ownkey 1.0.0 → 1.0.2

package/dist/core/apply/engine.js

@@ -1,194 +1,205 @@
-import { DiffParser, DiffValidator, DiffApplier } from '../diff/index.js';
+import { DiffParser, DiffApplier } from '../diff/index.js';
 import { BackupManager } from '../backup/index.js';
+import { InteractiveMode } from './interactive.js';
 import { dbClient } from '../../db/client.js';
 import { logger } from '../../utils/logger.js';
-import { join } from 'path';
+import { localStorage } from '../../storage/local.js';
+import { readFile, writeFile, mkdir } from 'fs/promises';
+import { existsSync, statSync } from 'fs';
+import { dirname, isAbsolute, relative, resolve } from 'path';
+const UUID_RE = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i;
 export class ApplyEngine {
     backupManager;
-    constructor() {
-        this.backupManager = new BackupManager();
+    constructor(backupManager) {
+        this.backupManager = backupManager ?? new BackupManager();
     }
-    /**
-     * Apply a suggestion to the codebase
-     */
     async applySuggestion(suggestionId, options = {}) {
-        const { dryRun = false, force = false, createBackup = true, } = options;
+        const { dryRun = false, force = false, createBackup = true, interactive = false } = options;
+        const fail = (error, warnings = []) => ({
+            success: false,
+            suggestionId,
+            filesModified: [],
+            error,
+            warnings,
+        });
         try {
-            logger.verbose(`Applying suggestion: ${suggestionId}`);
-            // 1. Load suggestion from database
+            // 1. Load
             const suggestion = await this.loadSuggestion(suggestionId);
             if (!suggestion) {
-                return {
-                    success: false,
-                    suggestionId,
-                    filesModified: [],
-                    error: 'Suggestion not found',
-                };
+                return fail(`Suggestion not found: ${suggestionId}. Run "ownkey apply" to list available IDs.`);
+            }
+            if (!suggestion.diff.trim()) {
+                return fail('This suggestion has no code change attached (the model gave advice only), so there is nothing to apply.');
             }
-            // 2. Parse diff
-            logger.verbose('Parsing diff...');
-            const diffs = DiffParser.parse(suggestion.diff);
+            if (suggestion.appliedAt && !dryRun && !force) {
+                return fail(`Already applied${suggestion.backupId ? ` (undo with: ownkey undo ${suggestion.backupId})` : ''}. Use --force to try again.`);
+            }
+            // 2. Parse
+            const diffs = DiffParser.parse(suggestion.diff).filter((d) => d.hunks.length > 0);
             if (diffs.length === 0) {
-                return {
-                    success: false,
-                    suggestionId,
-                    filesModified: [],
-                    error: 'No valid diff found in suggestion',
-                };
+                return fail('The suggestion diff could not be parsed as a unified diff');
+            }
+            // 3. Resolve paths against the project the suggestion was generated for
+            const root = this.resolveRoot(suggestion.projectPath);
+            const warnings = [];
+            const planned = [];
+            const errors = [];
+            for (const diff of diffs) {
+                let relPath = diff.filePath;
+                // Fall back to the suggestion's filePath when the diff header path does not exist
+                if (diffs.length === 1 &&
+                    suggestion.filePath &&
+                    diff.oldPath !== '/dev/null' &&
+                    !existsSync(resolve(root, relPath)) &&
+                    existsSync(resolve(root, suggestion.filePath))) {
+                    relPath = suggestion.filePath;
+                }
+                const absPath = resolve(root, relPath);
+                const rel = relative(root, absPath);
+                if (rel.startsWith('..') || isAbsolute(rel)) {
+                    errors.push(`Refusing to modify a file outside the project: ${relPath}`);
+                    continue;
+                }
+                const exists = existsSync(absPath);
+                if (!exists && diff.oldPath !== '/dev/null' && diff.hunks.some((h) => h.oldLines > 0)) {
+                    errors.push(`File not found: ${rel}`);
+                    continue;
+                }
+                const original = exists ? await readFile(absPath, 'utf-8') : null;
+                const result = DiffApplier.applyToContent(original, diff);
+                warnings.push(...result.warnings.map((w) => `${rel}: ${w}`));
+                if (!result.ok) {
+                    errors.push(...result.errors.map((e) => `${rel}: ${e}`));
+                    continue;
+                }
+                planned.push({ diff, absPath, relPath: rel, newContent: result.content });
+            }
+            if (errors.length > 0 && (!force || planned.length === 0)) {
+                return fail(`Cannot apply: ${errors.join('; ')}`, warnings);
             }
-            // 3. Validate all diffs
-            logger.verbose('Validating changes...');
-            const validationResults = await Promise.all(diffs.map((diff) => {
