feat: add directory support and .lnk tracking

- Add directory management support alongside individual files

- Implement .lnk tracking file to manage files and directories

- Update filesystem validation to allow directories

- Add MoveDirectory method for handling directory operations

- Use git rm --cached to properly handle directory removal

- Add comprehensive tests for directory operations

- Update README with directory support documentation

- All 20 integration tests passing

Breaking: None (backward compatible)

Resolves: Git limitation of not tracking directories

README.md

@@ -9,7 +9,7 @@ Git-native dotfiles management that won't break your setup. Zero config, zero bl
 lnk init && lnk add ~/.vimrc && lnk push
 ```
 
-[![Tests](https://img.shields.io/badge/tests-17%20passing-green)](./test) [![Go](https://img.shields.io/badge/go-1.21+-blue)](https://golang.org) [![License](https://img.shields.io/badge/license-MIT-blue)](LICENSE)
+[![Tests](https://img.shields.io/badge/tests-20%20passing-green)](./test) [![Go](https://img.shields.io/badge/go-1.21+-blue)](https://golang.org) [![License](https://img.shields.io/badge/license-MIT-blue)](LICENSE)
 
 ## Why Lnk?
 
@@ -22,8 +22,9 @@ While chezmoi offers 100+ features and Home Manager requires learning Nix, **Lnk
 - ⚡ **Zero friction**: No YAML configs, no templates, no learning curve
 - 🔧 **Git-native**: Clean commits, standard workflow, no abstractions
 - 📦 **Zero dependencies**: Single binary vs Python/Node/Ruby runtimes
-- 🚀 **Production ready**: 17 integration tests, proper error handling
+- 🚀 **Production ready**: 20 integration tests, proper error handling
 - 🔄 **Smart sync**: Built-in status tracking and seamless multi-machine workflow
+- 📁 **Directory support**: Manage entire config directories or individual files
 
 **The market gap**: Tools are either too simple (and unsafe) or too complex (and overwhelming). Lnk is the **Goldilocks solution** – just right for developers who want reliability without complexity.
 
@@ -98,10 +99,11 @@ lnk init -r git@github.com:username/dotfiles.git # With remote
 - ✅ Protects existing repositories from overwrite
 - ✅ Validates remote conflicts before changes
 
-### Manage Files
+### Manage Files & Directories
 
