@garyr/pt-cli 1.1.0 → 1.3.0

package/src/commands/learnCommand.ts

@@ -281,14 +281,21 @@ export async function learn(sourcePath: string, updateTemplate: string | null =
       folders = existingTemplate.folders;
     }
 
+    // selectedStructure should include ALL folders (existing + added) in additive mode
+    // so that the final filter doesn't drop user-selected new folders
+    selectedStructure = [
+      ...new Set([
+        ...existingTemplate.folders?.map((f: FolderNode) => f.name) || [],
+        ...folders.filter(f => !existingTemplate.folders?.some(ef => ef.name === f.name)).map(f => f.name),
+      ]),
+    ];
+
     // New files
     const newFiles = rootFiles.filter((f: string) => !existingTemplate.copy_files?.some((cf: CopyFileEntry) => cf.src === f));
     printNewFiles(newFiles.length, newFiles);
     const addedFiles = await promptNewFiles(newFiles, options);
     selectedFiles = [...(existingTemplate.copy_files?.filter((cf: CopyFileEntry) => !rootDirs.includes(cf.src)).map((cf: CopyFileEntry) => cf.src) || []), ...addedFiles];
 
-    // Structure
-    selectedStructure = existingTemplate.folders?.map((f: FolderNode) => f.name) || [];
     // Seed selectedFolders from existing copy_files directory entries
     selectedFolders = (existingTemplate.copy_files || [])
       .filter((f: CopyFileEntry) => rootDirs.includes(f.src))
@@ -311,7 +318,14 @@ export async function learn(sourcePath: string, updateTemplate: string | null =
 
   // --- COPY FILES ---
   const existingCopyFiles = isUpdate ? config.templates[updateTemplate].copy_files || [] : [];
-  const copy_files = buildCopyFiles(selectedFiles, selectedFolders, existingCopyFiles);
+  
+  // If JSON template config has copy_files, use those directly (for new templates)
+  let copy_files: CopyFileEntry[];
+  if (!isUpdate && fileTemplateConfig.copy_files && Array.isArray(fileTemplateConfig.copy_files)) {
+    copy_files = [...fileTemplateConfig.copy_files];
+  } else {
+    copy_files = buildCopyFiles(selectedFiles, selectedFolders, existingCopyFiles);
+  }
 
   const templateConfig: TemplateConfig = {
     description: description,
@@ -360,8 +374,18 @@ export async function learn(sourcePath: string, updateTemplate: string | null =
     .filter(file => isExecutable(path.join(resolvedPath, file), file))
     .filter(file => !shouldExcludeFile(file));
 
+  // In additive mode (isUpdate), only add executables that were explicitly selected by the user
+  let selectedExecutables: string[] = [];
+  if (isUpdate) {
+    // In additive mode, only include executables that are in selectedFiles (user explicitly chose them)
+    selectedExecutables = detectedExecutables.filter(exec => selectedFiles.includes(exec));
+  } else {
+    // In new template mode, include all detected executables (original behavior)
+    selectedExecutables = detectedExecutables;
+  }
+
   const existingPostCopy = isUpdate ? config.templates[updateTemplate].post_copy || [] : [];
-  const post_copy = mergePostCopyFiles(existingPostCopy, fileTemplateConfig.post_copy, detectedExecutables);
+  const post_copy = mergePostCopyFiles(existingPostCopy, fileTemplateConfig.post_copy, selectedExecutables);
 
   if (post_copy.length > 0) {
     templateConfig.post_copy = post_copy;
@@ -372,9 +396,7 @@ export async function learn(sourcePath: string, updateTemplate: string | null =
   // --- OUTPUT ---
   if (options.json) {
     const output = { name: targetName, ...templateConfig };
-    process.stdout.write(JSON.stringify(output, null, 2) + '\n', () => {
-      process.exit(0);
-    });
+    process.stdout.write(JSON.stringify(output, null, 2) + '\n');
     return;
   }
 

package/src/commands/template-utils.ts

@@ -151,7 +151,9 @@ export function getRootEntries(dirPath: string, ignorePatterns?: string[]): { fi
     .filter(e => !shouldExclude(dirPath, path.join(dirPath, e.name), ignorePatterns))
     .filter(e => !shouldIgnore(e.name, e.name, ignorePatterns));
 