-                const filePath = join(process.cwd(), diff.filePath);
-                return DiffValidator.validate(diff, filePath);
-            }));
-            const allValid = validationResults.every((r) => r.valid);
-            const warnings = validationResults.flatMap((r) => r.warnings);
-            if (!allValid && !force) {
-                const errors = validationResults.flatMap((r) => r.errors);
-                return {
-                    success: false,
-                    suggestionId,
-                    filesModified: [],
-                    error: `Validation failed: ${errors.join(', ')}`,
-                    warnings,
-                };
+            if (errors.length > 0) {
+                warnings.push(...errors.map((e) => `Skipped (--force): ${e}`));
             }
-            // 4. Dry run mode - just show what would change
+            // 4. Dry run: show the change, write nothing
             if (dryRun) {
-                logger.info('Dry run mode - no changes will be made');
-                return {
-                    success: true,
-                    suggestionId,
-                    filesModified: diffs.map((d) => d.filePath),
-                    warnings,
-                };
+                for (const change of planned)
+                    InteractiveMode.showFullDiff(change.diff);
+                return { success: true, suggestionId, filesModified: planned.map((p) => p.relPath), warnings };
             }
-            // 5. Create backup
+            // 5. Interactive confirmation
+            let toWrite = planned;
+            if (interactive) {
+                if (!process.stdin.isTTY) {
+                    return fail('No terminal to confirm in. Re-run with --auto to apply, or --dry-run to preview.', warnings);
+                }
+                toWrite = [];
+                for (const change of planned) {
+                    const answer = await InteractiveMode.confirmApply(change.diff, { showFullDiff: true });
+                    if (answer.skipAll) {
+                        return { success: false, suggestionId, filesModified: [], warnings, skipped: true, quit: true, error: 'Cancelled' };
+                    }
+                    if (answer.confirmed)
+                        toWrite.push(change);
+                }
+                if (toWrite.length === 0) {
+                    return { success: false, suggestionId, filesModified: [], warnings, skipped: true, error: 'Skipped' };
+                }
+            }
+            // 6. Backup
             let backupId;
             if (createBackup) {
-                logger.verbose('Creating backup...');
-                const filesToBackup = diffs.map((d) => join(process.cwd(), d.filePath));
-                backupId = await this.backupManager.createBackup(filesToBackup, `apply-${suggestionId}`);
+                backupId = await this.backupManager.createBackup(toWrite.map((c) => c.absPath), `apply-${suggestionId}`, root);
                 logger.verbose(`Backup created: ${backupId}`);
             }
-            // 6. Apply changes
-            logger.verbose('Applying changes...');
+            // 7. Write, rolling back on any failure
             const filesModified = [];
-            const applyErrors = [];
-            for (const diff of diffs) {
-                const filePath = join(process.cwd(), diff.filePath);
-                const result = await DiffApplier.apply(diff, filePath);
-                if (result.success) {
-                    filesModified.push(result.filePath);
-                    logger.verbose(`Applied changes to ${result.filePath}`);
+            try {
+                for (const change of toWrite) {
+                    await mkdir(dirname(change.absPath), { recursive: true });
+                    await writeFile(change.absPath, change.newContent, 'utf-8');
+                    filesModified.push(change.relPath);
                 }
-                else {
-                    applyErrors.push(result.error || 'Unknown error');
-                    logger.error(`Failed to apply changes to ${result.filePath}: ${result.error}`);
+            }
+            catch (error) {
+                if (backupId) {
+                    logger.warn('Write failed, restoring backup...');
+                    await this.backupManager.restore(backupId);
                 }
+                return fail(`Write failed: ${error.message}`, warnings);
             }
-            // 7. If any apply failed, rollback
-            if (applyErrors.length > 0 && backupId) {
-                logger.warn('Some changes failed, rolling back...');
-                await this.backupManager.restore(backupId);
-                return {
-                    success: false,
-                    suggestionId,
-                    filesModified: [],
-                    backupId,
-                    error: `Apply failed: ${applyErrors.join(', ')}`,
-                    warnings,
-                };
+            // 8. Record
+            if (suggestion.localId) {
+                await localStorage
+                    .updateSuggestion(suggestion.localId, { appliedAt: new Date().toISOString(), backupId })
+                    .catch(() => undefined);
             }
-            // 8. Record apply in database
-            if (dbClient.isConnected()) {
