@cregis-dev/cckit 0.4.0 → 0.4.1

package/src/commands/update.js

@@ -1,430 +1,430 @@
-import path from 'node:path'
-import { fileURLToPath } from 'node:url'
-import fse from 'fs-extra'
-import YAML from 'yaml'
-import { createLogger } from '../utils/logger.js'
-import { computeFileHash, interpolate, listFiles, TEXT_EXTENSIONS } from '../utils/fs.js'
-import { loadRegistry, resolveModules, getDefaultModules } from '../core/registry.js'
-import { ADAPTERS } from '../adapters/trae-adapter.js'
-
-const __dirname = path.dirname(fileURLToPath(import.meta.url))
-const CCKIT_ROOT = path.resolve(__dirname, '../..')
-
-/**
- * Extract the fileRegistry from a manifest, handling both formats:
- * - cckit.fileRegistry (produced by init command)
- * - top-level fileRegistry (legacy/manual)
- *
- * @param {object} manifest - Parsed manifest object
- * @returns {object} File registry map { relativePath: hash }
- */
-function extractFileRegistry(manifest) {
-  if (manifest.cckit && manifest.cckit.fileRegistry) {
-    return manifest.cckit.fileRegistry
-  }
-  if (manifest.fileRegistry) {
-    return manifest.fileRegistry
-  }
-  return {}
-}
-
-/**
- * Build a sourceMap from registry modules and config.
- *
- * Maps each target directory to its source template info:
- *   { templateDir, adapter, prefix, moduleId }
- *
- * @param {object} registry - Loaded registry
- * @param {object} config - Config from manifest (ides, languages, etc.)
- * @returns {object} sourceMap keyed by targetDir
- */
-function buildSourceMap(registry, config) {
-  const selectedIds = getDefaultModules(registry)
-  const resolved = resolveModules(registry, selectedIds)
-  const sourceMap = {}
-  const ides = config.ides || ['claude-code']
-
-  for (const mod of resolved) {
-    if (mod.targets) {
-      for (const ide of ides) {
-        const target = mod.targets[ide]
-        if (!target) continue
-
-        const templateDir = path.resolve(
-          CCKIT_ROOT,
-          target.templateDir || mod.templateDir
-        )
-        sourceMap[target.targetDir] = {
-          templateDir,
-          adapter: target.adapter ? ADAPTERS[target.adapter] : undefined,
-          prefix: target.prefix || undefined,
-          moduleId: mod.id
-        }
-      }
-    } else if (mod.ideTarget) {
-      if (ides.includes(mod.ideTarget)) {
-        sourceMap[mod.targetDir] = {
-          templateDir: path.resolve(CCKIT_ROOT, mod.templateDir),
-          adapter: undefined,
-          prefix: undefined,
-          moduleId: mod.id
-        }
-      }
-    } else {
-      sourceMap[mod.targetDir] = {
-        templateDir: path.resolve(CCKIT_ROOT, mod.templateDir),
-        adapter: undefined,
-        prefix: undefined,
-        moduleId: mod.id
-      }
-    }
-  }
-
-  return sourceMap
-}
-
-/**
- * Find the source template file for an installed file.
- *
- * @param {string} relPath - Relative path of the installed file (e.g. '.claude/rules/common/coding-style.md')
- * @param {object} sourceMap - Map from targetDir to source info
- * @returns {object|null} { srcAbsPath, adapter } or null if not found
- */
-function findSourceForFile(relPath, sourceMap) {
-  // Normalize to forward slashes for matching
-  const normalizedRel = relPath.replace(/\\/g, '/')
-
-  // Collect all matching entries, pick the one with the longest prefix (most specific)
-  let bestMatch = null
-  let bestPrefixLen = -1
-
-  for (const [targetDir, source] of Object.entries(sourceMap)) {
-    const normalizedTarget = targetDir.replace(/\\/g, '/')
-    // Check if file is under this target directory
-    // Handle both "dir/file" and "dir" == "." (root-level targets)
-    const prefix = normalizedTarget === '.'