 ```bash
 lnk add ~/.bashrc ~/.vimrc ~/.tmux.conf    # Add multiple files
+lnk add ~/.config/nvim ~/.ssh               # Add entire directories
 lnk rm ~/.bashrc                           # Remove from management
 ```
 
@@ -246,7 +248,7 @@ internal/
 
 ### What Makes It Robust
 
-- **17 integration tests** covering edge cases and error conditions
+- **20 integration tests** covering edge cases and error conditions
 - **Zero external dependencies** at runtime
 - **Atomic operations** with automatic rollback on failure
 - **Relative symlinks** for cross-platform compatibility

internal/core/lnk.go

@@ -4,6 +4,8 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"sort"
+	"strings"
 
 	"github.com/yarlson/lnk/internal/fs"
 	"github.com/yarlson/lnk/internal/git"
@@ -76,9 +78,9 @@ func (l *Lnk) AddRemote(name, url string) error {
 	return nil
 }
 
-// Add moves a file to the repository and creates a symlink
+// Add moves a file or directory to the repository and creates a symlink
 func (l *Lnk) Add(filePath string) error {
-	// Validate the file
+	// Validate the file or directory
 	if err := l.fs.ValidateFileForAdd(filePath); err != nil {
 		return err
 	}
@@ -93,30 +95,89 @@ func (l *Lnk) Add(filePath string) error {
 	basename := filepath.Base(absPath)
 	destPath := filepath.Join(l.repoPath, basename)
 
-	// Move file to repository
+	// Check if it's a directory or file
+	info, err := os.Stat(absPath)
+	if err != nil {
+		return fmt.Errorf("failed to stat path: %w", err)
+	}
+
+	// Move to repository (handles both files and directories)
+	if info.IsDir() {
+		if err := l.fs.MoveDirectory(absPath, destPath); err != nil {
+			return fmt.Errorf("failed to move directory to repository: %w", err)
+		}
+	} else {
 		if err := l.fs.MoveFile(absPath, destPath); err != nil {
 			return fmt.Errorf("failed to move file to repository: %w", err)
 		}
+	}
 
 	// Create symlink
 	if err := l.fs.CreateSymlink(destPath, absPath); err != nil {
-		// Try to restore the file if symlink creation fails
+		// Try to restore the original if symlink creation fails
+		if info.IsDir() {
+			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
+		} else {
 			_ = l.fs.MoveFile(destPath, absPath) // Ignore error in cleanup
+		}
 		return fmt.Errorf("failed to create symlink: %w", err)
 	}
 
-	// Stage and commit the file
-	if err := l.git.AddAndCommit(basename, fmt.Sprintf("lnk: added %s", basename)); err != nil {
+	// Add to .lnk tracking file
+	if err := l.addManagedItem(absPath); err != nil {
+		// Try to restore the original state if tracking fails
+		_ = os.Remove(absPath) // Ignore error in cleanup
+		if info.IsDir() {
+			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
+		} else {
+			_ = l.fs.MoveFile(destPath, absPath) // Ignore error in cleanup
+		}
+		return fmt.Errorf("failed to update tracking file: %w", err)
+	}
+
+	// Add both the item and .lnk file to git in a single commit
+	if err := l.git.Add(basename); err != nil {
+		// Try to restore the original state if git add fails
+		_ = os.Remove(absPath)           // Ignore error in cleanup
+		_ = l.removeManagedItem(absPath) // Ignore error in cleanup
+		if info.IsDir() {
+			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
+		} else {
+			_ = l.fs.MoveFile(destPath, absPath) // Ignore error in cleanup
+		}
+		return fmt.Errorf("failed to add item to git: %w", err)
+	}
+
+	// Add .lnk file to the same commit
+	if err := l.git.Add(".lnk"); err != nil {
+		// Try to restore the original state if git add fails
+		_ = os.Remove(absPath)           // Ignore error in cleanup
+		_ = l.removeManagedItem(absPath) // Ignore error in cleanup
+		if info.IsDir() {
+			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
+		} else {
+			_ = l.fs.MoveFile(destPath, absPath) // Ignore error in cleanup
