fix: recreate missing openspec template files in extend mode

src/core/init.ts

@@ -427,9 +427,11 @@ export class InitCommand {
     } else {
       ora({ stream: process.stdout }).info(
         PALETTE.midGray(
-          'ℹ OpenSpec already initialized. Skipping base scaffolding.'
+          'ℹ OpenSpec already initialized. Checking for missing files...'
         )
       );
+      await this.createDirectoryStructure(openspecPath);
+      await this.ensureTemplateFiles(openspecPath, config);
     }
 
     // Step 2: Configure AI tools
@@ -693,6 +695,31 @@ export class InitCommand {
     }
   }
 
+  private async ensureTemplateFiles(
+    openspecPath: string,
+    config: OpenSpecConfig
+  ): Promise<void> {
+    const context: ProjectContext = {
+      // Could be enhanced with prompts for project details
+    };
+
+    const templates = TemplateManager.getTemplates(context);
+
+    for (const template of templates) {
+      const filePath = path.join(openspecPath, template.path);
+
+      // Only write if file doesn't exist
+      if (!(await FileSystemUtils.fileExists(filePath))) {
+        const content =
+          typeof template.content === 'function'
+            ? template.content(context)
+            : template.content;
+
+        await FileSystemUtils.writeFile(filePath, content);
+      }
+    }
+  }
+
   private async configureAITools(
     projectPath: string,
     openspecDir: string,

test/core/init.test.ts

@@ -579,6 +579,48 @@ describe('InitCommand', () => {
       await expect(initCommand.execute(testDir)).resolves.toBeUndefined();
     });
 
+    it('should recreate deleted openspec/AGENTS.md in extend mode', async () => {
+      queueSelections('claude', DONE, DONE);
+
+      // First init
+      await initCommand.execute(testDir);
+
+      const openspecAgentsPath = path.join(testDir, 'openspec', 'AGENTS.md');
+      expect(await fileExists(openspecAgentsPath)).toBe(true);
+
+      // Delete the file
+      await fs.unlink(openspecAgentsPath);
+      expect(await fileExists(openspecAgentsPath)).toBe(false);
+
+      // Run init again - should recreate the file
+      await initCommand.execute(testDir);
+      expect(await fileExists(openspecAgentsPath)).toBe(true);
+
+      const content = await fs.readFile(openspecAgentsPath, 'utf-8');
+      expect(content).toContain('OpenSpec Instructions');
+    });
+
+    it('should recreate deleted openspec/project.md in extend mode', async () => {
+      queueSelections('claude', DONE, DONE);
+
+      // First init
+      await initCommand.execute(testDir);
+
+      const projectMdPath = path.join(testDir, 'openspec', 'project.md');
+      expect(await fileExists(projectMdPath)).toBe(true);
+
+      // Delete the file
+      await fs.unlink(projectMdPath);
+      expect(await fileExists(projectMdPath)).toBe(false);
+
+      // Run init again - should recreate the file
+      await initCommand.execute(testDir);
+      expect(await fileExists(projectMdPath)).toBe(true);
+
+      const content = await fs.readFile(projectMdPath, 'utf-8');
+      expect(content).toContain('Project Context');
+    });
+
     it('should handle non-existent target directory', async () => {
       queueSelections('claude', DONE);