-                await this.recordApply(suggestionId, filesModified, backupId);
+            if (dbClient.isConnected() && suggestion.dbId) {
+                await this.recordApply(suggestion.dbId, filesModified, backupId).catch((error) => logger.verbose(`Could not record apply in database: ${error.message}`));
             }
-            logger.success(`Successfully applied suggestion ${suggestionId}`);
-            return {
-                success: true,
-                suggestionId,
-                filesModified,
-                backupId,
-                warnings,
-            };
+            return { success: true, suggestionId, filesModified, backupId, warnings };
         }
         catch (error) {
-            logger.error('Apply engine error:', error);
-            return {
-                success: false,
-                suggestionId,
-                filesModified: [],
-                error: error.message,
-            };
+            logger.debug(`Apply engine error: ${error.stack}`);
+            return fail(error.message);
+        }
+    }
+    resolveRoot(projectPath) {
+        if (projectPath && existsSync(projectPath) && statSync(projectPath).isDirectory()) {
+            return projectPath;
+        }
+        if (projectPath && existsSync(projectPath)) {
+            return dirname(projectPath); // suggest was run on a single file
         }
+        return process.cwd();
     }
     /**
-     * Load suggestion from database OR local storage
+     * Load a suggestion from local storage (always written by suggest) or the optional database.
      */
     async loadSuggestion(suggestionId) {
-        // Try database first (if connected)
-        if (dbClient.isConnected()) {
-            try {
-                const sql = dbClient.getClient();
-                if (sql) {
-                    const results = await sql `
-                        SELECT diff FROM suggestions WHERE id = ${suggestionId}
-                    `;
-                    if (results.length > 0) {
-                        logger.verbose('Loaded suggestion from database');
-                        return results[0];
-                    }
-                }
-            }
-            catch (error) {
-                logger.warn(`Failed to load from database: ${error.message}`);
-            }
+        const stored = await localStorage.loadSuggestion(suggestionId).catch(() => null);
+        if (stored) {
+            return {
+                id: stored.id,
+                diff: stored.diff || '',
+                filePath: stored.filePath,
+                projectPath: stored.projectPath,
+                localId: stored.id,
+                dbId: stored.dbId,
+                appliedAt: stored.appliedAt,
+                backupId: stored.backupId,
+            };
         }
-        // Fall back to local storage
-        try {
-            const { localStorage } = await import('../../storage/local.js');
-            const stored = await localStorage.loadSuggestion(suggestionId);
-            if (stored && stored.diff) {
-                logger.verbose('Loaded suggestion from local storage');
-                return { diff: stored.diff };
+        if (dbClient.isConnected() && UUID_RE.test(suggestionId)) {
+            const sql = dbClient.getClient();
+            if (sql) {
+                const rows = await sql `
+                    SELECT s.id, s.diff, s.file_path, p.root_path
+                    FROM suggestions s JOIN projects p ON p.id = s.project_id
+                    WHERE s.id = ${suggestionId}
+                `;
+                if (rows.length > 0) {
+                    const row = rows[0];
+                    return {
+                        id: row.id,
+                        diff: row.diff || '',
+                        filePath: row.file_path,
+                        projectPath: row.root_path,
+                        dbId: row.id,
+                    };
+                }
             }
         }
-        catch (error) {
-            logger.warn(`Failed to load from local storage: ${error.message}`);
-        }
         return null;
     }
-    /**
-     * Record apply operation in database
-     */
-    async recordApply(suggestionId, filesModified, backupId) {
+    async recordApply(dbSuggestionId, filesModified, backupId) {
         const sql = dbClient.getClient();
-        if (!sql) {
+        if (!sql)
             return;
-        }
-        await sql `
-            INSERT INTO applies (
-                id,
-                suggestion_id,
-                files_modified,
-                backup_id,
-                applied_at,
-                status
-            ) VALUES (
-                gen_random_uuid(),
-                ${suggestionId},
-                ${JSON.stringify(filesModified)},
-                ${backupId || null},
-                NOW(),
-                'success'
-            )
+        await sql `
+            INSERT INTO applies (id, suggestion_id, files_modified, backup_id, applied_at, status)
+            VALUES (gen_random_uuid(), ${dbSuggestionId}, ${JSON.stringify(filesModified)}::jsonb, ${backupId || null}, NOW(), 'success')
         `;
     }
-    /**
-     * Get backup manager instance
-     */
     getBackupManager() {
         return this.backupManager;
     }

