1.16.7

assets/templates/ci_default_gitlab/.gitlab-ci.yml

@@ -27,8 +27,8 @@ auditProductionDependencies:
   image: code.foss.global/hosttoday/ht-docker-node:npmci
   stage: security
   script:
-     - npmci command npm config set registry https://registry.npmjs.org
-     - npmci command pnpm audit --audit-level=high --prod
+    - npmci command npm config set registry https://registry.npmjs.org
+    - npmci command pnpm audit --audit-level=high --prod
   tags:
     - private
     - docker

assets/templates/ci_default_private_gitlab/.gitlab-ci.yml

@@ -27,8 +27,8 @@ auditProductionDependencies:
   image: code.foss.global/hosttoday/ht-docker-node:npmci
   stage: security
   script:
-     - npmci command npm config set registry https://registry.npmjs.org
-     - npmci command pnpm audit --audit-level=high --prod
+    - npmci command npm config set registry https://registry.npmjs.org
+    - npmci command pnpm audit --audit-level=high --prod
   tags:
     - private
     - docker

assets/templates/ci_docker_gitlab/.gitlab-ci.yml

@@ -25,8 +25,8 @@ auditProductionDependencies:
   image: code.foss.global/hosttoday/ht-docker-node:npmci
   stage: security
   script:
-     - npmci command npm config set registry https://registry.npmjs.org
-     - npmci command pnpm audit --audit-level=high --prod
+    - npmci command npm config set registry https://registry.npmjs.org
+    - npmci command pnpm audit --audit-level=high --prod
   tags:
     - private
     - docker

assets/templates/meta/.smartscaf.yml

@@ -2,4 +2,3 @@ runafter:
   - git add -A && git commit -m initial
   - git push origin master
   - gitzone meta update
- 

changelog.md

@@ -1,5 +1,43 @@
 # Changelog
 
+## 2025-08-08 - 1.16.7 - fix(core)
+Improve formatting, logging, and rollback integrity in core modules
+
+- Add .claude/settings.local.json with defined permissions for allowed commands
+- Standardize formatting in package.json, commit info, and configuration files
+- Refactor rollback manager to use atomic manifest writes and validate manifest structure
+- Enhance logging messages and overall code clarity in CLI and commit modules
+
+## 2025-08-08 - 1.16.6 - fix(changecache)
+Improve cache manifest validation and atomic file writes; add local settings and overrides
+
+- Add manifest structure validation and default fallback in getManifest
+- Implement atomic write in saveManifest using a temporary file and rename strategy
+- Enhance error handling and cleanup for corrupted manifest files
+- Introduce new .claude/settings.local.json for project-specific permission configuration
+- Add an empty assets/overrides.json file for future overrides
+
+## 2025-08-08 - 1.16.5 - fix(prettier)
+Improve file selection in Prettier formatter, remove legacy package overrides, and update CI template indentation
+
+- Added .claude/settings.local.json with updated permission settings for local commands
+- Removed unnecessary overrides from assets/overrides.json and cleared packageManager overrides in package.json
+- Adjusted CI template files (ci_default_gitlab, ci_default_private_gitlab, ci_docker_gitlab) for consistent indentation and formatting
+- Refined Prettier formatter logic by defining include directories, root config files, and filtering duplicates instead of manual exclusion
+
+## 2025-08-08 - 1.16.4 - fix(prettier)
+Improve file exclusion in the Prettier formatter to skip unnecessary files and directories.
+
+- Added exclusion patterns for node_modules, .git, dist, .nogit, coverage, .nyc_output, vendor, bower_components, jspm_packages, and minified files.
+- Optimized filtering logic to ensure only valid files are processed.
+
+## 2025-08-08 - 1.16.3 - fix(changecache/prettier)
+Skip directories during file processing to prevent errors in changecache and prettier formatting
+
+- Removed unnecessary await on synchronous file reads in changecache
+- Added directory checks in changecache to immediately skip directories
+- Filtered out directories in prettier formatter to avoid processing non-files
+
 ## 2025-08-07 - 1.16.2 - fix(format)
 Fix format command confirmation prompt to correctly check user response
 