-      ? ''
-      : normalizedTarget + '/'
-
-    if (prefix === '' ? true : normalizedRel.startsWith(prefix)) {
-      if (prefix.length > bestPrefixLen) {
-        const remainder = prefix === ''
-          ? normalizedRel
-          : normalizedRel.slice(prefix.length)
-
-        // If a prefix was applied to the filename during install, strip it to find source
-        let srcRelPath = remainder
-        if (source.prefix) {
-          const fileName = path.basename(remainder)
-          if (fileName.startsWith(source.prefix)) {
-            const originalName = fileName.slice(source.prefix.length)
-            const dir = path.dirname(remainder)
-            srcRelPath = dir === '.' ? originalName : path.join(dir, originalName)
-          }
-        }
-
-        const srcAbsPath = path.join(source.templateDir, srcRelPath)
-        bestPrefixLen = prefix.length
-        bestMatch = {
-          srcAbsPath,
-          adapter: source.adapter
-        }
-      }
-    }
-  }
-  return bestMatch
-}
-
-/**
- * Reinstall a single file from its template source.
- *
- * @param {string} targetDir - Project root directory
- * @param {string} relPath - Relative path of the file
- * @param {object} source - { srcAbsPath, adapter }
- * @param {object} variables - Template interpolation variables
- * @returns {Promise<boolean>} true if successfully reinstalled
- */
-async function reinstallFile(targetDir, relPath, source, variables) {
-  const destPath = path.join(targetDir, relPath)
-  const ext = path.extname(relPath).toLowerCase()
-
-  if (!await fse.pathExists(source.srcAbsPath)) {
-    return false
-  }
-
-  await fse.ensureDir(path.dirname(destPath))
-
-  if (TEXT_EXTENSIONS.has(ext)) {
-    let content = await fse.readFile(source.srcAbsPath, 'utf8')
-    content = interpolate(content, variables)
-    if (source.adapter) {
-      content = source.adapter(content, path.basename(relPath))
-    }
-    await fse.writeFile(destPath, content, 'utf8')
-  } else {
-    await fse.copy(source.srcAbsPath, destPath)
-  }
-
-  return true
-}
-
-/**
- * Discover new files from templates that are not yet tracked in fileRegistry.
- * This handles newly added modules/skills in cckit updates.
- *
- * @param {object} sourceMap - Map from targetDir to source info
- * @param {object} fileRegistry - Current file registry from manifest
- * @returns {Promise<Array<{ relPath: string, source: { srcAbsPath: string, adapter?: Function } }>>}
- */
-async function discoverNewFiles(sourceMap, fileRegistry) {
-  const newFiles = []
-
-  for (const [targetDir, source] of Object.entries(sourceMap)) {
-    if (!await fse.pathExists(source.templateDir)) continue
-
-    const templateFiles = await listFiles(source.templateDir)
-
-    for (const relPath of templateFiles) {
-      const fileName = path.basename(relPath)
-      const dir = path.dirname(relPath)
-
-      // Apply prefix if configured (e.g. ecc-agent- prefix)
-      const installedName = source.prefix
-        ? `${source.prefix}${fileName}`
-        : fileName
-
-      // Build the installed relative path
-      const installedRelPath = targetDir === '.'
-        ? (dir === '.' ? installedName : `${dir}/${installedName}`)
-        : (dir === '.' ? `${targetDir}/${installedName}` : `${targetDir}/${dir}/${installedName}`)
-
-      const normalizedPath = installedRelPath.replace(/\\/g, '/')
-
-      if (!(normalizedPath in fileRegistry)) {
-        newFiles.push({
-          relPath: normalizedPath,
-          source: {
-            srcAbsPath: path.join(source.templateDir, relPath),
-            adapter: source.adapter,
-          },
-        })
-      }
-    }
-  }
-
-  return newFiles
-}
-
-/**
- * Run the update command.