-  const files = entries.filter(e => e.isFile()).map(e => e.name);
+  const files = entries.filter(e => e.isFile())
+    .map(e => e.name)
+    .filter(fileName => !shouldExcludeFile(fileName));
   const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
   return { files, dirs };
 }
@@ -207,16 +209,25 @@ export function mergePostConfigTasks(
   if (jsonTasks && Array.isArray(jsonTasks)) {
     return [...jsonTasks];
   }
-  return detectedTasks.length > 0 ? detectedTasks : existingTasks;
+  // Merge detected tasks with existing, avoiding duplicates
+  const merged = [...existingTasks];
+  for (const dt of detectedTasks) {
+    const exists = merged.some(et => et.command === dt.command && et.script === dt.script);
+    if (!exists) {
+      merged.push(dt);
+    }
+  }
+  return merged;
 }
 
 /**
  * Merge post_copy files from existing, JSON file, and detected executables
+ * Only adds executables that were explicitly selected by the user
  */
 export function mergePostCopyFiles(
   existingPostCopy: PostCopyFile[],
   jsonPostCopy: PostCopyFile[] | undefined,
-  detectedExecutables: string[]
+  selectedExecutables: string[]
 ): PostCopyFile[] {
   let post_copy = [...existingPostCopy];
 
@@ -228,11 +239,9 @@ export function mergePostCopyFiles(
     }
   }
 
-  const newExecutables = detectedExecutables.filter(file => !post_copy.some(existing => existing.src === file));
-  
-  if (newExecutables.length > 0) {
-    // In interactive mode, we'd prompt to add these - for now just auto-add
-    for (const file of newExecutables) {
+  // Only add executables that were explicitly selected by the user
+  for (const file of selectedExecutables) {
+    if (!post_copy.some(existing => existing.src === file)) {
       post_copy.push({ src: file, dest: file });
     }
   }

package/src/commands/updateCommand.ts

@@ -170,6 +170,7 @@ export async function update(sourcePath: string, templateName: string, options:
   if (!isFullMode) {
     // Additive mode: only present new variables for selection
     const existingVarNames = new Set(config.templates[templateName].variables?.map(v => v.name) || []);
+    // newVars are NOT added to variables yet - only existing variables + JSON variables are in variables
     const newVars = variables.filter(v => !existingVarNames.has(v.name));
     
     if (newVars.length > 0) {
@@ -177,6 +178,7 @@ export async function update(sourcePath: string, templateName: string, options:
       console.log(chalk.green(`  + ${newVars.length} new variable(s): ${newVars.map(v => v.name).join(', ')}`));
       
       const selectedNewVars = await promptNewVariables(newVars, options);
+      // Only add the selected new variables (not all newVars)
       variables.push(...selectedNewVars);
     } else {
       printNoNewVariables();
@@ -197,106 +199,119 @@ export async function update(sourcePath: string, templateName: string, options:
       variables.push(...selectedGlobals);
     }
   } else {
-    // Full mode: original behavior with optional default/global variables prompt
-    const globalVarsToPrompt: TemplateVariable[] = [];
-    if (config.variables && Array.isArray(config.variables)) {
-      for (const v of config.variables) {
-        if (!variables.some(existing => existing.name === v.name)) {
-          globalVarsToPrompt.push({ ...v });
+    // Full mode: replace all variables with detected ones (no additive)
+    variables = [];
+    // Add detected variables
+    for (const varName of detectedVars) {
+      variables.push({
+        name: varName,
+        prompt: `Enter ${varName}:`,
+        required: true
+      });
+    }
+    // Also include JSON variables
+    if (fileTemplateConfig.variables && Array.isArray(fileTemplateConfig.variables)) {
+      for (const v of fileTemplateConfig.variables) {
+        const existingIndex = variables.findIndex(existing => existing.name === v.name);
+        if (existingIndex !== -1) {
+          variables[existingIndex] = { ...variables[existingIndex], ...v };
+        } else {
+          variables.push({ ...v });
         }
       }
     }
-
-    if (globalVarsToPrompt.length > 0) {
-      const selectedGlobals = await promptGlobalVariables(globalVarsToPrompt, options);
-      variables.push(...selectedGlobals);
-    }
-
-    const additionalVars = await promptAdditionalVariables(variables, options);
-    variables.push(...additionalVars);
   }
 