package/dist/core/apply/engine.js.map

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package/dist/core/apply/index.d.ts

@@ -1,3 +1,5 @@
-export { ApplyEngine, ApplyOptions, ApplyEngineResult } from './engine.js';
-export { InteractiveMode, InteractiveOptions, InteractiveResult } from './interactive.js';
+export { ApplyEngine } from './engine.js';
+export type { ApplyOptions, ApplyEngineResult } from './engine.js';
+export { InteractiveMode } from './interactive.js';
+export type { InteractiveOptions, InteractiveResult } from './interactive.js';
 //# sourceMappingURL=index.d.ts.map

package/dist/core/apply/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/core/apply/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAC3E,OAAO,EAAE,eAAe,EAAE,kBAAkB,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/core/apply/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAC1C,YAAY,EAAE,YAAY,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AACnE,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AACnD,YAAY,EAAE,kBAAkB,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC"}

package/dist/core/apply/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/core/apply/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAmC,MAAM,aAAa,CAAC;AAC3E,OAAO,EAAE,eAAe,EAAyC,MAAM,kBAAkB,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/core/apply/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAE1C,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC"}

package/dist/core/apply/interactive.d.ts

@@ -20,7 +20,7 @@ export declare class InteractiveMode {
     /**
      * Show full diff with syntax highlighting
      */
-    private static showFullDiff;
+    static showFullDiff(diff: ParsedDiff): void;
     /**
      * Print a single change line with color
      */

package/dist/core/apply/interactive.d.ts.map

@@ -1 +1 @@
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package/dist/core/apply/interactive.js.map

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package/dist/core/backup/index.d.ts