+		}
+		return fmt.Errorf("failed to add .lnk file to git: %w", err)
+	}
+
+	// Commit both changes together
+	if err := l.git.Commit(fmt.Sprintf("lnk: added %s", basename)); err != nil {
 		// Try to restore the original state if commit fails
 		_ = os.Remove(absPath)           // Ignore error in cleanup
+		_ = l.removeManagedItem(absPath) // Ignore error in cleanup
+		if info.IsDir() {
+			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
+		} else {
 			_ = l.fs.MoveFile(destPath, absPath) // Ignore error in cleanup
+		}
 		return fmt.Errorf("failed to commit changes: %w", err)
 	}
 
 	return nil
 }
 
-// Remove removes a symlink and restores the original file
+// Remove removes a symlink and restores the original file or directory
 func (l *Lnk) Remove(filePath string) error {
 	// Get absolute path
 	absPath, err := filepath.Abs(filePath)
@@ -142,22 +203,46 @@ func (l *Lnk) Remove(filePath string) error {
 
 	basename := filepath.Base(target)
 
+	// Check if target is a directory or file
+	info, err := os.Stat(target)
+	if err != nil {
+		return fmt.Errorf("failed to stat target: %w", err)
+	}
+
 	// Remove the symlink
 	if err := os.Remove(absPath); err != nil {
 		return fmt.Errorf("failed to remove symlink: %w", err)
 	}
 
-	// Move file back from repository
+	// Remove from .lnk tracking file
+	if err := l.removeManagedItem(absPath); err != nil {
+		return fmt.Errorf("failed to update tracking file: %w", err)
+	}
+
+	// Remove from Git first (while the item is still in the repository)
+	if err := l.git.Remove(basename); err != nil {
+		return fmt.Errorf("failed to remove from git: %w", err)
+	}
+
+	// Add .lnk file to the same commit
+	if err := l.git.Add(".lnk"); err != nil {
+		return fmt.Errorf("failed to add .lnk file to git: %w", err)
+	}
+
+	// Commit both changes together
+	if err := l.git.Commit(fmt.Sprintf("lnk: removed %s", basename)); err != nil {
+		return fmt.Errorf("failed to commit changes: %w", err)
+	}
+
+	// Move back from repository (handles both files and directories)
+	if info.IsDir() {
+		if err := l.fs.MoveDirectory(target, absPath); err != nil {
+			return fmt.Errorf("failed to restore directory: %w", err)
+		}
+	} else {
 		if err := l.fs.MoveFile(target, absPath); err != nil {
 			return fmt.Errorf("failed to restore file: %w", err)
 		}
-
-	// Remove from Git and commit
-	if err := l.git.RemoveAndCommit(basename, fmt.Sprintf("lnk: removed %s", basename)); err != nil {
-		// Try to restore the symlink if commit fails
-		_ = l.fs.MoveFile(absPath, target)      // Ignore error in cleanup
-		_ = l.fs.CreateSymlink(target, absPath) // Ignore error in cleanup
-		return fmt.Errorf("failed to commit changes: %w", err)
 	}
 
 	return nil
@@ -249,30 +334,24 @@ func (l *Lnk) Pull() ([]string, error) {
 	return restored, nil
 }
 
-// RestoreSymlinks finds all files in the repository and ensures they have proper symlinks
+// RestoreSymlinks finds all managed items from .lnk file and ensures they have proper symlinks
 func (l *Lnk) RestoreSymlinks() ([]string, error) {
 	var restored []string
 
-	// Read all files in the repository
-	entries, err := os.ReadDir(l.repoPath)
+	// Get managed items from .lnk file
+	managedItems, err := l.getManagedItems()
 	if err != nil {
-		return nil, fmt.Errorf("failed to read repository directory: %w", err)
+		return nil, fmt.Errorf("failed to get managed items: %w", err)
 	}
 
-	for _, entry := range entries {
-		// Skip hidden files and directories (like .git)
-		if entry.Name()[0] == '.' {
-			continue
-		}
+	for _, itemName := range managedItems {
+		repoItem := filepath.Join(l.repoPath, itemName)
 
-		// Skip directories
-		if entry.IsDir() {
-			continue
+		// Check if item exists in repository
+		if _, err := os.Stat(repoItem); os.IsNotExist(err) {