   // 1. Structure (skeleton) - Additive mode
-  let folders: FolderNode[] = [];
-  if (!isFullMode) {
-    // Additive mode: only add new folders
-    const detectedFolders = fileTemplateConfig.folders && Array.isArray(fileTemplateConfig.folders)
-      ? fileTemplateConfig.folders
-      : extractStructure(resolvedPath, resolvedPath, ignorePatterns);
+    let folders: FolderNode[] = [];
+    let selectedStructure: string[] = [];
+    let selectedFiles: string[] = [];
+    let selectedFolders: string[] = [];
+  
+    if (!isFullMode) {
+      // Additive mode: only add new folders
+      const detectedFolders = fileTemplateConfig.folders && Array.isArray(fileTemplateConfig.folders)
+        ? fileTemplateConfig.folders
+        : extractStructure(resolvedPath, resolvedPath, ignorePatterns);
 
-    const existingFolders = config.templates[templateName].folders || [];
-    const newFolders = detectedFolders.filter(f => !existingFolders.some(ef => ef.name === f.name));
-    
-    if (newFolders.length > 0) {
-      console.log(chalk.cyan(`\n📊 New Folders:`));
-      console.log(chalk.green(`  + ${newFolders.length} new folder(s): ${newFolders.map(f => f.name).join(', ')}`));
-      
-      const addedFolders = await promptNewFolders(newFolders, options);
-      folders = [...existingFolders, ...addedFolders];
-    } else {
-      printNoNewFolders();
-      folders = existingFolders;
-    }
-  } else {
-    // Full mode: original behavior
-    folders = fileTemplateConfig.folders && Array.isArray(fileTemplateConfig.folders)
-      ? fileTemplateConfig.folders
-      : extractStructure(resolvedPath, resolvedPath, ignorePatterns);
-  }
+      const existingFolders = config.templates[templateName].folders || [];
+      const newFolders = detectedFolders.filter(f => !existingFolders.some(ef => ef.name === f.name));
 
-  // 2. Content Selection (Root only)
-  const rootEntries = fs.readdirSync(resolvedPath, { withFileTypes: true })
-    .filter(e => !shouldExclude(resolvedPath, path.join(resolvedPath, e.name), ignorePatterns))
-    .filter(e => !shouldIgnore(e.name, e.name, ignorePatterns));
+      if (newFolders.length > 0) {
+        console.log(chalk.cyan(`\n📊 New Folders:`));
+        console.log(chalk.green(`  + ${newFolders.length} new folder(s): ${newFolders.map(f => f.name).join(', ')}`));
 
-  const rootFiles = rootEntries.filter(e => e.isFile()).map(e => e.name);
-  const rootDirs = rootEntries.filter(e => e.isDirectory()).map(e => e.name);
+        const addedFolders = await promptNewFolders(newFolders, options);
+        folders = [...existingFolders, ...addedFolders];
+      } else {
+        printNoNewFolders();
+        folders = existingFolders;
+      }
 
-  let selectedFiles: string[] = [];
-  let selectedFolders: string[] = [];
-  let selectedStructure: string[] = [];
+      // selectedStructure should include ALL folders (existing + added) in additive mode
+      // so that the final filter doesn't drop user-selected new folders
+      selectedStructure = [
+        ...new Set([
+          ...existingFolders.map(f => f.name),
+          ...folders.filter(f => !existingFolders.some(ef => ef.name === f.name)).map(f => f.name),
+        ]),
+      ];
+    } else {
+        // Full mode: original behavior
+        folders = fileTemplateConfig.folders && Array.isArray(fileTemplateConfig.folders)
+          ? fileTemplateConfig.folders
+          : extractStructure(resolvedPath, resolvedPath, ignorePatterns);
+      }
 
