fix(init): add .gitkeep files to empty directories

After running openspec init, the specs/, changes/, and changes/archive/
directories are empty. Since git does not track empty directories, these
folders are lost when the repository is cloned, causing openspec list to
recommend re-initialization.

Added .gitkeep file creation to createDirectoryStructure() for both
normal and extend modes, ensuring empty directories are preserved in
version control.

Fixes #269

Author: Br1an67

src/core/init.ts

@@ -465,6 +465,17 @@ export class InitCommand {
       for (const dir of directories) {
         await FileSystemUtils.createDirectory(dir);
       }
+
+      // Add .gitkeep to empty directories so they are tracked by git
+      const emptyDirs = [
+        path.join(openspecPath, 'specs'),
+        path.join(openspecPath, 'changes'),
+        path.join(openspecPath, 'changes', 'archive'),
+      ];
+      for (const dir of emptyDirs) {
+        const gitkeepPath = path.join(dir, '.gitkeep');
+        await FileSystemUtils.writeFile(gitkeepPath, '');
+      }
       return;
     }
 
@@ -481,6 +492,17 @@ export class InitCommand {
       await FileSystemUtils.createDirectory(dir);
     }
 
+    // Add .gitkeep to empty directories so they are tracked by git
+    const emptyDirs = [
+      path.join(openspecPath, 'specs'),
+      path.join(openspecPath, 'changes'),
+      path.join(openspecPath, 'changes', 'archive'),
+    ];
+    for (const dir of emptyDirs) {
+      const gitkeepPath = path.join(dir, '.gitkeep');
+      await FileSystemUtils.writeFile(gitkeepPath, '');
+    }
+
     spinner.stopAndPersist({
       symbol: PALETTE.white('▌'),
       text: PALETTE.white('OpenSpec structure created'),

test/core/init.test.ts

@@ -65,6 +65,17 @@ describe('InitCommand', () => {
       expect(await directoryExists(path.join(openspecPath, 'changes', 'archive'))).toBe(true);
     });
 
+    it('should create .gitkeep files in empty directories', async () => {
+      const initCommand = new InitCommand({ tools: 'claude', force: true });
+
+      await initCommand.execute(testDir);
+
+      const openspecPath = path.join(testDir, 'openspec');
+      expect(await fileExists(path.join(openspecPath, 'specs', '.gitkeep'))).toBe(true);
+      expect(await fileExists(path.join(openspecPath, 'changes', '.gitkeep'))).toBe(true);
+      expect(await fileExists(path.join(openspecPath, 'changes', 'archive', '.gitkeep'))).toBe(true);
+    });
+
     it('should create config.yaml with default schema', async () => {
       const initCommand = new InitCommand({ tools: 'claude', force: true });