+			continue // Skip missing items
 		}
 
-		filename := entry.Name()
-		repoFile := filepath.Join(l.repoPath, filename)
-
 		// Determine where the symlink should be
 		// For config files, we'll place them in the user's home directory
 		homeDir, err := os.UserHomeDir()
@@ -280,26 +359,26 @@ func (l *Lnk) RestoreSymlinks() ([]string, error) {
 			return nil, fmt.Errorf("failed to get home directory: %w", err)
 		}
 
-		symlinkPath := filepath.Join(homeDir, filename)
+		symlinkPath := filepath.Join(homeDir, itemName)
 
 		// Check if symlink already exists and is correct
-		if l.isValidSymlink(symlinkPath, repoFile) {
+		if l.isValidSymlink(symlinkPath, repoItem) {
 			continue
 		}
 
 		// Remove existing file/symlink if it exists
 		if _, err := os.Lstat(symlinkPath); err == nil {
-			if err := os.Remove(symlinkPath); err != nil {
-				return nil, fmt.Errorf("failed to remove existing file %s: %w", symlinkPath, err)
+			if err := os.RemoveAll(symlinkPath); err != nil {
+				return nil, fmt.Errorf("failed to remove existing item %s: %w", symlinkPath, err)
 			}
 		}
 
 		// Create symlink
-		if err := l.fs.CreateSymlink(repoFile, symlinkPath); err != nil {
-			return nil, fmt.Errorf("failed to create symlink for %s: %w", filename, err)
+		if err := l.fs.CreateSymlink(repoItem, symlinkPath); err != nil {
+			return nil, fmt.Errorf("failed to create symlink for %s: %w", itemName, err)
 		}
 
-		restored = append(restored, filename)
+		restored = append(restored, itemName)
 	}
 
 	return restored, nil
@@ -341,3 +420,99 @@ func (l *Lnk) isValidSymlink(symlinkPath, expectedTarget string) bool {
 
 	return targetAbs == expectedAbs
 }
+
+// getManagedItems returns the list of managed files and directories from .lnk file
+func (l *Lnk) getManagedItems() ([]string, error) {
+	lnkFile := filepath.Join(l.repoPath, ".lnk")
+
+	// If .lnk file doesn't exist, return empty list
+	if _, err := os.Stat(lnkFile); os.IsNotExist(err) {
+		return []string{}, nil
+	}
+
+	content, err := os.ReadFile(lnkFile)
+	if err != nil {
+		return nil, fmt.Errorf("failed to read .lnk file: %w", err)
+	}
+
+	if len(content) == 0 {
+		return []string{}, nil
+	}
+
+	lines := strings.Split(strings.TrimSpace(string(content)), "\n")
+	var items []string
+	for _, line := range lines {
+		line = strings.TrimSpace(line)
+		if line != "" {
+			items = append(items, line)
+		}
+	}
+
+	return items, nil
+}
+
+// addManagedItem adds an item to the .lnk tracking file
+func (l *Lnk) addManagedItem(itemPath string) error {
+	// Get current items
+	items, err := l.getManagedItems()
+	if err != nil {
+		return fmt.Errorf("failed to get managed items: %w", err)
+	}
+
+	// Get the basename for storage
+	basename := filepath.Base(itemPath)
+
+	// Check if already exists
+	for _, item := range items {
+		if item == basename {
+			return nil // Already managed
+		}
+	}
+
+	// Add new item
+	items = append(items, basename)
+
+	// Sort for consistent ordering
+	sort.Strings(items)
+
+	return l.writeManagedItems(items)
+}
+
+// removeManagedItem removes an item from the .lnk tracking file
+func (l *Lnk) removeManagedItem(itemPath string) error {
+	// Get current items
+	items, err := l.getManagedItems()
+	if err != nil {
+		return fmt.Errorf("failed to get managed items: %w", err)
+	}
+
+	// Get the basename for removal
+	basename := filepath.Base(itemPath)
+
+	// Remove item
+	var newItems []string
+	for _, item := range items {
+		if item != basename {
+			newItems = append(newItems, item)
+		}
+	}
+
+	return l.writeManagedItems(newItems)
+}
+
+// writeManagedItems writes the list of managed items to .lnk file
+func (l *Lnk) writeManagedItems(items []string) error {
+	lnkFile := filepath.Join(l.repoPath, ".lnk")
+
+	content := strings.Join(items, "\n")
+	if len(items) > 0 {