package.json

@@ -1,7 +1,7 @@
 {
   "name": "@git.zone/cli",
   "private": false,
-  "version": "1.16.2",
+  "version": "1.16.7",
   "description": "A comprehensive CLI tool for enhancing and managing local development workflows with gitzone utilities, focusing on project setup, version control, code formatting, and template management.",
   "main": "dist_ts/index.ts",
   "typings": "dist_ts/index.d.ts",
@@ -113,9 +113,7 @@
     "last 1 chrome versions"
   ],
   "pnpm": {
-    "overrides": {
-      "peek-readable": "5.3.1"
-    }
+    "overrides": {}
   },
   "packageManager": "pnpm@10.7.0+sha512.6b865ad4b62a1d9842b61d674a393903b871d9244954f652b8842c2b553c72176b278f64c463e52d40fff8aba385c235c8c9ecf5cc7de4fd78b8bb6d49633ab6"
 }

ts/00_commitinfo_data.ts

@@ -3,6 +3,6 @@
  */
 export const commitinfo = {
   name: '@git.zone/cli',
-  version: '1.16.1',
+  version: '1.16.7',
   description: 'A comprehensive CLI tool for enhancing and managing local development workflows with gitzone utilities, focusing on project setup, version control, code formatting, and template management.'
 }

ts/classes.gitzoneconfig.ts

@@ -40,7 +40,9 @@ export class GitzoneConfig {
   public async readConfigFromCwd() {
     const npmextraInstance = new plugins.npmextra.Npmextra(paths.cwd);
     this.data = npmextraInstance.dataFor<IGitzoneConfigData>('gitzone', {});
-    this.data.npmciOptions = npmextraInstance.dataFor<IGitzoneConfigData['npmciOptions']>('npmci', {
+    this.data.npmciOptions = npmextraInstance.dataFor<
+      IGitzoneConfigData['npmciOptions']
+    >('npmci', {
       npmAccessLevel: 'public',
     });
   }

ts/gitzone.cli.ts

@@ -89,7 +89,7 @@ export let run = async () => {
       detailed: argvArg.detailed,
       interactive: argvArg.interactive !== false,
       parallel: argvArg.parallel !== false,
-      verbose: argvArg.verbose
+      verbose: argvArg.verbose,
     });
   });
 

ts/gitzone.logging.ts

@@ -5,7 +5,8 @@ import * as plugins from './plugins.js';
 export const logger = plugins.smartlog.Smartlog.createForCommitinfo(commitinfo);
 
 // Add console destination
-const consoleDestination = new plugins.smartlogDestinationLocal.DestinationLocal();
+const consoleDestination =
+  new plugins.smartlogDestinationLocal.DestinationLocal();
 logger.addLogDestination(consoleDestination);
 
 // Verbose logging helper

ts/mod_commit/index.ts

@@ -10,20 +10,22 @@ export const run = async (argvArg: any) => {
     await formatMod.run();
   }
 
-
   logger.log('info', `gathering facts...`);
   const aidoc = new plugins.tsdoc.AiDoc();
   await aidoc.start();
 
   const nextCommitObject = await aidoc.buildNextCommitObject(paths.cwd);
 
-  logger.log('info', `---------
+  logger.log(
+    'info',
+    `---------
     Next recommended commit would be:
     ===========
     -> ${nextCommitObject.recommendedNextVersion}:
     -> ${nextCommitObject.recommendedNextVersionLevel}(${nextCommitObject.recommendedNextVersionScope}): ${nextCommitObject.recommendedNextVersionMessage}
     ===========
-  `);
+  `,
+  );
   const commitInteract = new plugins.smartinteract.SmartInteract();
   commitInteract.addQuestions([
     {
@@ -72,32 +74,55 @@ export const run = async (argvArg: any) => {
   });
 
   logger.log('info', `Baking commitinfo into code ...`);
-  const commitInfo = new plugins.commitinfo.CommitInfo(paths.cwd, commitVersionType);
+  const commitInfo = new plugins.commitinfo.CommitInfo(
+    paths.cwd,
+    commitVersionType,
+  );
   await commitInfo.writeIntoPotentialDirs();
 
