[auto] fix: bootstrap --yes vs --force separation + backup + orphan detection

.gitignore

@@ -27,3 +27,8 @@ C:*
 node_modules/
 .pnpm-store/
 __pycache__/
+# cc-taskrunner worktree protection
+C:*
+node_modules/
+.pnpm-store/
+__pycache__/

packages/cli/src/__tests__/bootstrap.test.ts

@@ -52,7 +52,9 @@ CONTEXT:
     expect(fs.existsSync(path.join('.ai', '.backup'))).toBe(false);
     expect(fs.existsSync(path.join('.ai', 'manifest.adf'))).toBe(true);
     expect(fs.existsSync(path.join('.ai', 'state.adf'))).toBe(true);
-    expect(logs).toContain('  Warning: .ai/core.adf has custom content; skipping scaffold overwrite');
+    const skipWarning = logs.find(l => l.includes('.ai/core.adf has custom content') && l.includes('skipping scaffold overwrite'));
+    expect(skipWarning).toBeDefined();
+    expect(skipWarning).toMatch(/\d+ bytes/);
   });
 
   it('backs up and overwrites custom ADF files when run with --force', async () => {
@@ -75,15 +77,26 @@ STATE:
     );
 
     expect(exitCode).toBe(0);
-    expect(fs.readFileSync(path.join('.ai', '.backup', 'core.adf'), 'utf-8')).toBe(customCore);
-    expect(fs.readFileSync(path.join('.ai', '.backup', 'state.adf'), 'utf-8')).toBe(customState);
+
+    // Backup files should exist with timestamp suffix
+    const backupDir = path.join('.ai', '.backup');
+    expect(fs.existsSync(backupDir)).toBe(true);
+    const backupFiles = fs.readdirSync(backupDir);
+    const coreBackup = backupFiles.find(f => f.startsWith('core.adf.'));
+    const stateBackup = backupFiles.find(f => f.startsWith('state.adf.'));
+    expect(coreBackup).toBeDefined();
+    expect(stateBackup).toBeDefined();
+    expect(fs.readFileSync(path.join(backupDir, coreBackup!), 'utf-8')).toBe(customCore);
+    expect(fs.readFileSync(path.join(backupDir, stateBackup!), 'utf-8')).toBe(customState);
+
+    // Originals should be overwritten with scaffold content
     expect(fs.readFileSync(path.join('.ai', 'core.adf'), 'utf-8')).not.toBe(customCore);
     expect(fs.readFileSync(path.join('.ai', 'state.adf'), 'utf-8')).not.toBe(customState);
     expect(logs).toContain('  Backed up 2 files to .ai/.backup/');
   });
 
-  it('detects orphaned .adf modules not in manifest (--yes mode prints warning)', async () => {
-    // Pre-create .ai/ with an extra module that won't be in the scaffold manifest
+  it('detects orphaned .adf modules and auto-registers them in --yes mode', async () => {
+    // Pre-create .ai/ with extra modules that won't be in the scaffold manifest
     fs.mkdirSync('.ai', { recursive: true });
     fs.writeFileSync(path.join('.ai', 'agent.adf'), 'ADF: 0.1\n\nCONTEXT:\n  - Agent rules\n');
     fs.writeFileSync(path.join('.ai', 'persona.adf'), 'ADF: 0.1\n\nCONTEXT:\n  - Persona rules\n');
@@ -99,8 +112,14 @@ STATE:
     expect(orphanWarning).toBeDefined();
     expect(orphanWarning).toContain('agent.adf');
     expect(orphanWarning).toContain('persona.adf');
-    // Should suggest the register command
-    const registerHint = logs.find(l => l.includes('charter adf register'));
-    expect(registerHint).toBeDefined();
+
+    // In --yes mode, orphans should be auto-registered in manifest
+    const registerLog = logs.find(l => l.includes('Registered 2 module(s) as ON_DEMAND'));
+    expect(registerLog).toBeDefined();
+
+    // Verify manifest contains the orphan entries
+    const manifest = fs.readFileSync(path.join('.ai', 'manifest.adf'), 'utf-8');
+    expect(manifest).toContain('agent.adf');
+    expect(manifest).toContain('persona.adf');
   });
 });

packages/cli/src/commands/adf.ts

@@ -299,7 +299,7 @@ See .ai/manifest.adf for the module routing manifest.
 `;
 
