feat(cli,core,config): Add --include-full-directory-structure and full repository tree

README.md

@@ -627,6 +627,7 @@ Instruction
 - `--header-text <text>`: Custom text to include at the beginning of the output
 - `--instruction-file-path <path>`: Path to file containing custom instructions to include in output
 - `--include-empty-directories`: Include folders with no files in directory structure
+- `--include-full-directory-structure`: Show complete directory tree in output, including files not matched by --include patterns
 - `--no-git-sort-by-changes`: Don't sort files by git change frequency (default: most changed files first)
 - `--include-diffs`: Add git diff section showing working tree and staged changes
 - `--include-logs`: Add git commit history with messages and changed files

biome.json

@@ -1,5 +1,5 @@
 {
-  "$schema": "https://biomejs.dev/schemas/2.2.4/schema.json",
+  "$schema": "https://biomejs.dev/schemas/2.2.6/schema.json",
   "files": {
     "includes": [
       "bin/**",

src/cli/actions/defaultAction.ts

@@ -234,6 +234,13 @@ export const buildCliConfig = (options: CliOptions): RepomixConfigCli => {
     };
   }
 
+  if (options.includeFullDirectoryStructure) {
+    cliConfig.output = {
+      ...cliConfig.output,
+      includeFullDirectoryStructure: options.includeFullDirectoryStructure,
+    };
+  }
+
   // Only apply gitSortByChanges setting if explicitly set to false
   if (options.gitSortByChanges === false) {
     cliConfig.output = {

src/cli/cliRun.ts

@@ -117,6 +117,10 @@ export const run = async () => {
       .option('--header-text <text>', 'Custom text to include at the beginning of the output')
       .option('--instruction-file-path <path>', 'Path to file containing custom instructions to include in output')
       .option('--include-empty-directories', 'Include folders with no files in directory structure')
+      .option(
+        '--include-full-directory-structure',
+        'Show entire repository tree in the Directory Structure section, even when using --include patterns',
+      )
       .option(
         '--no-git-sort-by-changes',
         "Don't sort files by git change frequency (default: most changed files first)",

src/cli/types.ts

@@ -22,6 +22,7 @@ export interface CliOptions extends OptionValues {
   headerText?: string;
   instructionFilePath?: string;
   includeEmptyDirectories?: boolean;
+  includeFullDirectoryStructure?: boolean;
   gitSortByChanges?: boolean;
   includeDiffs?: boolean;
   includeLogs?: boolean;

src/config/configSchema.ts

@@ -39,6 +39,7 @@ export const repomixConfigBaseSchema = z.object({
       truncateBase64: z.boolean().optional(),
       copyToClipboard: z.boolean().optional(),
       includeEmptyDirectories: z.boolean().optional(),
+      includeFullDirectoryStructure: z.boolean().optional(),
       tokenCountTree: z.union([z.boolean(), z.number(), z.string()]).optional(),
       git: z
         .object({
@@ -100,6 +101,7 @@ export const repomixConfigDefaultSchema = z.object({
       truncateBase64: z.boolean().default(false),
       copyToClipboard: z.boolean().default(false),
       includeEmptyDirectories: z.boolean().optional(),
+      includeFullDirectoryStructure: z.boolean().default(false),
       tokenCountTree: z.union([z.boolean(), z.number(), z.string()]).default(false),
       git: z
         .object({

src/core/file/fileSearch.ts

@@ -304,8 +304,8 @@ export const getIgnorePatterns = async (rootDir: string, config: RepomixConfigMe
 
   // Add patterns from .git/info/exclude if useGitignore is enabled
   if (config.ignore.useGitignore) {
+    // Read .git/info/exclude file
     const excludeFilePath = path.join(rootDir, '.git', 'info', 'exclude');
-
     try {
       const excludeFileContent = await fs.readFile(excludeFilePath, 'utf8');
       const excludePatterns = parseIgnoreContent(excludeFileContent);
@@ -321,3 +321,93 @@ export const getIgnorePatterns = async (rootDir: string, config: RepomixConfigMe
 