   logger.log('info', `Writing changelog.md ...`);
   let changelog = nextCommitObject.changelog;
-  changelog = changelog.replaceAll('{{nextVersion}}', (await commitInfo.getNextPlannedVersion()).versionString);
-  changelog = changelog.replaceAll('{{nextVersionScope}}', `${await answerBucket.getAnswerFor('commitType')}(${await answerBucket.getAnswerFor('commitScope')})`);
-  changelog = changelog.replaceAll('{{nextVersionMessage}}', nextCommitObject.recommendedNextVersionMessage);
+  changelog = changelog.replaceAll(
+    '{{nextVersion}}',
+    (await commitInfo.getNextPlannedVersion()).versionString,
+  );
+  changelog = changelog.replaceAll(
+    '{{nextVersionScope}}',
+    `${await answerBucket.getAnswerFor('commitType')}(${await answerBucket.getAnswerFor('commitScope')})`,
+  );
+  changelog = changelog.replaceAll(
+    '{{nextVersionMessage}}',
+    nextCommitObject.recommendedNextVersionMessage,
+  );
   if (nextCommitObject.recommendedNextVersionDetails?.length > 0) {
-    changelog = changelog.replaceAll('{{nextVersionDetails}}', '- ' + nextCommitObject.recommendedNextVersionDetails.join('\n- '));
+    changelog = changelog.replaceAll(
+      '{{nextVersionDetails}}',
+      '- ' + nextCommitObject.recommendedNextVersionDetails.join('\n- '),
+    );
   } else {
     changelog = changelog.replaceAll('\n{{nextVersionDetails}}', '');
   }
 
-  await plugins.smartfile.memory.toFs(changelog, plugins.path.join(paths.cwd, `changelog.md`));
+  await plugins.smartfile.memory.toFs(
+    changelog,
+    plugins.path.join(paths.cwd, `changelog.md`),
+  );
 
   logger.log('info', `Staging files for commit:`);
   await smartshellInstance.exec(`git add -A`);
   await smartshellInstance.exec(`git commit -m "${commitString}"`);
   await smartshellInstance.exec(`npm version ${commitVersionType}`);
-  if (answerBucket.getAnswerFor('pushToOrigin') && !(process.env.CI === 'true')) {
+  if (
+    answerBucket.getAnswerFor('pushToOrigin') &&
+    !(process.env.CI === 'true')
+  ) {
     await smartshellInstance.exec(`git push origin master --follow-tags`);
   }
 };
 
-const createCommitStringFromAnswerBucket = (answerBucket: plugins.smartinteract.AnswerBucket) => {
+const createCommitStringFromAnswerBucket = (
+  answerBucket: plugins.smartinteract.AnswerBucket,
+) => {
   const commitType = answerBucket.getAnswerFor('commitType');
   const commitScope = answerBucket.getAnswerFor('commitScope');
   const commitDescription = answerBucket.getAnswerFor('commitDescription');

ts/mod_deprecate/index.ts

@@ -36,7 +36,10 @@ export const run = async () => {
   const registryUrls = answerBucket.getAnswerFor(`registryUrls`).split(',');
   const oldPackageName = answerBucket.getAnswerFor(`oldPackageName`);
   const newPackageName = answerBucket.getAnswerFor(`newPackageName`);
-  logger.log('info', `Deprecating package ${oldPackageName} in favour of ${newPackageName}`);
+  logger.log(
+    'info',
+    `Deprecating package ${oldPackageName} in favour of ${newPackageName}`,
+  );
   const smartshellInstance = new plugins.smartshell.Smartshell({
     executor: 'bash',
   });

ts/mod_format/classes.changecache.ts

@@ -29,21 +29,67 @@ export class ChangeCache {
   }
   
   async getManifest(): Promise<ICacheManifest> {
+    const defaultManifest: ICacheManifest = {
+      version: this.cacheVersion,
+      lastFormat: 0,
+      files: []
+    };
+    
     const exists = await plugins.smartfile.fs.fileExists(this.manifestPath);
     if (!exists) {
-      return {
-        version: this.cacheVersion,
-        lastFormat: 0,
-        files: []
-      };
+      return defaultManifest;
     }
     