-  if (!isFullMode) {
-    // Additive mode for files and folders
-    const existingCopyFiles = config.templates[templateName].copy_files || [];
+      // 2. Content Selection (Root only)
+      const rootEntries = fs.readdirSync(resolvedPath, { withFileTypes: true })
+        .filter(e => !shouldExclude(resolvedPath, path.join(resolvedPath, e.name), ignorePatterns))
+        .filter(e => !shouldIgnore(e.name, e.name, ignorePatterns));
+
+      const rootFiles = rootEntries.filter(e => e.isFile())
+        .map(e => e.name)
+        .filter(fileName => !shouldExcludeFile(fileName));
+      const rootDirs = rootEntries.filter(e => e.isDirectory()).map(e => e.name);
+
+      if (!isFullMode) {
+        // Additive mode for files and folders
+        const existingCopyFiles = config.templates[templateName].copy_files || [];
     
-    // New files
-    const newFiles = rootFiles.filter(f => !existingCopyFiles.some(cf => cf.src === f));
-    printNewFiles(newFiles.length, newFiles);
-    const addedFiles = await promptNewFiles(newFiles, options);
-    selectedFiles = [...existingCopyFiles.filter(cf => !rootDirs.includes(cf.src)).map(cf => cf.src), ...addedFiles];
-
-    // Structure
-    selectedStructure = config.templates[templateName].folders?.map(f => f.name) || [];
-    // Seed selectedFolders from existing copy_files directory entries
-    selectedFolders = existingCopyFiles
-      .filter(f => rootDirs.includes(f.src))
-      .map(f => f.src);
-
-    if (rootDirs.length > 0) {
-      const detectedFolders = fileTemplateConfig.folders && Array.isArray(fileTemplateConfig.folders)
-        ? fileTemplateConfig.folders
-        : extractStructure(resolvedPath, resolvedPath, ignorePatterns);
-      const newFolders = detectedFolders.filter(f => !config.templates[templateName].folders?.some(ef => ef.name === f.name));
+        // New files
+        const newFiles = rootFiles.filter(f => !existingCopyFiles.some(cf => cf.src === f));
+        printNewFiles(newFiles.length, newFiles);
+        const addedFiles = await promptNewFiles(newFiles, options);
+        selectedFiles = [...existingCopyFiles.filter(cf => !rootDirs.includes(cf.src)).map(cf => cf.src), ...addedFiles];
+
+        // Seed selectedFolders from existing copy_files directory entries
+        selectedFolders = existingCopyFiles
+          .filter(f => rootDirs.includes(f.src))
+          .map(f => f.src);
+
+        if (rootDirs.length > 0) {
+          const detectedFolders = fileTemplateConfig.folders && Array.isArray(fileTemplateConfig.folders)
+            ? fileTemplateConfig.folders
+            : extractStructure(resolvedPath, resolvedPath, ignorePatterns);
+          const newFolders = detectedFolders.filter(f => !config.templates[templateName].folders?.some(ef => ef.name === f.name));
       
-      const addedDirs = newFolders
-        .filter(f => ['APP', 'scripts', 'bin'].some(p => f.name === p))
-        .map(f => f.name);
-      selectedStructure = [...new Set([...selectedStructure, ...addedDirs])];
-      selectedFolders = [...new Set([...selectedFolders, ...addedDirs])];
-    }
-  } else {
-    // Full mode: original behavior
-    if (options.yes || options.json) {
-      selectedFiles = rootFiles.filter(f => ['.makerc', 'readme.md', 'README.md', '.gitattributes', '.gitignore', 'Makefile', 'makefile', 'package.json'].some(p => f.toLowerCase() === p.toLowerCase()));
-      selectedStructure = rootDirs;
-      selectedFolders = rootDirs.filter(d => ['APP', 'scripts', 'bin'].some(p => d === p));
-    } else {
-      selectedFiles = await promptRootFiles(rootFiles, undefined, options);
-      selectedStructure = await promptStructureFolders(rootDirs, options);
-      selectedFolders = await promptCopyFolders(selectedStructure, undefined, options);
-    }
-  }
+          const addedDirs = newFolders
+            .filter(f => ['APP', 'scripts', 'bin'].some(p => f.name === p))
+            .map(f => f.name);
+          selectedStructure = [...new Set([...selectedStructure, ...addedDirs])];
+          selectedFolders = [...new Set([...selectedFolders, ...addedDirs])];
+        }
+      } else {
+          // Full mode: original behavior - pick up all files like a fresh learn
+          if (options.yes || options.json) {
+            selectedFiles = rootFiles;
+            selectedStructure = rootDirs;
+            selectedFolders = rootDirs.filter(d => ['APP', 'scripts', 'bin'].some(p => d === p));
+          } else {
+            selectedFiles = await promptRootFiles(rootFiles, undefined, options);
+            selectedStructure = await promptStructureFolders(rootDirs, options);
+            selectedFolders = await promptCopyFolders(selectedStructure, undefined, options);
+          }
+        }
 