   return Array.from(ignorePatterns);
 };
+
+/**
+ * Lists all directories in the given root directory, respecting ignore patterns.
+ * This function does not apply include patterns - it returns the full directory set subject to ignore rules.
+ *
+ * @param rootDir The root directory to scan
+ * @param config The merged configuration
+ * @returns Array of directory paths relative to rootDir
+ */
+export const listDirectories = async (rootDir: string, config: RepomixConfigMerged): Promise<string[]> => {
+  const [ignorePatterns, ignoreFilePatterns] = await Promise.all([
+    getIgnorePatterns(rootDir, config),
+    getIgnoreFilePatterns(config),
+  ]);
+
+  // Normalize ignore patterns to handle trailing slashes consistently
+  const normalizedIgnorePatterns = ignorePatterns.map(normalizeGlobPattern);
+
+  // Check if .git is a worktree reference
+  const gitPath = path.join(rootDir, '.git');
+  const isWorktree = await isGitWorktreeRef(gitPath);
+
+  // Modify ignore patterns for git worktree
+  const adjustedIgnorePatterns = [...normalizedIgnorePatterns];
+  if (isWorktree) {
+    // Remove '.git/**' pattern and add '.git' to ignore the reference file
+    const gitIndex = adjustedIgnorePatterns.indexOf('.git/**');
+    if (gitIndex !== -1) {
+      adjustedIgnorePatterns.splice(gitIndex, 1);
+      adjustedIgnorePatterns.push('.git');
+    }
+  }
+
+  const directories = await globby(['**/*'], {
+    cwd: rootDir,
+    onlyDirectories: true,
+    absolute: false,
+    dot: true,
+    followSymbolicLinks: false,
+    ignore: [...adjustedIgnorePatterns],
+    ignoreFiles: [...ignoreFilePatterns],
+  });
+
+  return sortPaths(directories);
+};
+
+/**
+ * Lists all files in the given root directory, respecting ignore patterns.
+ * This function does not apply include patterns - it returns the full file set subject to ignore rules.
+ *
+ * @param rootDir The root directory to scan
+ * @param config The merged configuration
+ * @returns Array of file paths relative to rootDir
+ */
+export const listFiles = async (rootDir: string, config: RepomixConfigMerged): Promise<string[]> => {
+  const [ignorePatterns, ignoreFilePatterns] = await Promise.all([
+    getIgnorePatterns(rootDir, config),
+    getIgnoreFilePatterns(config),
+  ]);
+
+  // Normalize ignore patterns to handle trailing slashes consistently
+  const normalizedIgnorePatterns = ignorePatterns.map(normalizeGlobPattern);
+
+  // Check if .git is a worktree reference
+  const gitPath = path.join(rootDir, '.git');
+  const isWorktree = await isGitWorktreeRef(gitPath);
+
+  // Modify ignore patterns for git worktree
+  const adjustedIgnorePatterns = [...normalizedIgnorePatterns];
+  if (isWorktree) {
+    // Remove '.git/**' pattern and add '.git' to ignore the reference file
+    const gitIndex = adjustedIgnorePatterns.indexOf('.git/**');
+    if (gitIndex !== -1) {
+      adjustedIgnorePatterns.splice(gitIndex, 1);
+      adjustedIgnorePatterns.push('.git');
+    }
+  }
+
+  const files = await globby(['**/*'], {
+    cwd: rootDir,
+    onlyFiles: true,
+    absolute: false,
+    dot: true,
+    followSymbolicLinks: false,
+    ignore: [...adjustedIgnorePatterns],
+    ignoreFiles: [...ignoreFilePatterns],
+  });
+
+  return sortPaths(files);
+};

src/core/output/outputGenerate.ts

@@ -4,7 +4,7 @@ import { XMLBuilder } from 'fast-xml-parser';
 import Handlebars from 'handlebars';
 import type { RepomixConfigMerged } from '../../config/configSchema.js';
 import { RepomixError } from '../../shared/errorHandle.js';
-import { type FileSearchResult, searchFiles } from '../file/fileSearch.js';
+import { type FileSearchResult, listDirectories, listFiles, searchFiles } from '../file/fileSearch.js';
 import { generateTreeString } from '../file/fileTreeGenerate.js';
 import type { ProcessedFile } from '../file/fileTypes.js';
 import type { GitDiffResult } from '../git/gitDiffHandle.js';
@@ -268,6 +268,11 @@ export const buildOutputGeneratorContext = async (
   processedFiles: ProcessedFile[],
   gitDiffResult: GitDiffResult | undefined = undefined,
   gitLogResult: GitLogResult | undefined = undefined,
+  deps = {
+    listDirectories,
+    listFiles,
+    searchFiles,
+  },
 ): Promise<OutputGeneratorContext> => {
   let repositoryInstruction = '';
 
@@ -280,27 +285,63 @@ export const buildOutputGeneratorContext = async (
     }
   }
 