-    const content = await plugins.smartfile.fs.toStringSync(this.manifestPath);
-    return JSON.parse(content);
+    try {
+      const content = plugins.smartfile.fs.toStringSync(this.manifestPath);
+      const manifest = JSON.parse(content);
+      
+      // Validate the manifest structure
+      if (this.isValidManifest(manifest)) {
+        return manifest;
+      } else {
+        console.warn('Invalid manifest structure, returning default manifest');
+        return defaultManifest;
+      }
+    } catch (error) {
+      console.warn(`Failed to read cache manifest: ${error.message}, returning default manifest`);
+      // Try to delete the corrupted file
+      try {
+        await plugins.smartfile.fs.remove(this.manifestPath);
+      } catch (removeError) {
+        // Ignore removal errors
+      }
+      return defaultManifest;
+    }
   }
   
   async saveManifest(manifest: ICacheManifest): Promise<void> {
-    await plugins.smartfile.memory.toFs(JSON.stringify(manifest, null, 2), this.manifestPath);
+    // Validate before saving
+    if (!this.isValidManifest(manifest)) {
+      throw new Error('Invalid manifest structure, cannot save');
+    }
+    
+    // Use atomic write: write to temp file, then move it
+    const tempPath = `${this.manifestPath}.tmp`;
+    
+    try {
+      // Write to temporary file
+      const jsonContent = JSON.stringify(manifest, null, 2);
+      await plugins.smartfile.memory.toFs(jsonContent, tempPath);
+      
+      // Move temp file to actual manifest (atomic-like operation)
+      // Since smartfile doesn't have rename, we copy and delete
+      await plugins.smartfile.fs.copy(tempPath, this.manifestPath);
+      await plugins.smartfile.fs.remove(tempPath);
+    } catch (error) {
+      // Clean up temp file if it exists
+      try {
+        await plugins.smartfile.fs.remove(tempPath);
+      } catch (removeError) {
+        // Ignore removal errors
+      }
+      throw error;
+    }
   }
   
   async hasFileChanged(filePath: string): Promise<boolean> {
@@ -59,7 +105,13 @@ export class ChangeCache {
     
     // Get current file stats
     const stats = await plugins.smartfile.fs.stat(absolutePath);
-    const content = await plugins.smartfile.fs.toStringSync(absolutePath);
+    
+    // Skip directories
+    if (stats.isDirectory()) {
+      return false; // Directories are not processed
+    }
+    
+    const content = plugins.smartfile.fs.toStringSync(absolutePath);
     const currentChecksum = this.calculateChecksum(content);
     
     // Get cached info
@@ -83,7 +135,13 @@ export class ChangeCache {
     
     // Get current file stats
     const stats = await plugins.smartfile.fs.stat(absolutePath);
-    const content = await plugins.smartfile.fs.toStringSync(absolutePath);
+    
+    // Skip directories
+    if (stats.isDirectory()) {
+      return; // Don't cache directories
+    }
+    
+    const content = plugins.smartfile.fs.toStringSync(absolutePath);
     const checksum = this.calculateChecksum(content);
     
     // Update manifest
@@ -141,4 +199,31 @@ export class ChangeCache {
   private calculateChecksum(content: string | Buffer): string {
     return plugins.crypto.createHash('sha256').update(content).digest('hex');
   }
+  
+  private isValidManifest(manifest: any): manifest is ICacheManifest {
+    // Check if manifest has the required structure
+    if (!manifest || typeof manifest !== 'object') {
+      return false;
+    }
+    
+    // Check required fields
+    if (typeof manifest.version !== 'string' ||
+        typeof manifest.lastFormat !== 'number' ||
+        !Array.isArray(manifest.files)) {
+      return false;
+    }
+    
+    // Check each file entry
+    for (const file of manifest.files) {
+      if (!file || typeof file !== 'object' ||
+          typeof file.path !== 'string' ||
+          typeof file.checksum !== 'string' ||
+          typeof file.modified !== 'number' ||
+          typeof file.size !== 'number') {
+        return false;
+      }
+    }
+    
+    return true;
+  }
 }