@@ -1,2 +1,3 @@
-export { BackupManager, BackupMetadata, BackupInfo } from './manager.js';
+export { BackupManager } from './manager.js';
+export type { BackupMetadata, BackupInfo } from './manager.js';
 //# sourceMappingURL=index.d.ts.map

package/dist/core/backup/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/core/backup/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/core/backup/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC;AAC7C,YAAY,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC"}

package/dist/core/backup/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/core/backup/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAA8B,MAAM,cAAc,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/core/backup/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,cAAc,CAAC"}

package/dist/core/backup/manager.d.ts

@@ -1,8 +1,13 @@
 export interface BackupMetadata {
     id: string;
     timestamp: Date;
+    /** Paths relative to `root` that existed and were copied */
     files: string[];
     reason: string;
+    /** Project root the paths are relative to (older backups: the cwd at restore time) */
+    root?: string;
+    /** Paths relative to `root` that did not exist before the apply; undo deletes them */
+    created?: string[];
 }
 export interface BackupInfo {
     id: string;
@@ -16,7 +21,7 @@ export declare class BackupManager {
     /**
      * Create a backup of files before applying changes
      */
-    createBackup(files: string[], reason?: string): Promise<string>;
+    createBackup(files: string[], reason?: string, root?: string): Promise<string>;
     /**
      * List all available backups
      */

package/dist/core/backup/manager.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"manager.d.ts","sourceRoot":"","sources":["../../../src/core/backup/manager.ts"],"names":[],"mappings":"AAKA,MAAM,WAAW,cAAc;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,SAAS,EAAE,IAAI,CAAC;IAChB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,UAAU;IACvB,EAAE,EAAE,MAAM,CAAC;IACX,SAAS,EAAE,IAAI,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;CAClB;AAED,qBAAa,aAAa;IACtB,OAAO,CAAC,SAAS,CAAS;gBAEd,SAAS,CAAC,EAAE,MAAM;IAI9B;;OAEG;IACG,YAAY,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE,MAAM,GAAE,MAAgB,GAAG,OAAO,CAAC,MAAM,CAAC;IAsC9E;;OAEG;IACG,WAAW,IAAI,OAAO,CAAC,UAAU,EAAE,CAAC;IAyB1C;;OAEG;IACG,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,GAAG,IAAI,CAAC;IAUzE;;OAEG;IACG,OAAO,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC;IAuBhE;;OAEG;IACG,YAAY,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAOnD;;OAEG;IACG,eAAe,CAAC,IAAI,GAAE,MAAW,GAAG,OAAO,CAAC,MAAM,CAAC;IAezD;;OAEG;IACH,OAAO,CAAC,gBAAgB;IAMxB;;OAEG;IACH,YAAY,IAAI,MAAM;CAGzB"}
+{"version":3,"file":"manager.d.ts","sourceRoot":"","sources":["../../../src/core/backup/manager.ts"],"names":[],"mappings":"AAKA,MAAM,WAAW,cAAc;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,SAAS,EAAE,IAAI,CAAC;IAChB,4DAA4D;IAC5D,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,sFAAsF;IACtF,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,sFAAsF;IACtF,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;CACtB;AAED,MAAM,WAAW,UAAU;IACvB,EAAE,EAAE,MAAM,CAAC;IACX,SAAS,EAAE,IAAI,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;CAClB;AAED,qBAAa,aAAa;IACtB,OAAO,CAAC,SAAS,CAAS;gBAEd,SAAS,CAAC,EAAE,MAAM;IAI9B;;OAEG;IACG,YAAY,CACd,KAAK,EAAE,MAAM,EAAE,EACf,MAAM,GAAE,MAAgB,EACxB,IAAI,GAAE,MAAsB,GAC7B,OAAO,CAAC,MAAM,CAAC;IAiClB;;OAEG;IACG,WAAW,IAAI,OAAO,CAAC,UAAU,EAAE,CAAC;IAyB1C;;OAEG;IACG,iBAAiB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,GAAG,IAAI,CAAC;IAUzE;;OAEG;IACG,OAAO,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC;IA2BhE;;OAEG;IACG,YAAY,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAOnD;;OAEG;IACG,eAAe,CAAC,IAAI,GAAE,MAAW,GAAG,OAAO,CAAC,MAAM,CAAC;IAezD;;OAEG;IACH,OAAO,CAAC,gBAAgB;IAMxB;;OAEG;IACH,YAAY,IAAI,MAAM;CAGzB"}