-  let emptyDirPaths: string[] = [];
-  if (config.output.includeEmptyDirectories) {
+  // Determine if full-tree mode applies (only when directory structure is rendered)
+  const shouldUseFullTree =
+    config.output.directoryStructure === true &&
+    !!config.output.includeFullDirectoryStructure &&
+    (config.include?.length ?? 0) > 0;
+
+  // Paths to include in the directory tree visualization
+  let directoryPathsForTree: string[] = [];
+  let filePathsForTree: string[] = allFilePaths;
+
+  if (shouldUseFullTree) {
     try {
-      emptyDirPaths = (await Promise.all(rootDirs.map((rootDir) => searchFiles(rootDir, config)))).reduce(
+      // Collect all directories and all files from all roots
+      const [allDirectoriesByRoot, allFilesByRoot] = await Promise.all([
+        Promise.all(rootDirs.map((rootDir) => deps.listDirectories(rootDir, config))),
+        Promise.all(rootDirs.map((rootDir) => deps.listFiles(rootDir, config))),
+      ]);
+
+      // Merge, deduplicate, and sort for deterministic output
+      const allDirectories = Array.from(new Set(allDirectoriesByRoot.flat())).sort();
+      const allRepoFiles = Array.from(new Set(allFilesByRoot.flat()));
+
+      // Merge in any files that weren't part of the included files so they appear in the tree
+      const includedSet = new Set(allFilePaths);
+      const additionalFiles = allRepoFiles.filter((p) => !includedSet.has(p));
+
+      directoryPathsForTree = allDirectories;
+      filePathsForTree = Array.from(new Set([...allFilePaths, ...additionalFiles]));
+    } catch (error) {
+      throw new RepomixError(
+        `Failed to build full directory structure: ${error instanceof Error ? error.message : String(error)}`,
+        error instanceof Error ? { cause: error } : undefined,
+      );
+    }
+  } else if (config.output.directoryStructure && config.output.includeEmptyDirectories) {
+    // Default behavior: include empty directories only
+    try {
+      const merged = (await Promise.all(rootDirs.map((rootDir) => deps.searchFiles(rootDir, config)))).reduce(
         (acc: FileSearchResult, curr: FileSearchResult) =>
           ({
             filePaths: [...acc.filePaths, ...curr.filePaths],
             emptyDirPaths: [...acc.emptyDirPaths, ...curr.emptyDirPaths],
           }) as FileSearchResult,
         { filePaths: [], emptyDirPaths: [] },
       ).emptyDirPaths;
+      directoryPathsForTree = [...new Set(merged)].sort();
     } catch (error) {
-      if (error instanceof Error) {
-        throw new RepomixError(`Failed to search for empty directories: ${error.message}`);
-      }
+      throw new RepomixError(
+        `Failed to search for empty directories: ${error instanceof Error ? error.message : String(error)}`,
+        error instanceof Error ? { cause: error } : undefined,
+      );
     }
   }
 
   return {
     generationDate: new Date().toISOString(),
-    treeString: generateTreeString(allFilePaths, emptyDirPaths),
+    treeString: generateTreeString(filePathsForTree, directoryPathsForTree),
     processedFiles,
     config,
     instruction: repositoryInstruction,

src/core/security/workers/secretlint.d.ts

@@ -0,0 +1,6 @@
+declare module '@secretlint/secretlint-rule-preset-recommend' {
+  import type { SecretLintRulePresetCreator } from '@secretlint/types';
+
+  // Re-export as a preset creator without importing runtime Secretlint modules.
+  export const creator: SecretLintRulePresetCreator;
+}

tests/cli/actions/workers/defaultActionWorker.test.ts

@@ -51,6 +51,7 @@ describe('defaultActionWorker', () => {
       truncateBase64: false,
       copyToClipboard: false,
       includeEmptyDirectories: false,
+      includeFullDirectoryStructure: false,
       tokenCountTree: false,
       git: {
         sortByChanges: true,

tests/config/configSchema.test.ts

@@ -113,6 +113,7 @@ describe('configSchema', () => {
           showLineNumbers: false,
           truncateBase64: true,
           copyToClipboard: true,
+          includeFullDirectoryStructure: false,
           tokenCountTree: '100',
           git: {
             sortByChanges: true,
@@ -211,6 +212,7 @@ describe('configSchema', () => {
           showLineNumbers: true,
           truncateBase64: true,
           copyToClipboard: false,
+          includeFullDirectoryStructure: false,
           tokenCountTree: false,
           git: {
             sortByChanges: true,

tests/core/metrics/calculateGitDiffMetrics.test.ts

@@ -41,6 +41,7 @@ describe('calculateGitDiffMetrics', () => {
       truncateBase64: false,
       copyToClipboard: false,
       includeEmptyDirectories: false,
+      includeFullDirectoryStructure: false,
       tokenCountTree: false,
       git: {
         sortByChanges: true,

tests/core/metrics/calculateGitLogMetrics.test.ts

@@ -41,6 +41,7 @@ describe('calculateGitLogMetrics', () => {
       truncateBase64: false,
       copyToClipboard: false,
       includeEmptyDirectories: false,
+      includeFullDirectoryStructure: false,
       tokenCountTree: false,
       git: {
         sortByChanges: true,