   const copy_files: CopyFileEntry[] = [];
   if (fileTemplateConfig.copy_files && Array.isArray(fileTemplateConfig.copy_files)) {
@@ -371,8 +386,29 @@ export async function update(sourcePath: string, templateName: string, options:
     .filter(file => isExecutable(path.join(resolvedPath, file), file))
     .filter(file => !shouldExcludeFile(file));
 
+  // In additive mode, only add executables that were explicitly selected by the user
+  let selectedExecutables: string[] = [];
+  if (!isFullMode) {
+    // In additive mode, only include executables that are in selectedFiles (user explicitly chose them)
+    // BUT exclude files that already exist in copy_files with custom settings (chmod, substitute_variables: false)
+    const existingCopyFiles = config.templates[templateName].copy_files || [];
+    const existingCopySrcs = new Set(existingCopyFiles.map(cf => cf.src));
+    const existingCustomSettings = new Set(
+      existingCopyFiles
+        .filter(cf => cf.chmod || cf.substitute_variables === false)
+        .map(cf => cf.src)
+    );
+    
+    selectedExecutables = detectedExecutables.filter(exec => 
+      selectedFiles.includes(exec) && !existingCustomSettings.has(exec)
+    );
+  } else {
+    // In full mode, include all detected executables (original behavior)
+    selectedExecutables = detectedExecutables;
+  }
+
   const existingPostCopy = config.templates[templateName].post_copy || [];
-  const post_copy = mergePostCopyFiles(existingPostCopy, fileTemplateConfig.post_copy, detectedExecutables);
+  const post_copy = mergePostCopyFiles(existingPostCopy, fileTemplateConfig.post_copy, selectedExecutables);
 
   if (post_copy.length > 0) {
     templateConfig.post_copy = post_copy;
@@ -386,9 +422,7 @@ export async function update(sourcePath: string, templateName: string, options:
       ...templateConfig
     };
 
-    process.stdout.write(JSON.stringify(output, null, 2) + '\n', () => {
-      process.exit(0);
-    });
+    process.stdout.write(JSON.stringify(output, null, 2) + '\n');
     return;
   }
 

package/src/config.ts

@@ -285,6 +285,7 @@ export const DEFAULT_EXCLUDES = [
   'dist',
   'build',
   'bin',
+  '.vscode',
   '.DS_Store',
   'Thumbs.db',
 ];
@@ -397,6 +398,8 @@ export function shouldExcludeFile(fileName: string): boolean {
     'yarn.lock',
     'pnpm-lock.yaml',
     'composer.lock',
+    'post_config.sh',
+    'post_config.bat',
   ];
 
   for (const pattern of excludePatterns) {

package/src/index.ts

@@ -25,7 +25,7 @@ const program = new Command();
 program
   .name('pt')
   .description('Project Template CLI - Learn project structures and initialize new ones')
-  .version(pkg.version, '-v', 'output the version number');
+  .version(pkg.version, '-v, --version', 'output the version number');
 
 program
   .command('learn [path]')
@@ -72,15 +72,31 @@ program
   });
 
 program
-  .command('init [templateName] [destPath]')
-  .description('Initialize a new project from a learned template')
+  .command('init [args...]')
+  .description('Initialize a new project from one or more learned templates')
   .option('-f, --file <jsonPath>', 'Initialize directly from a JSON template file without adding it to local config')
   .option('--skip-post-config', 'Skip running post-config tasks')
   .option('--dry-run', 'Show what would be created without making changes')
   .option('-y, --yes', 'Automatically answer yes to prompts')
   .option('--vars <variables>', 'Comma-separated key=value variables (e.g. key1=val1,key2=val2)')
-  .action(async (typeName: string | undefined, destPath: string | undefined, options) => {
-    await init(typeName, destPath, options);
+  .option('--collision <mode>', 'File collision resolution strategy (overwrite, newest)', 'overwrite')
+  .option('--json', 'Output result as JSON')
+  .action(async (args: string[], options) => {
+    try {
+      await init(args, options);
+    } catch (err: any) {
+      if (options.json) {
+        process.stdout.write(JSON.stringify({
+          status: 'error',
+          message: err.message || String(err)
+        }) + '\n', () => {
+          process.exit(1);
+        });
+      } else {
+        console.error(chalk.red(`Error: ${err.message || err}`));
+        process.exit(1);
+      }
+    }
   });
 