package/dist/core/backup/manager.js

@@ -1,5 +1,5 @@
 import { mkdir, copyFile, readdir, rm, readFile, writeFile } from 'fs/promises';
-import { join, dirname, relative } from 'path';
+import { join, dirname, relative, resolve } from 'path';
 import { homedir } from 'os';
 import { existsSync } from 'fs';
 export class BackupManager {
@@ -10,28 +10,31 @@ export class BackupManager {
     /**
      * Create a backup of files before applying changes
      */
-    async createBackup(files, reason = 'apply') {
+    async createBackup(files, reason = 'apply', root = process.cwd()) {
         const backupId = this.generateBackupId();
         const backupPath = join(this.backupDir, backupId);
-        // Create backup directory
         await mkdir(backupPath, { recursive: true });
-        // Copy each file
         const copiedFiles = [];
+        const createdFiles = [];
         for (const file of files) {
-            const relativePath = relative(process.cwd(), file);
-            const targetPath = join(backupPath, relativePath);
-            // Create parent directories
+            const relativePath = relative(root, resolve(root, file));
+            if (!existsSync(file)) {
+                // New file: nothing to copy, remember it so undo can remove it
+                createdFiles.push(relativePath);
+                continue;
+            }
+            const targetPath = join(backupPath, 'files', relativePath);
             await mkdir(dirname(targetPath), { recursive: true });
-            // Copy file
             await copyFile(file, targetPath);
             copiedFiles.push(relativePath);
         }
-        // Save metadata
         const metadata = {
             id: backupId,
             timestamp: new Date(),
             files: copiedFiles,
+            created: createdFiles,
             reason,
+            root,
         };
         await writeFile(join(backupPath, 'metadata.json'), JSON.stringify(metadata, null, 2), 'utf-8');
         return backupId;
@@ -52,7 +55,7 @@ export class BackupManager {
                 backups.push({
                     id: metadata.id,
                     timestamp: new Date(metadata.timestamp),
-                    fileCount: metadata.files.length,
+                    fileCount: metadata.files.length + (metadata.created?.length ?? 0),
                     reason: metadata.reason,
                 });
             }
@@ -80,17 +83,22 @@ export class BackupManager {
             throw new Error(`Backup not found: ${backupId}`);
         }
         const backupPath = join(this.backupDir, backupId);
-        const filesToRestore = files || metadata.files;
-        for (const file of filesToRestore) {
-            const sourcePath = join(backupPath, file);
-            const targetPath = join(process.cwd(), file);
+        const root = metadata.root || process.cwd();
+        // v1.0.0 backups stored files at the top level; v1.0.1+ under files/
+        const storeDir = existsSync(join(backupPath, 'files')) ? join(backupPath, 'files') : backupPath;
+        for (const file of files || metadata.files) {
+            const sourcePath = join(storeDir, file);
+            const targetPath = join(root, file);
             if (existsSync(sourcePath)) {
-                // Create parent directories
                 await mkdir(dirname(targetPath), { recursive: true });
-                // Restore file
                 await copyFile(sourcePath, targetPath);
             }
         }
+        if (!files) {
+            for (const file of metadata.created || []) {
+                await rm(join(root, file), { force: true });
+            }
+        }
     }
     /**
      * Delete a backup
@@ -120,8 +128,8 @@ export class BackupManager {
      */
     generateBackupId() {
         const now = new Date();
-        const timestamp = now.toISOString().replace(/[:.]/g, '-').slice(0, -5);
-        return timestamp;
+        const timestamp = now.toISOString().replace(/[:.]/g, '-').slice(0, -1);
+        return existsSync(join(this.backupDir, timestamp)) ? `${timestamp}-${Math.random().toString(36).slice(2, 6)}` : timestamp;
     }
     /**
      * Get backup directory path