- *
- * Reads the installed manifest, compares current file hashes against
- * the recorded fileRegistry, and reports which files are unchanged,
- * modified by the user, or missing.
- *
- * When --apply is set, reinstalls files from cckit templates.
- *
- * @param {object} opts - Command options
- * @param {string} [opts.dir] - Target directory (default: cwd)
- * @param {boolean} [opts.dryRun] - Preview changes without applying
- * @param {boolean} [opts.apply] - Reinstall files from templates
- * @param {boolean} [opts.force] - Force overwrite modified files without backup
- * @param {boolean} [opts.debug] - Enable debug output
- * @returns {Promise<object>} Result with { checked, modified, unchanged, missing, applied? }
- * @throws {Error} If cckit is not installed
- */
-export async function runUpdate(opts = {}) {
-  const logger = createLogger({ debug: opts.debug })
-  const targetDir = path.resolve(opts.dir || process.cwd())
-  const manifestPath = path.join(targetDir, '_bmad', '_config', 'manifest.yaml')
-
-  if (!await fse.pathExists(manifestPath)) {
-    throw new Error('cckit is not installed. Run `cckit init` first.')
-  }
-
-  const manifestContent = await fse.readFile(manifestPath, 'utf8')
-  const manifest = YAML.parse(manifestContent)
-
-  logger.banner('cckit update')
-
-  const fileRegistry = extractFileRegistry(manifest)
-  const modified = []
-  const unchanged = []
-  const missing = []
-
-  for (const [relPath, expectedHash] of Object.entries(fileRegistry)) {
-    const fullPath = path.join(targetDir, relPath)
-
-    if (!await fse.pathExists(fullPath)) {
-      missing.push(relPath)
-      continue
-    }
-
-    const currentHash = await computeFileHash(fullPath)
-    if (currentHash !== expectedHash) {
-      modified.push(relPath)
-    } else {
-      unchanged.push(relPath)
-    }
-  }
-
-  // Report results
-  const totalFiles = Object.keys(fileRegistry).length
-  if (totalFiles > 0) {
-    logger.info(`  Checked ${totalFiles} registered file(s)`)
-  }
-
-  if (unchanged.length > 0) {
-    logger.success(`${unchanged.length} file(s) unchanged`)
-  }
-
-  if (modified.length > 0) {
-    logger.warn(`${modified.length} file(s) modified by user:`)
-    for (const f of modified) {
-      logger.info(`    ${f}`)
-    }
-  }
-
-  if (missing.length > 0) {
-    logger.warn(`${missing.length} file(s) missing:`)
-    for (const f of missing) {
-      logger.info(`    ${f}`)
-    }
-  }
-
-  if (totalFiles === 0) {
-    logger.info('  No files registered in manifest.')
-  } else if (modified.length === 0 && missing.length === 0) {
-    logger.success('All files match. Nothing to update.')
-  }
-
-  if (opts.dryRun) {
-    logger.info('\n  (dry run - no changes made)')
-    return { checked: true, modified, unchanged, missing }
-  }
-
-  // Apply mode: reinstall files from templates
-  if (opts.apply) {
-    const applied = { updated: 0, backedUp: 0, restored: 0, added: 0, failed: 0, orphaned: 0 }
-
-    let registry
-    let sourceMap
-    let variables
-
-    try {
-      registry = await loadRegistry()
-      const config = manifest.cckit && manifest.cckit.config
-        ? manifest.cckit.config
-        : {}
-
-      sourceMap = buildSourceMap(registry, config)
-      variables = {
-        user_name: config.user_name || '',
-        communication_language: config.communication_language || '',
-        document_output_language: config.document_output_language || '',
-        languages: Array.isArray(config.languages)
-          ? config.languages.join(', ')
-          : (config.languages || ''),
-        'project-root': '.'