+		content += "\n"
+	}
+
+	err := os.WriteFile(lnkFile, []byte(content), 0644)
+	if err != nil {
+		return fmt.Errorf("failed to write .lnk file: %w", err)
+	}
+
+	return nil
+}

internal/fs/filesystem.go

@@ -15,7 +15,7 @@ func New() *FileSystem {
 	return &FileSystem{}
 }
 
-// ValidateFileForAdd validates that a file can be added to lnk
+// ValidateFileForAdd validates that a file or directory can be added to lnk
 func (fs *FileSystem) ValidateFileForAdd(filePath string) error {
 	// Check if file exists
 	info, err := os.Stat(filePath)
@@ -26,14 +26,9 @@ func (fs *FileSystem) ValidateFileForAdd(filePath string) error {
 		return fmt.Errorf("failed to stat file: %w", err)
 	}
 
-	// Check if it's a directory
-	if info.IsDir() {
-		return fmt.Errorf("directories are not supported: %s", filePath)
-	}
-
-	// Check if it's a regular file
-	if !info.Mode().IsRegular() {
-		return fmt.Errorf("only regular files are supported: %s", filePath)
+	// Allow both regular files and directories
+	if !info.Mode().IsRegular() && !info.IsDir() {
+		return fmt.Errorf("only regular files and directories are supported: %s", filePath)
 	}
 
 	return nil
@@ -110,3 +105,29 @@ func (fs *FileSystem) CreateSymlink(target, linkPath string) error {
 
 	return nil
 }
+
+// MoveDirectory moves a directory from source to destination recursively
+func (fs *FileSystem) MoveDirectory(src, dst string) error {
+	// Check if source is a directory
+	info, err := os.Stat(src)
+	if err != nil {
+		return fmt.Errorf("failed to stat source: %w", err)
+	}
+
+	if !info.IsDir() {
+		return fmt.Errorf("source is not a directory: %s", src)
+	}
+
+	// Ensure destination parent directory exists
+	dstParent := filepath.Dir(dst)
+	if err := os.MkdirAll(dstParent, 0755); err != nil {
+		return fmt.Errorf("failed to create destination parent directory: %w", err)
+	}
+
+	// Use os.Rename which works for directories
+	if err := os.Rename(src, dst); err != nil {
+		return fmt.Errorf("failed to move directory from %s to %s: %w", src, dst, err)
+	}
+
+	return nil
+}

internal/git/git.go

@@ -130,7 +130,7 @@ func (g *Git) IsLnkRepository() bool {
 // AddAndCommit stages a file and commits it
 func (g *Git) AddAndCommit(filename, message string) error {
 	// Stage the file
-	if err := g.add(filename); err != nil {
+	if err := g.Add(filename); err != nil {
 		return err
 	}
 
@@ -145,7 +145,7 @@ func (g *Git) AddAndCommit(filename, message string) error {
 // RemoveAndCommit removes a file from Git and commits the change
 func (g *Git) RemoveAndCommit(filename, message string) error {
 	// Remove the file from Git
-	if err := g.remove(filename); err != nil {
+	if err := g.Remove(filename); err != nil {
 		return err
 	}
 
@@ -157,8 +157,8 @@ func (g *Git) RemoveAndCommit(filename, message string) error {
 	return nil
 }
 
-// add stages a file
-func (g *Git) add(filename string) error {
+// Add stages a file
+func (g *Git) Add(filename string) error {
 	cmd := exec.Command("git", "add", filename)
 	cmd.Dir = g.repoPath
 
@@ -170,9 +170,21 @@ func (g *Git) add(filename string) error {
 	return nil
 }
 
-// remove removes a file from Git tracking
-func (g *Git) remove(filename string) error {
-	cmd := exec.Command("git", "rm", filename)
+// Remove removes a file from Git tracking
+func (g *Git) Remove(filename string) error {
+	// Check if it's a directory that needs -r flag
+	fullPath := filepath.Join(g.repoPath, filename)
+	info, err := os.Stat(fullPath)
+
+	var cmd *exec.Cmd
+	if err == nil && info.IsDir() {
+		// Use -r and --cached flags for directories (only remove from git, not filesystem)
+		cmd = exec.Command("git", "rm", "-r", "--cached", filename)
+	} else {
+		// Regular file (only remove from git, not filesystem)
+		cmd = exec.Command("git", "rm", "--cached", filename)
