feat(cli-flags): add --include-empty-directories flag

README.md

@@ -423,6 +423,7 @@ This format provides a clean, readable structure that is both human-friendly and
 - `--token-count-encoding <encoding>`: Specify token count encoding (e.g., `o200k_base`, `cl100k_base`)
 - `--verbose`: Enable verbose logging
 - `--instruction-file-path <path>`: Path to a file containing detailed custom instructions
+- `--include-empty-directories`: Include empty directories in the output
 
 Examples:
 

src/cli/actions/defaultAction.ts

@@ -145,6 +145,9 @@ const buildCliConfig = (options: CliOptions): RepomixConfigCli => {
   if (options.instructionFilePath) {
     cliConfig.output = { ...cliConfig.output, instructionFilePath: options.instructionFilePath };
   }
+  if (options.includeEmptyDirectories) {
+    cliConfig.output = { ...cliConfig.output, includeEmptyDirectories: options.includeEmptyDirectories };
+  }
 
   try {
     return repomixConfigCliSchema.parse(cliConfig);

src/cli/cliRun.ts

@@ -36,6 +36,7 @@ export interface CliOptions extends OptionValues {
   removeEmptyLines?: boolean;
   tokenCountEncoding?: string;
   instructionFilePath?: string;
+  includeEmptyDirectories?: boolean;
 }
 
 export const run = async () => {
@@ -71,6 +72,7 @@ export const run = async () => {
       )
       .option('--no-security-check', 'disable security check')
       .option('--instruction-file-path <path>', 'path to a file containing detailed custom instructions')
+      .option('--include-empty-directories', 'include empty directories in the output')
       .action((directory = '.', options: CliOptions = {}) => executeAction(directory, process.cwd(), options));
 
     await program.parseAsync(process.argv);

tests/cli/actions/defaultAction.test.ts

@@ -437,4 +437,24 @@ describe('defaultAction', () => {
       );
     });
   });
+
+  describe('includeEmptyDirectories flag', () => {
+    it('should handle --include-empty-directories flag', async () => {
+      const options: CliOptions = {
+        includeEmptyDirectories: true,
+      };
+
+      await runDefaultAction('.', process.cwd(), options);
+
+      expect(configLoader.mergeConfigs).toHaveBeenCalledWith(
+        process.cwd(),
+        expect.anything(),
+        expect.objectContaining({
+          output: {
+            includeEmptyDirectories: true,
+          },
+        }),
+      );
+    });
+  });
 });

tests/cli/cliRun.test.ts

@@ -268,5 +268,17 @@ describe('cliRun', () => {
         }),
       );
     });
+
+    test('should handle --include-empty-directories flag', async () => {
+      await executeAction('.', process.cwd(), { includeEmptyDirectories: true });
+
+      expect(defaultAction.runDefaultAction).toHaveBeenCalledWith(
+        '.',
+        process.cwd(),
+        expect.objectContaining({
+          includeEmptyDirectories: true,
+        }),
+      );
+    });
   });
 });