-      }
-    } catch (err) {
-      logger.debug(`Failed to load registry for apply: ${err.message}`)
-      // Return result with empty applied if registry cannot be loaded
-      if (manifest.cckit) {
-        manifest.cckit.lastUpdated = new Date().toISOString()
-      }
-      await fse.writeFile(manifestPath, YAML.stringify(manifest), 'utf8')
-      logger.success('Update complete.')
-      return { checked: true, modified, unchanged, missing, applied }
-    }
-
-    // Process all files: unchanged + modified + missing
-    const allFiles = [...unchanged, ...modified, ...missing]
-
-    for (const relPath of allFiles) {
-      const source = findSourceForFile(relPath, sourceMap)
-      if (!source || !await fse.pathExists(source.srcAbsPath)) {
-        logger.debug(`No source template found for: ${relPath} (orphaned)`)
-        applied.orphaned += 1
-        // Remove orphaned file from registry so it's no longer tracked
-        delete fileRegistry[relPath]
-        continue
-      }
-
-      const fullPath = path.join(targetDir, relPath)
-      const isModified = modified.includes(relPath)
-
-      // Backup modified files unless --force
-      if (isModified && !opts.force) {
-        const bakPath = `${fullPath}.bak.${Date.now()}`
-        try {
-          await fse.copy(fullPath, bakPath)
-          applied.backedUp += 1
-          logger.debug(`Backed up: ${relPath} -> ${path.basename(bakPath)}`)
-        } catch (err) {
-          logger.debug(`Failed to backup ${relPath}: ${err.message}`)
-        }
-      }
-
-      // Reinstall file
-      const success = await reinstallFile(targetDir, relPath, source, variables)
-      if (success) {
-        applied.updated += 1
-        // Recompute hash for updated file
-        const newHash = await computeFileHash(fullPath)
-        fileRegistry[relPath] = newHash
-
-        if (missing.includes(relPath)) {
-          applied.restored += 1
-        }
-      } else {
-        applied.failed += 1
-        logger.debug(`Source not found for: ${relPath}`)
-      }
-    }
-
-    // Discover and install new files from templates not yet in fileRegistry
-    const newFiles = await discoverNewFiles(sourceMap, fileRegistry)
-    if (newFiles.length > 0) {
-      logger.info(`  Discovered ${newFiles.length} new file(s) from updated templates`)
-      for (const { relPath, source } of newFiles) {
-        const success = await reinstallFile(targetDir, relPath, source, variables)
-        if (success) {
-          applied.added += 1
-          const fullPath = path.join(targetDir, relPath)
-          const newHash = await computeFileHash(fullPath)
-          fileRegistry[relPath] = newHash
-        } else {
-          applied.failed += 1
-          logger.debug(`Failed to install new file: ${relPath}`)
-        }
-      }
-    }
-
-    // Update manifest with new fileRegistry
-    if (manifest.cckit) {
-      manifest.cckit.fileRegistry = fileRegistry
-      manifest.cckit.lastUpdated = new Date().toISOString()
-    }
-    await fse.writeFile(manifestPath, YAML.stringify(manifest), 'utf8')
-
-    logger.newline()
-    if (applied.orphaned > 0) {
-      logger.warn(`${applied.orphaned} file(s) orphaned (module removed, no longer tracked)`)
-    }
-    logger.success(
-      `Applied: ${applied.updated} updated, ${applied.added} added, ${applied.restored} restored, ${applied.backedUp} backed up, ${applied.failed} failed`
-    )
-
-    return { checked: true, modified, unchanged, missing, applied }
-  }
-
-  // Non-dry-run, non-apply: update the lastUpdated timestamp only
-  if (manifest.cckit) {
-    manifest.cckit.lastUpdated = new Date().toISOString()
-  }
-  await fse.writeFile(manifestPath, YAML.stringify(manifest), 'utf8')
-
-  logger.success('Update complete.')
