdir as readdir32, writeFile as writeFile30 } from "node:fs/promises";
 import { join as join105, relative as relative19 } from "node:path";
 var TRANSFORMABLE_FILE_PATTERNS = [
   ".md",
@@ -89383,7 +89507,7 @@ async function transformFileContents(dir, compiledReplacements, options2) {
       if (!shouldTransform)
         continue;
       try {
-        const content = await readFile50(fullPath, "utf-8");
+        const content = await readFile49(fullPath, "utf-8");
         let newContent = content;
         let changeCount = 0;
         for (const { regex: regex2, replacement } of compiledReplacements) {
@@ -89505,7 +89629,7 @@ async function transformFolderPaths(extractDir, folders, options2 = {}) {
 
 // src/services/transformers/global-path-transformer.ts
 init_logger();
-import { readFile as readFile51, readdir as readdir33, writeFile as writeFile31 } from "node:fs/promises";
+import { readFile as readFile50, readdir as readdir33, writeFile as writeFile31 } from "node:fs/promises";
 import { platform as platform13 } from "node:os";
 import { extname as extname5, join as join106 } from "node:path";
 var IS_WINDOWS3 = platform13() === "win32";
@@ -89625,7 +89749,7 @@ async function transformPathsForGlobalInstall(directory, options2 = {}) {
         await processDirectory2(fullPath);
       } else if (entry.isFile() && shouldTransformFile3(entry.name)) {
         try {
-          const content = await readFile51(fullPath, "utf-8");
+          const content = await readFile50(fullPath, "utf-8");
           const { transformed, changes } = transformContent(content);
           if (changes > 0) {
             await writeFile31(fullPath, transformed, "utf-8");
@@ -89887,7 +90011,7 @@ init_checksum_utils();
 init_config_discovery();
 var import_picocolors25 = __toESM(require_picocolors(), 1);
 import { existsSync as existsSync51 } from "node:fs";
-import { readFile as readFile52, rm as rm13, unlink as unlink12 } from "node:fs/promises";
+import { readFile as readFile51, rm as rm13, unlink as unlink12 } from "node:fs/promises";
 import { resolve as resolve22 } from "node:path";
 
 // src/commands/portable/conflict-resolver.ts
@@ -90461,7 +90585,7 @@ async function migrateCommand(options2) {
       for (const action of conflictActions) {
         if (!action.diff && action.targetPath && existsSync51(action.targetPath)) {
           try {
-            const targetContent = await readFile52(action.targetPath, "utf-8");
+            const targetContent = await readFile51(action.targetPath, "utf-8");
             const sourceItem = agents2.find((a3) => a3.name === action.item) || commands.find((c2) => c2.name === action.item) || (configItem?.name === action.item ? configItem : null) || ruleItems.find((r2) => r2.name === action.item);
             if (sourceItem) {
               const providerConfig = providers[action.provider];
@@ -90653,26 +90777,27 @@ async function computeTargetStates(selectedProviders, global3) {
       continue;
     if (entry.global !== global3)
       continue;
-    try {
-      if (existsSync51(entry.path)) {
-        const content = await readFile52(entry.path, "utf-8");
-        states.set(entry.path, {
-          path: entry.path,
-          exists: true,
-          currentChecksum: computeContentChecksum(content)
-        });
-      } else {
-        states.set(entry.path, {
-          path: entry.path,
-          exists: false
-        });
-      }
-    } catch {
+    if (entry.type === "skill")
+      continue;
+    const exists = existsSync51(entry.path);
+    if (!exists) {
       states.set(entry.path, {
         path: entry.path,
         exists: false
       });
+      continue;
+    }
+    const state = {
+      path: entry.path,
+      exists: true
+    };
+    try {
+      const content = await readFile51(entry.path, "utf-8");
+      state.currentChecksum = computeContentChecksum(content);
+    } catch (error) {
+      logger.debug(`[migrate] Failed to read target for checksum: ${entry.path} (${String(error)})`);
     }
+    states.set(entry.path, state);
   }
   return states;
 }
@@ -92573,7 +92698,7 @@ function registerCommands(cli) {
     }
     await newCommand(options2);
   });
-  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, all, or comma-separated").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("--with-sudo", "Include system packages requiring sudo (Linux: ffmpeg, imagemagick)").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)").option("--sync", "Sync config files from upstream with interactive hunk-by-hunk merge").option("--use-git", "Use git clone instead of GitHub API (uses SSH/HTTPS credentials)").option("--archive <path>", "Use local archive file instead of downloading (zip/tar.gz)").option("--kit-path <path>", "Use local kit directory instead of downloading").action(async (options2) => {
+  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, all, or comma-separated").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", "Full reset: remove CK files, replace settings.json and CLAUDE.md, reinstall from scratch").option("--install-skills", "Install skills dependencies (non-interactive mode)").option("--with-sudo", "Include system packages requiring sudo (Linux: ffmpeg, imagemagick)").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)").option("--sync", "Sync config files from upstream with interactive hunk-by-hunk merge").option("--use-git", "Use git clone instead of GitHub API (uses SSH/HTTPS credentials)").option("--archive <path>", "Use local archive file instead of downloading (zip/tar.gz)").option("--kit-path <path>", "Use local kit directory instead of downloading").action(async (options2) => {
     if (options2.exclude && !Array.isArray(options2.exclude)) {
       options2.exclude = [options2.exclude];
     }

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "claudekit-cli",
-	"version": "3.35.0-dev.23",
+	"version": "3.35.0-dev.25",
 	"description": "CLI tool for bootstrapping and updating ClaudeKit projects",
 	"type": "module",
 	"repository": {