 function adfInit(options: CLIOptions, args: string[]): number {
-  const force = options.yes || args.includes('--force');
+  const force = args.includes('--force');
   const aiDir = getFlag(args, '--ai-dir') || '.ai';
   const moduleFlag = getFlag(args, '--module');
   const presetFlag = getFlag(args, '--preset');
@@ -323,7 +323,7 @@ function adfInit(options: CLIOptions, args: string[]): number {
       console.log('');
       console.log('  .ai/ directory already exists. Run \'charter doctor\' to check for issues.');
       console.log('');
-      console.log('  Use --force (or --yes) to overwrite.');
+      console.log('  Use --force to overwrite existing files.');
       console.log('  To add a single module: charter adf init --module <name>');
     }
     return EXIT_CODE.SUCCESS;
@@ -566,7 +566,7 @@ function adfCreate(options: CLIOptions, args: string[]): number {
   }
 
   const aiDir = getFlag(args, '--ai-dir') || '.ai';
-  const force = options.yes || args.includes('--force');
+  const force = args.includes('--force');
   const load = (getFlag(args, '--load') || 'on-demand').toLowerCase();
   if (load !== 'default' && load !== 'on-demand') {
     throw new CLIError(`Invalid --load value: ${load}. Use default or on-demand.`);

packages/cli/src/commands/bootstrap.ts

@@ -165,15 +165,22 @@ export async function bootstrapCommand(options: CLIOptions, args: string[]): Pro
     console.log('');
   }
 
-  // Orphan registration prompt (interactive only)
+  // Orphan registration: auto-register in --yes mode, prompt interactively otherwise
   const orphans = adfResult.step.details.orphans as string[] || [];
-  if (orphans.length > 0 && !nonInteractive && options.format === 'text') {
-    const shouldRegister = await promptYesNo('  Register these modules now? (y/N) ');
+  if (orphans.length > 0) {
+    let shouldRegister = false;
+    if (nonInteractive) {
+      shouldRegister = true;
+    } else if (options.format === 'text') {
+      shouldRegister = await promptYesNo('  Register these modules now? (y/N) ');
+    }
     if (shouldRegister) {
       registerOrphansInManifest(path.join('.ai', 'manifest.adf'), orphans);
       updateModuleIndex('CLAUDE.md', '.ai');
-      console.log(`  Registered ${orphans.length} module(s) as ON_DEMAND in manifest.adf`);
-      console.log('');
+      if (options.format === 'text') {
+        console.log(`  Registered ${orphans.length} module(s) as ON_DEMAND in manifest.adf`);
+        console.log('');
+      }
     }
   }
 
@@ -514,6 +521,7 @@ function writeAdfScaffolds(
   const warnings: string[] = [];
   let backedUp = 0;
   let backupDir: string | undefined;
+  const timestamp = new Date().toISOString().replace(/[:.]/g, '-');
 
   for (const scaffold of getAdfScaffolds(preset)) {
     const targetPath = path.join(aiDir, scaffold.name);
@@ -530,14 +538,18 @@ function writeAdfScaffolds(
       continue;
     }
 
+    const byteCount = Buffer.byteLength(existing, 'utf-8');
+
     if (!force) {
-      warnings.push(`${label} has custom content; skipping scaffold overwrite`);
+      warnings.push(`${label} has custom content (${byteCount} bytes); skipping scaffold overwrite`);
       continue;
     }
 
     backupDir ||= path.join(aiDir, '.backup');
     fs.mkdirSync(backupDir, { recursive: true });
-    fs.copyFileSync(targetPath, path.join(backupDir, scaffold.name));
+    const backupName = `${scaffold.name}.${timestamp}`;
+    fs.copyFileSync(targetPath, path.join(backupDir, backupName));
+    warnings.push(`Backed up ${label} (${byteCount} bytes) → .ai/.backup/${backupName}`);
     backedUp++;
 
     fs.writeFileSync(targetPath, scaffold.content);

packages/cli/src/commands/setup.ts

@@ -178,7 +178,7 @@ export async function setupCommand(options: CLIOptions, args: string[]): Promise
   const presetFlag = getFlag(args, '--preset');
   const detectOnly = args.includes('--detect-only');
   const explicitForce = args.includes('--force');
-  const force = options.yes || explicitForce;
+  const force = explicitForce;
   const noDependencySync = args.includes('--no-dependency-sync');
 
   if (ciMode && ciMode !== 'github') {
@@ -645,7 +645,7 @@ export function detectStack(contexts: PackageContext[]): DetectionResult {
 export function loadPackageContexts(): PackageContext[] {
   const candidates = new Set<string>(['package.json']);
 
-  for (const dir of ['client', 'frontend', 'web']) {
+  for (const dir of ['client', 'frontend', 'web', 'worker', 'src', 'app']) {
     candidates.add(path.join(dir, 'package.json'));
   }
   candidates.add(path.join('apps', 'web', 'package.json'));