-  return { checked: true, modified, unchanged, missing }
-}
+import path from 'node:path'
+import { fileURLToPath } from 'node:url'
+import fse from 'fs-extra'
+import YAML from 'yaml'
+import { createLogger } from '../utils/logger.js'
+import { computeFileHash, interpolate, listFiles, TEXT_EXTENSIONS } from '../utils/fs.js'
+import { loadRegistry, resolveModules, getDefaultModules } from '../core/registry.js'
+import { ADAPTERS } from '../adapters/trae-adapter.js'
+
+const __dirname = path.dirname(fileURLToPath(import.meta.url))
+const CCKIT_ROOT = path.resolve(__dirname, '../..')
+
+/**
+ * Extract the fileRegistry from a manifest, handling both formats:
+ * - cckit.fileRegistry (produced by init command)
+ * - top-level fileRegistry (legacy/manual)
+ *
+ * @param {object} manifest - Parsed manifest object
+ * @returns {object} File registry map { relativePath: hash }
+ */
+function extractFileRegistry(manifest) {
+  if (manifest.cckit && manifest.cckit.fileRegistry) {
+    return manifest.cckit.fileRegistry
+  }
+  if (manifest.fileRegistry) {
+    return manifest.fileRegistry
+  }
+  return {}
+}
+
+/**
+ * Build a sourceMap from registry modules and config.
+ *
+ * Maps each target directory to its source template info:
+ *   { templateDir, adapter, prefix, moduleId }
+ *
+ * @param {object} registry - Loaded registry
+ * @param {object} config - Config from manifest (ides, languages, etc.)
+ * @returns {object} sourceMap keyed by targetDir
+ */
+function buildSourceMap(registry, config) {
+  const selectedIds = getDefaultModules(registry)
+  const resolved = resolveModules(registry, selectedIds)
+  const sourceMap = {}
+  const ides = config.ides || ['claude-code']
+
+  for (const mod of resolved) {
+    if (mod.targets) {
+      for (const ide of ides) {
+        const target = mod.targets[ide]
+        if (!target) continue
+
+        const templateDir = path.resolve(
+          CCKIT_ROOT,
+          target.templateDir || mod.templateDir
+        )
+        sourceMap[target.targetDir] = {
+          templateDir,
+          adapter: target.adapter ? ADAPTERS[target.adapter] : undefined,
+          prefix: target.prefix || undefined,
+          moduleId: mod.id
+        }
+      }
+    } else if (mod.ideTarget) {
+      if (ides.includes(mod.ideTarget)) {
+        sourceMap[mod.targetDir] = {
+          templateDir: path.resolve(CCKIT_ROOT, mod.templateDir),
+          adapter: undefined,
+          prefix: undefined,
+          moduleId: mod.id
+        }
+      }
+    } else {
+      sourceMap[mod.targetDir] = {
+        templateDir: path.resolve(CCKIT_ROOT, mod.templateDir),
+        adapter: undefined,
+        prefix: undefined,
+        moduleId: mod.id
+      }
+    }
+  }
+
+  return sourceMap
+}
+
+/**
+ * Find the source template file for an installed file.
+ *
+ * @param {string} relPath - Relative path of the installed file (e.g. '.claude/rules/common/coding-style.md')
+ * @param {object} sourceMap - Map from targetDir to source info
+ * @returns {object|null} { srcAbsPath, adapter } or null if not found
+ */
+function findSourceForFile(relPath, sourceMap) {
+  // Normalize to forward slashes for matching
+  const normalizedRel = relPath.replace(/\\/g, '/')
+
+  // Collect all matching entries, pick the one with the longest prefix (most specific)
+  let bestMatch = null
+  let bestPrefixLen = -1
+
+  for (const [targetDir, source] of Object.entries(sourceMap)) {
+    const normalizedTarget = targetDir.replace(/\\/g, '/')
+    // Check if file is under this target directory
+    // Handle both "dir/file" and "dir" == "." (root-level targets)
+    const prefix = normalizedTarget === '.'