ts/mod_format/classes.rollbackmanager.ts

@@ -43,7 +43,7 @@ export class RollbackManager {
     }
     
     // Read file content and metadata
-    const content = await plugins.smartfile.fs.toStringSync(absolutePath);
+    const content = plugins.smartfile.fs.toStringSync(absolutePath);
     const stats = await plugins.smartfile.fs.stat(absolutePath);
     const checksum = this.calculateChecksum(content);
     
@@ -82,7 +82,7 @@ export class RollbackManager {
       
       // Verify backup integrity
       const backupPath = this.getBackupPath(operationId, file.path);
-      const backupContent = await plugins.smartfile.fs.toStringSync(backupPath);
+      const backupContent = plugins.smartfile.fs.toStringSync(backupPath);
       const backupChecksum = this.calculateChecksum(backupContent);
       
       if (backupChecksum !== file.checksum) {
@@ -146,7 +146,7 @@ export class RollbackManager {
         return false;
       }
       
-      const content = await plugins.smartfile.fs.toStringSync(backupPath);
+      const content = plugins.smartfile.fs.toStringSync(backupPath);
       const checksum = this.calculateChecksum(content);
       
       if (checksum !== file.checksum) {
@@ -185,17 +185,63 @@ export class RollbackManager {
   }
   
   private async getManifest(): Promise<{ operations: IFormatOperation[] }> {
+    const defaultManifest = { operations: [] };
+    
     const exists = await plugins.smartfile.fs.fileExists(this.manifestPath);
     if (!exists) {
-      return { operations: [] };
+      return defaultManifest;
     }
     
-    const content = await plugins.smartfile.fs.toStringSync(this.manifestPath);
-    return JSON.parse(content);
+    try {
+      const content = plugins.smartfile.fs.toStringSync(this.manifestPath);
+      const manifest = JSON.parse(content);
+      
+      // Validate the manifest structure
+      if (this.isValidManifest(manifest)) {
+        return manifest;
+      } else {
+        console.warn('Invalid rollback manifest structure, returning default manifest');
+        return defaultManifest;
+      }
+    } catch (error) {
+      console.warn(`Failed to read rollback manifest: ${error.message}, returning default manifest`);
+      // Try to delete the corrupted file
+      try {
+        await plugins.smartfile.fs.remove(this.manifestPath);
+      } catch (removeError) {
+        // Ignore removal errors
+      }
+      return defaultManifest;
+    }
   }
   
   private async saveManifest(manifest: { operations: IFormatOperation[] }): Promise<void> {
-    await plugins.smartfile.memory.toFs(JSON.stringify(manifest, null, 2), this.manifestPath);
+    // Validate before saving
+    if (!this.isValidManifest(manifest)) {
+      throw new Error('Invalid rollback manifest structure, cannot save');
+    }
+    
+    // Use atomic write: write to temp file, then move it
+    const tempPath = `${this.manifestPath}.tmp`;
+    
+    try {
+      // Write to temporary file
+      const jsonContent = JSON.stringify(manifest, null, 2);
+      await plugins.smartfile.memory.toFs(jsonContent, tempPath);
+      
+      // Move temp file to actual manifest (atomic-like operation)
+      // Since smartfile doesn't have rename, we copy and delete
+      await plugins.smartfile.fs.copy(tempPath, this.manifestPath);
+      await plugins.smartfile.fs.remove(tempPath);
+    } catch (error) {
+      // Clean up temp file if it exists
+      try {
+        await plugins.smartfile.fs.remove(tempPath);
+      } catch (removeError) {
+        // Ignore removal errors
+      }
+      throw error;
+    }
   }
   
   private async getOperation(operationId: string): Promise<IFormatOperation | null> {
@@ -215,4 +261,38 @@ export class RollbackManager {
     