+	}
+
 	cmd.Dir = g.repoPath
 
 	output, err := cmd.CombinedOutput()

test/integration_test.go

@@ -169,14 +169,230 @@ func (suite *LnkIntegrationTestSuite) TestAddDirectory() {
 	err := suite.lnk.Init()
 	suite.Require().NoError(err)
 
-	// Create a directory
+	// Create a directory with files
 	testDir := filepath.Join(suite.tempDir, "testdir")
 	err = os.MkdirAll(testDir, 0755)
 	suite.Require().NoError(err)
 
+	// Add files to the directory
+	testFile1 := filepath.Join(testDir, "file1.txt")
+	err = os.WriteFile(testFile1, []byte("content1"), 0644)
+	suite.Require().NoError(err)
+
+	testFile2 := filepath.Join(testDir, "file2.txt")
+	err = os.WriteFile(testFile2, []byte("content2"), 0644)
+	suite.Require().NoError(err)
+
+	// Add the directory - should now succeed
 	err = suite.lnk.Add(testDir)
-	suite.Error(err)
-	suite.Contains(err.Error(), "directories are not supported")
+	suite.Require().NoError(err)
+
+	// Check that the directory is now a symlink
+	info, err := os.Lstat(testDir)
+	suite.Require().NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	// Check that the directory exists in the repo
+	repoDir := filepath.Join(suite.tempDir, "lnk", "testdir")
+	suite.DirExists(repoDir)
+
+	// Check that files are preserved
+	repoFile1 := filepath.Join(repoDir, "file1.txt")
+	repoFile2 := filepath.Join(repoDir, "file2.txt")
+	suite.FileExists(repoFile1)
+	suite.FileExists(repoFile2)
+
+	content1, err := os.ReadFile(repoFile1)
+	suite.Require().NoError(err)
+	suite.Equal("content1", string(content1))
+
+	content2, err := os.ReadFile(repoFile2)
+	suite.Require().NoError(err)
+	suite.Equal("content2", string(content2))
+
+	// Check that .lnk file was created and contains the directory
+	lnkFile := filepath.Join(suite.tempDir, "lnk", ".lnk")
+	suite.FileExists(lnkFile)
+
+	lnkContent, err := os.ReadFile(lnkFile)
+	suite.Require().NoError(err)
+	suite.Contains(string(lnkContent), "testdir")
+
+	// Check that Git commit was made
+	commits, err := suite.lnk.GetCommits()
+	suite.Require().NoError(err)
+	suite.Len(commits, 1)
+	suite.Contains(commits[0], "lnk: added testdir")
+}
+
+func (suite *LnkIntegrationTestSuite) TestRemoveDirectory() {
+	// Initialize and add a directory first
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	testDir := filepath.Join(suite.tempDir, "testdir")
+	err = os.MkdirAll(testDir, 0755)
+	suite.Require().NoError(err)
+
+	testFile := filepath.Join(testDir, "config.txt")
+	content := "test config"
+	err = os.WriteFile(testFile, []byte(content), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add(testDir)
+	suite.Require().NoError(err)
+
+	// Now remove the directory
+	err = suite.lnk.Remove(testDir)
+	suite.Require().NoError(err)
+
+	// Check that the symlink is gone and regular directory is restored
+	info, err := os.Lstat(testDir)
+	suite.Require().NoError(err)
+	suite.Equal(os.FileMode(0), info.Mode()&os.ModeSymlink) // Not a symlink
+	suite.True(info.IsDir())                                // Is a directory
+
+	// Check that content is preserved
+	restoredContent, err := os.ReadFile(testFile)
+	suite.Require().NoError(err)
+	suite.Equal(content, string(restoredContent))
+
+	// Check that directory is removed from repo
+	repoDir := filepath.Join(suite.tempDir, "lnk", "testdir")
+	suite.NoDirExists(repoDir)
+
+	// Check that .lnk file no longer contains the directory
+	lnkFile := filepath.Join(suite.tempDir, "lnk", ".lnk")
+	if suite.FileExists(lnkFile) {
+		lnkContent, err := os.ReadFile(lnkFile)
+		suite.Require().NoError(err)
+		suite.NotContains(string(lnkContent), "testdir")
+	}
+
+	// Check that Git commit was made
+	commits, err := suite.lnk.GetCommits()
+	suite.Require().NoError(err)
+	suite.Len(commits, 2) // add + remove
+	suite.Contains(commits[0], "lnk: removed testdir")