+      ? ''
+      : normalizedTarget + '/'
+
+    if (prefix === '' ? true : normalizedRel.startsWith(prefix)) {
+      if (prefix.length > bestPrefixLen) {
+        const remainder = prefix === ''
+          ? normalizedRel
+          : normalizedRel.slice(prefix.length)
+
+        // If a prefix was applied to the filename during install, strip it to find source
+        let srcRelPath = remainder
+        if (source.prefix) {
+          const fileName = path.basename(remainder)
+          if (fileName.startsWith(source.prefix)) {
+            const originalName = fileName.slice(source.prefix.length)
+            const dir = path.dirname(remainder)
+            srcRelPath = dir === '.' ? originalName : path.join(dir, originalName)
+          }
+        }
+
+        const srcAbsPath = path.join(source.templateDir, srcRelPath)
+        bestPrefixLen = prefix.length
+        bestMatch = {
+          srcAbsPath,
+          adapter: source.adapter
+        }
+      }
+    }
+  }
+  return bestMatch
+}
+
+/**
+ * Reinstall a single file from its template source.
+ *
+ * @param {string} targetDir - Project root directory
+ * @param {string} relPath - Relative path of the file
+ * @param {object} source - { srcAbsPath, adapter }
+ * @param {object} variables - Template interpolation variables
+ * @returns {Promise<boolean>} true if successfully reinstalled
+ */
+async function reinstallFile(targetDir, relPath, source, variables) {
+  const destPath = path.join(targetDir, relPath)
+  const ext = path.extname(relPath).toLowerCase()
+
+  if (!await fse.pathExists(source.srcAbsPath)) {
+    return false
+  }
+
+  await fse.ensureDir(path.dirname(destPath))
+
+  if (TEXT_EXTENSIONS.has(ext)) {
+    let content = await fse.readFile(source.srcAbsPath, 'utf8')
+    content = interpolate(content, variables)
+    if (source.adapter) {
+      content = source.adapter(content, path.basename(relPath))
+    }
+    await fse.writeFile(destPath, content, 'utf8')
+  } else {
+    await fse.copy(source.srcAbsPath, destPath)
+  }
+
+  return true
+}
+
+/**
+ * Discover new files from templates that are not yet tracked in fileRegistry.
+ * This handles newly added modules/skills in cckit updates.
+ *
+ * @param {object} sourceMap - Map from targetDir to source info
+ * @param {object} fileRegistry - Current file registry from manifest
+ * @returns {Promise<Array<{ relPath: string, source: { srcAbsPath: string, adapter?: Function } }>>}
+ */
+async function discoverNewFiles(sourceMap, fileRegistry) {
+  const newFiles = []
+
+  for (const [targetDir, source] of Object.entries(sourceMap)) {
+    if (!await fse.pathExists(source.templateDir)) continue
+
+    const templateFiles = await listFiles(source.templateDir)
+
+    for (const relPath of templateFiles) {
+      const fileName = path.basename(relPath)
+      const dir = path.dirname(relPath)
+
+      // Apply prefix if configured (e.g. ecc-agent- prefix)
+      const installedName = source.prefix
+        ? `${source.prefix}${fileName}`
+        : fileName
+
+      // Build the installed relative path
+      const installedRelPath = targetDir === '.'
+        ? (dir === '.' ? installedName : `${dir}/${installedName}`)
+        : (dir === '.' ? `${targetDir}/${installedName}` : `${targetDir}/${dir}/${installedName}`)
+
+      const normalizedPath = installedRelPath.replace(/\\/g, '/')
+
+      if (!(normalizedPath in fileRegistry)) {
+        newFiles.push({
+          relPath: normalizedPath,
+          source: {
+            srcAbsPath: path.join(source.templateDir, relPath),
+            adapter: source.adapter,
+          },
+        })
+      }
+    }
+  }
+
+  return newFiles
+}
+
+/**
+ * Run the update command.