 program

package/src/substitute.ts

@@ -50,7 +50,9 @@ export async function processCopyFiles(
   resolvedDest: string,
   template: TemplateConfig,
   variables: Record<string, string>,
-  dryRun: boolean = false
+  dryRun: boolean = false,
+  collisionMode: 'overwrite' | 'newest' = 'overwrite',
+  silent: boolean = false
 ): Promise<void> {
   if (!template.copy_files) return;
 
@@ -59,7 +61,7 @@ export async function processCopyFiles(
     const destPath = path.join(resolvedDest, sanitizePath(copyFile.dest));
 
     if (!fs.existsSync(srcPath)) {
-      console.warn(chalk.yellow(`Warning: ${copyFile.src} not found in template`));
+      if (!silent) console.warn(chalk.yellow(`Warning: ${copyFile.src} not found in template`));
       continue;
     }
 
@@ -67,7 +69,7 @@ export async function processCopyFiles(
     if (stat.isDirectory()) {
       // Recursive directory copy
       if (dryRun) {
-        console.log(chalk.gray(`  [DRY RUN] Would recursively copy directory ${copyFile.src} → ${copyFile.dest}`));
+        if (!silent) console.log(chalk.gray(`  [DRY RUN] Would recursively copy directory ${copyFile.src} → ${copyFile.dest}`));
       } else {
         const dirSubstitute = !!(copyFile.substitute_variables === true || (
           copyFile.substitute_variables === undefined &&
@@ -75,24 +77,39 @@ export async function processCopyFiles(
           template.variables.length > 0 &&
           Object.keys(variables).length > 0
         ));
-        copyDirRecursive(srcPath, destPath, variables, dirSubstitute, copyFile.chmod);
+        copyDirRecursive(srcPath, destPath, variables, dirSubstitute, copyFile.chmod, collisionMode, silent);
       }
-      console.log(chalk.green(`  ✓ ${copyFile.dest} (recursive)`));
+      if (!silent) console.log(chalk.green(`  ✓ ${copyFile.dest} (recursive)`));
     } else {
+      // Check collision mode
+      if (collisionMode === 'newest' && fs.existsSync(destPath)) {
+        const destStat = fs.statSync(destPath);
+        if (destStat.mtimeMs > stat.mtimeMs) {
+          if (dryRun && !silent) {
+            console.log(chalk.yellow(`  [DRY RUN] [COLLISION] Destination is newer, keeping ${copyFile.dest}`));
+          } else if (!silent) {
+            console.log(chalk.yellow(`  [COLLISION] Destination is newer, keeping ${copyFile.dest}`));
+          }
+          continue;
+        }
+      }
+
       // Single file copy
       if (dryRun) {
-        console.log(chalk.gray(`  [DRY RUN] Would copy ${copyFile.src} → ${copyFile.dest}`));
-        const drySubstitute = !!(copyFile.substitute_variables === true || (
-          copyFile.substitute_variables === undefined &&
-          template.variables &&
-          template.variables.length > 0 &&
-          Object.keys(variables).length > 0
-        ));
-        if (drySubstitute) {
-          console.log(chalk.gray(`  [DRY RUN] Would substitute variables in ${copyFile.dest}`));
-        }
-        if (copyFile.chmod) {
-          console.log(chalk.gray(`  [DRY RUN] Would chmod ${copyFile.chmod} ${copyFile.dest}`));
+        if (!silent) {
+          console.log(chalk.gray(`  [DRY RUN] Would copy ${copyFile.src} → ${copyFile.dest}`));
+          const drySubstitute = !!(copyFile.substitute_variables === true || (
+            copyFile.substitute_variables === undefined &&
+            template.variables &&
+            template.variables.length > 0 &&
+            Object.keys(variables).length > 0
+          ));
+          if (drySubstitute) {
+            console.log(chalk.gray(`  [DRY RUN] Would substitute variables in ${copyFile.dest}`));
+          }
+          if (copyFile.chmod) {
+            console.log(chalk.gray(`  [DRY RUN] Would chmod ${copyFile.chmod} ${copyFile.dest}`));
+          }
         }
         continue;
       }
@@ -119,13 +136,13 @@ export async function processCopyFiles(
         try {
           fs.chmodSync(destPath, parseInt(copyFile.chmod, 8));
         } catch (e) {
-          if (process.platform !== 'win32') {
+          if (process.platform !== 'win32' && !silent) {
             console.error(chalk.red(`Failed to set chmod ${copyFile.chmod} on ${copyFile.dest}`));
           }
         }
       }
 