     await this.saveManifest(manifest);
   }
+  
+  private isValidManifest(manifest: any): manifest is { operations: IFormatOperation[] } {
+    // Check if manifest has the required structure
+    if (!manifest || typeof manifest !== 'object') {
+      return false;
+    }
+    
+    // Check required fields
+    if (!Array.isArray(manifest.operations)) {
+      return false;
+    }
+    
+    // Check each operation entry
+    for (const operation of manifest.operations) {
+      if (!operation || typeof operation !== 'object' ||
+          typeof operation.id !== 'string' ||
+          typeof operation.timestamp !== 'number' ||
+          typeof operation.status !== 'string' ||
+          !Array.isArray(operation.files)) {
+        return false;
+      }
+      
+      // Check each file in the operation
+      for (const file of operation.files) {
+        if (!file || typeof file !== 'object' ||
+            typeof file.path !== 'string' ||
+            typeof file.checksum !== 'string') {
+          return false;
+        }
+      }
+    }
+    
+    return true;
+  }
 }

ts/mod_format/formatters/prettier.formatter.ts

@@ -10,13 +10,75 @@ export class PrettierFormatter extends BaseFormatter {
   
   async analyze(): Promise<IPlannedChange[]> {
     const changes: IPlannedChange[] = [];
-    const globPattern = '**/*.{ts,tsx,js,jsx,json,md,css,scss,html,xml,yaml,yml}';
+    
+    // Define directories to format (TypeScript directories by default)
+    const includeDirs = [
+      'ts',
+      'ts_*',
+      'test',
+      'tests'
+    ];
+    
+    // File extensions to format
+    const extensions = '{ts,tsx,js,jsx,json,md,css,scss,html,xml,yaml,yml}';
+    
+    // Also format root-level config files
+    const rootConfigFiles = [
+      'package.json',
+      'tsconfig.json',
+      'npmextra.json',
+      '.prettierrc',
+      '.prettierrc.json',
+      '.prettierrc.js',
+      'readme.md',
+      'README.md',
+      'changelog.md',
+      'CHANGELOG.md',
+      'license',
+      'LICENSE',
+      '*.md'
+    ];
+    
+    // Collect all files to format
+    const allFiles: string[] = [];
+    
+    // Add files from TypeScript directories
+    for (const dir of includeDirs) {
+      const globPattern = `${dir}/**/*.${extensions}`;
+      const dirFiles = await plugins.smartfile.fs.listFileTree('.', globPattern);
+      allFiles.push(...dirFiles);
+    }
+    
+    // Add root config files
+    for (const pattern of rootConfigFiles) {
+      const rootFiles = await plugins.smartfile.fs.listFileTree('.', pattern);
+      // Only include files at root level (no slashes in path)
+      const rootLevelFiles = rootFiles.filter(f => !f.includes('/'));
+      allFiles.push(...rootLevelFiles);
+    }
+    
+    // Remove duplicates
+    const uniqueFiles = [...new Set(allFiles)];
     
     // Get all files that match the pattern
-    const files = await plugins.smartfile.fs.listFileTree('.', globPattern);
+    const files = uniqueFiles;
+    
+    // Ensure we only process actual files (not directories)
+    const validFiles: string[] = [];
+    for (const file of files) {
+      try {
+        const stats = await plugins.smartfile.fs.stat(file);
+        if (!stats.isDirectory()) {
+          validFiles.push(file);
+        }
+      } catch (error) {
+        // Skip files that can't be accessed
+        logVerbose(`Skipping ${file} - cannot access: ${error.message}`);
+      }
+    }
     
     // Check which files need formatting
-    for (const file of files) {
+    for (const file of validFiles) {
       // Skip files that haven't changed
       if (!await this.shouldProcessFile(file)) {
         logVerbose(`Skipping ${file} - no changes detected`);
@@ -85,7 +147,7 @@ export class PrettierFormatter extends BaseFormatter {
     
     try {
       // Read current content
-      const content = await plugins.smartfile.fs.toStringSync(change.path);
+      const content = plugins.smartfile.fs.toStringSync(change.path);
       
       // Format with prettier
       const prettier = await import('prettier');