+ *
+ * Reads the installed manifest, compares current file hashes against
+ * the recorded fileRegistry, and reports which files are unchanged,
+ * modified by the user, or missing.
+ *
+ * When --apply is set, reinstalls files from cckit templates.
+ *
+ * @param {object} opts - Command options
+ * @param {string} [opts.dir] - Target directory (default: cwd)
+ * @param {boolean} [opts.dryRun] - Preview changes without applying
+ * @param {boolean} [opts.apply] - Reinstall files from templates
+ * @param {boolean} [opts.force] - Force overwrite modified files without backup
+ * @param {boolean} [opts.debug] - Enable debug output
+ * @returns {Promise<object>} Result with { checked, modified, unchanged, missing, applied? }
+ * @throws {Error} If cckit is not installed
+ */
+export async function runUpdate(opts = {}) {
+  const logger = createLogger({ debug: opts.debug })
+  const targetDir = path.resolve(opts.dir || process.cwd())
+  const manifestPath = path.join(targetDir, '_bmad', '_config', 'manifest.yaml')
+
+  if (!await fse.pathExists(manifestPath)) {
+    throw new Error('cckit is not installed. Run `cckit init` first.')
+  }
+
+  const manifestContent = await fse.readFile(manifestPath, 'utf8')
+  const manifest = YAML.parse(manifestContent)
+
+  logger.banner('cckit update')
+
+  const fileRegistry = extractFileRegistry(manifest)
+  const modified = []
+  const unchanged = []
+  const missing = []
+
+  for (const [relPath, expectedHash] of Object.entries(fileRegistry)) {
+    const fullPath = path.join(targetDir, relPath)
+
+    if (!await fse.pathExists(fullPath)) {
+      missing.push(relPath)
+      continue
+    }
+
+    const currentHash = await computeFileHash(fullPath)
+    if (currentHash !== expectedHash) {
+      modified.push(relPath)
+    } else {
+      unchanged.push(relPath)
+    }
+  }
+
+  // Report results
+  const totalFiles = Object.keys(fileRegistry).length
+  if (totalFiles > 0) {
+    logger.info(`  Checked ${totalFiles} registered file(s)`)
+  }
+
+  if (unchanged.length > 0) {
+    logger.success(`${unchanged.length} file(s) unchanged`)
+  }
+
+  if (modified.length > 0) {
+    logger.warn(`${modified.length} file(s) modified by user:`)
+    for (const f of modified) {
+      logger.info(`    ${f}`)
+    }
+  }
+
+  if (missing.length > 0) {
+    logger.warn(`${missing.length} file(s) missing:`)
+    for (const f of missing) {
+      logger.info(`    ${f}`)
+    }
+  }
+
+  if (totalFiles === 0) {
+    logger.info('  No files registered in manifest.')
+  } else if (modified.length === 0 && missing.length === 0) {
+    logger.success('All files match. Nothing to update.')
+  }
+
+  if (opts.dryRun) {
+    logger.info('\n  (dry run - no changes made)')
+    return { checked: true, modified, unchanged, missing }
+  }
+
+  // Apply mode: reinstall files from templates
+  if (opts.apply) {
+    const applied = { updated: 0, backedUp: 0, restored: 0, added: 0, failed: 0, orphaned: 0 }
+
+    let registry
+    let sourceMap
+    let variables
+
+    try {
+      registry = await loadRegistry()
+      const config = manifest.cckit && manifest.cckit.config
+        ? manifest.cckit.config
+        : {}
+
+      sourceMap = buildSourceMap(registry, config)
+      variables = {
+        user_name: config.user_name || '',
+        communication_language: config.communication_language || '',
+        document_output_language: config.document_output_language || '',
+        languages: Array.isArray(config.languages)
+          ? config.languages.join(', ')
+          : (config.languages || ''),
+        'project-root': '.'