-      console.log(chalk.green(`  ✓ ${copyFile.dest}`));
+      if (!silent) console.log(chalk.green(`  ✓ ${copyFile.dest}`));
     }
   }
 }
@@ -135,7 +152,9 @@ function copyDirRecursive(
   dest: string,
   variables: Record<string, string>,
   substitute: boolean,
-  chmod?: string
+  chmod?: string,
+  collisionMode: 'overwrite' | 'newest' = 'overwrite',
+  silent: boolean = false
 ) {
   fs.mkdirSync(dest, { recursive: true });
   const entries = fs.readdirSync(src, { withFileTypes: true });
@@ -145,8 +164,16 @@ function copyDirRecursive(
     const destPath = path.join(dest, entry.name);
 
     if (entry.isDirectory()) {
-      copyDirRecursive(srcPath, destPath, variables, substitute, chmod);
+      copyDirRecursive(srcPath, destPath, variables, substitute, chmod, collisionMode, silent);
     } else {
+      if (collisionMode === 'newest' && fs.existsSync(destPath)) {
+        const destStat = fs.statSync(destPath);
+        const srcStat = fs.statSync(srcPath);
+        if (destStat.mtimeMs > srcStat.mtimeMs) {
+          continue;
+        }
+      }
+
       let content = fs.readFileSync(srcPath, 'utf-8');
       if (substitute) {
         content = substituteVariables(content, variables);

package/tests/config-utils.test.ts

@@ -147,9 +147,9 @@ test('DEFAULT_EXCLUDES contains expected patterns', () => {
   assert.ok(DEFAULT_EXCLUDES.includes('node_modules'), 'Should include node_modules');
   assert.ok(DEFAULT_EXCLUDES.includes('dist'), 'Should include dist');
   assert.ok(DEFAULT_EXCLUDES.includes('build'), 'Should include build');
+  assert.ok(DEFAULT_EXCLUDES.includes('.vscode'), 'Should include .vscode');
   assert.ok(DEFAULT_EXCLUDES.includes('.DS_Store'), 'Should include .DS_Store');
   assert.ok(DEFAULT_EXCLUDES.includes('Thumbs.db'), 'Should include Thumbs.db');
-  assert.ok(!DEFAULT_EXCLUDES.includes('.vscode'), 'Should NOT include .vscode');
   assert.ok(!DEFAULT_EXCLUDES.includes('.gitea'), 'Should NOT include .gitea');
   assert.ok(!DEFAULT_EXCLUDES.includes('.stignore'), 'Should NOT include .stignore');
 });

package/tests/learn.test.ts

@@ -38,15 +38,16 @@ function cleanConfig() {
 
 /** Capture console.log output during an async callback. */
 async function captureStdout(fn: () => Promise<void>): Promise<string> {
-  const original = console.log;
+  const originalWrite = process.stdout.write;
   let captured = '';
-  console.log = (...args: unknown[]) => {
-    captured += args.map(a => (typeof a === 'string' ? a : JSON.stringify(a))).join(' ') + '\n';
+  process.stdout.write = (chunk: any) => {
+    captured += chunk.toString();
+    return true;
   };
   try {
     await fn();
   } finally {
-    console.log = original;
+    process.stdout.write = originalWrite;
   }
   return captured;
 }