+	suite.Contains(commits[1], "lnk: added testdir")
+}
+
+func (suite *LnkIntegrationTestSuite) TestLnkFileTracking() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Add a file
+	testFile := filepath.Join(suite.tempDir, ".bashrc")
+	err = os.WriteFile(testFile, []byte("export PATH=/usr/local/bin:$PATH"), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add(testFile)
+	suite.Require().NoError(err)
+
+	// Add a directory
+	testDir := filepath.Join(suite.tempDir, ".ssh")
+	err = os.MkdirAll(testDir, 0700)
+	suite.Require().NoError(err)
+
+	configFile := filepath.Join(testDir, "config")
+	err = os.WriteFile(configFile, []byte("Host example.com"), 0600)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add(testDir)
+	suite.Require().NoError(err)
+
+	// Check .lnk file contains both entries
+	lnkFile := filepath.Join(suite.tempDir, "lnk", ".lnk")
+	suite.FileExists(lnkFile)
+
+	lnkContent, err := os.ReadFile(lnkFile)
+	suite.Require().NoError(err)
+
+	lines := strings.Split(strings.TrimSpace(string(lnkContent)), "\n")
+	suite.Len(lines, 2)
+	suite.Contains(lines, ".bashrc")
+	suite.Contains(lines, ".ssh")
+
+	// Remove a file and check .lnk is updated
+	err = suite.lnk.Remove(testFile)
+	suite.Require().NoError(err)
+
+	lnkContent, err = os.ReadFile(lnkFile)
+	suite.Require().NoError(err)
+
+	lines = strings.Split(strings.TrimSpace(string(lnkContent)), "\n")
+	suite.Len(lines, 1)
+	suite.Contains(lines, ".ssh")
+	suite.NotContains(lines, ".bashrc")
+}
+
+func (suite *LnkIntegrationTestSuite) TestPullWithDirectories() {
+	// Initialize repo
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Add remote for pull to work
+	err = suite.lnk.AddRemote("origin", "https://github.com/test/dotfiles.git")
+	suite.Require().NoError(err)
+
+	// Create a directory and .lnk file in the repo directly to simulate a pull
+	repoDir := filepath.Join(suite.tempDir, "lnk", ".config")
+	err = os.MkdirAll(repoDir, 0755)
+	suite.Require().NoError(err)
+
+	configFile := filepath.Join(repoDir, "app.conf")
+	content := "setting=value"
+	err = os.WriteFile(configFile, []byte(content), 0644)
+	suite.Require().NoError(err)
+
+	// Create .lnk file
+	lnkFile := filepath.Join(suite.tempDir, "lnk", ".lnk")
+	err = os.WriteFile(lnkFile, []byte(".config\n"), 0644)
+	suite.Require().NoError(err)
+
+	// Get home directory for the test
+	homeDir, err := os.UserHomeDir()
+	suite.Require().NoError(err)
+
+	targetDir := filepath.Join(homeDir, ".config")
+
+	// Clean up the test directory after the test
+	defer func() {
+		_ = os.RemoveAll(targetDir)
+	}()
+
+	// Create a regular directory in home to simulate conflict scenario
+	err = os.MkdirAll(targetDir, 0755)
+	suite.Require().NoError(err)
+	err = os.WriteFile(filepath.Join(targetDir, "different.conf"), []byte("different"), 0644)
+	suite.Require().NoError(err)
+
+	// Pull should restore symlinks and handle conflicts
+	restored, err := suite.lnk.Pull()
+	// In tests, pull will fail because we don't have real remotes, but that's expected
+	// We can still test the symlink restoration part
+	if err != nil {
+		suite.Contains(err.Error(), "git pull failed")
+		// Test symlink restoration directly
+		restored, err = suite.lnk.RestoreSymlinks()
+		suite.Require().NoError(err)
+	}
+
+	// Should have restored the symlink
+	suite.GreaterOrEqual(len(restored), 1)
+	if len(restored) > 0 {
+		suite.Equal(".config", restored[0])
+	}
+
+	// Check that directory is back to being a symlink
+	info, err := os.Lstat(targetDir)
+	suite.Require().NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	// Check content is preserved from repo
+	repoContent, err := os.ReadFile(configFile)
+	suite.Require().NoError(err)
+	suite.Equal(content, string(repoContent))
 }
 
 func (suite *LnkIntegrationTestSuite) TestRemoveNonSymlink() {