+      }
+    } catch (err) {
+      logger.debug(`Failed to load registry for apply: ${err.message}`)
+      // Return result with empty applied if registry cannot be loaded
+      if (manifest.cckit) {
+        manifest.cckit.lastUpdated = new Date().toISOString()
+      }
+      await fse.writeFile(manifestPath, YAML.stringify(manifest), 'utf8')
+      logger.success('Update complete.')
+      return { checked: true, modified, unchanged, missing, applied }
+    }
+
+    // Process all files: unchanged + modified + missing
+    const allFiles = [...unchanged, ...modified, ...missing]
+
+    for (const relPath of allFiles) {
+      const source = findSourceForFile(relPath, sourceMap)
+      if (!source || !await fse.pathExists(source.srcAbsPath)) {
+        logger.debug(`No source template found for: ${relPath} (orphaned)`)
+        applied.orphaned += 1
+        // Remove orphaned file from registry so it's no longer tracked
+        delete fileRegistry[relPath]
+        continue
+      }
+
+      const fullPath = path.join(targetDir, relPath)
+      const isModified = modified.includes(relPath)
+
+      // Backup modified files unless --force
+      if (isModified && !opts.force) {
+        const bakPath = `${fullPath}.bak.${Date.now()}`
+        try {
+          await fse.copy(fullPath, bakPath)
+          applied.backedUp += 1
+          logger.debug(`Backed up: ${relPath} -> ${path.basename(bakPath)}`)
+        } catch (err) {
+          logger.debug(`Failed to backup ${relPath}: ${err.message}`)
+        }
+      }
+
+      // Reinstall file
+      const success = await reinstallFile(targetDir, relPath, source, variables)
+      if (success) {
+        applied.updated += 1
+        // Recompute hash for updated file
+        const newHash = await computeFileHash(fullPath)
+        fileRegistry[relPath] = newHash
+
+        if (missing.includes(relPath)) {
+          applied.restored += 1
+        }
+      } else {
+        applied.failed += 1
+        logger.debug(`Source not found for: ${relPath}`)
+      }
+    }
+
+    // Discover and install new files from templates not yet in fileRegistry
+    const newFiles = await discoverNewFiles(sourceMap, fileRegistry)
+    if (newFiles.length > 0) {
+      logger.info(`  Discovered ${newFiles.length} new file(s) from updated templates`)
+      for (const { relPath, source } of newFiles) {
+        const success = await reinstallFile(targetDir, relPath, source, variables)
+        if (success) {
+          applied.added += 1
+          const fullPath = path.join(targetDir, relPath)
+          const newHash = await computeFileHash(fullPath)
+          fileRegistry[relPath] = newHash
+        } else {
+          applied.failed += 1
+          logger.debug(`Failed to install new file: ${relPath}`)
+        }
+      }
+    }
+
+    // Update manifest with new fileRegistry
+    if (manifest.cckit) {
+      manifest.cckit.fileRegistry = fileRegistry
+      manifest.cckit.lastUpdated = new Date().toISOString()
+    }
+    await fse.writeFile(manifestPath, YAML.stringify(manifest), 'utf8')
+
+    logger.newline()
+    if (applied.orphaned > 0) {
+      logger.warn(`${applied.orphaned} file(s) orphaned (module removed, no longer tracked)`)
+    }
+    logger.success(
+      `Applied: ${applied.updated} updated, ${applied.added} added, ${applied.restored} restored, ${applied.backedUp} backed up, ${applied.failed} failed`
+    )
+
+    return { checked: true, modified, unchanged, missing, applied }
+  }
+
+  // Non-dry-run, non-apply: update the lastUpdated timestamp only
+  if (manifest.cckit) {
+    manifest.cckit.lastUpdated = new Date().toISOString()
+  }
+  await fse.writeFile(manifestPath, YAML.stringify(manifest), 'utf8')
+
+  logger.success('Update complete.')
+  return { checked: true, modified, unchanged, missing }
+}