feat(cmd): add 'list' command to display managed files

Implements a new 'list' command that shows all files and directories managed by lnk, improving visibility and user experience.

fixes #4

.github/workflows/ci.yml

@@ -6,6 +6,9 @@ on:
   pull_request:
     branches: [ main ]
 
+permissions:
+  contents: read
+
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -38,7 +41,7 @@ jobs:
         run: go vet ./...
 
       - name: Test
-        run: go test -v -race -coverprofile=coverage.out ./test
+        run: go test -v -race -coverprofile=coverage.out ./...
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3

.github/workflows/release.yml

@@ -23,7 +23,7 @@ jobs:
           go-version: '1.24'
 
       - name: Run tests
-        run: go test ./test
+        run: go test ./...
 
       - name: Run GoReleaser
         uses: goreleaser/goreleaser-action@v6

Makefile

@@ -60,19 +60,19 @@ build:
 ## test: Run tests
 test:
 	@echo "$(BLUE)Running tests...$(NC)"
-	@go test ./test
+	@go test ./...
 	@echo "$(GREEN)✓ Tests passed$(NC)"
 
 ## test-v: Run tests with verbose output
 test-v:
 	@echo "$(BLUE)Running tests (verbose)...$(NC)"
-	@go test -v ./test
+	@go test -v ./...
 
 ## test-cover: Run tests with coverage
 test-cover:
 	@echo "$(BLUE)Running tests with coverage...$(NC)"
-	@go test -v -cover ./test
+	@go test -v -cover ./...
-	@go test -coverprofile=coverage.out ./test
+	@go test -coverprofile=coverage.out ./
 	@go tool cover -html=coverage.out -o coverage.html
 	@echo "$(GREEN)✓ Coverage report generated: coverage.html$(NC)"
 

README.md

@@ -52,6 +52,9 @@ lnk init -r git@github.com:user/dotfiles.git
 # Add files/directories
 lnk add ~/.vimrc ~/.config/nvim ~/.gitconfig
 
+# List managed files
+lnk list
+
 # Check status
 lnk status
 
@@ -99,6 +102,7 @@ lnk pull  # auto-creates symlinks
 
 ```bash
 vim ~/.vimrc           # edit normally
+lnk list               # see what's managed
 lnk status             # check what changed
 lnk push "new plugins" # commit & push
 ```
@@ -108,6 +112,7 @@ lnk push "new plugins" # commit & push
 - `lnk init [-r remote]` - Create repo
 - `lnk add <files>` - Move files to repo, create symlinks
 - `lnk rm <files>` - Move files back, remove symlinks
+- `lnk list` - List files managed by lnk
 - `lnk status` - Git status + sync info
 - `lnk push [msg]` - Stage all, commit, push
 - `lnk pull` - Pull + restore missing symlinks
@@ -115,10 +120,8 @@ lnk push "new plugins" # commit & push
 ## Technical bits
 
 - **Single binary** (~8MB, no deps)
-- **Atomic operations** (rollback on failure)
 - **Relative symlinks** (portable)
 - **XDG compliant** (`~/.config/lnk`)
-- **20 integration tests**
 
 ## Alternatives
 

cmd/add.go

@@ -8,7 +8,8 @@ import (
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var addCmd = &cobra.Command{
+func newAddCmd() *cobra.Command {
+	return &cobra.Command{
 		Use:          "add <file>",
 		Short:        "✨ Add a file to lnk management",
 		Long:         "Moves a file to the lnk repository and creates a symlink in its place.",
@@ -23,13 +24,10 @@ var addCmd = &cobra.Command{
 			}
 
 			basename := filepath.Base(filePath)
-		fmt.Printf("✨ \033[1mAdded %s to lnk\033[0m\n", basename)
+			printf(cmd, "✨ \033[1mAdded %s to lnk\033[0m\n", basename)
-		fmt.Printf("   🔗 \033[90m%s\033[0m → \033[36m~/.config/lnk/%s\033[0m\n", filePath, basename)
+			printf(cmd, "   🔗 \033[90m%s\033[0m → \033[36m~/.config/lnk/%s\033[0m\n", filePath, basename)
-		fmt.Printf("   📝 Use \033[1mlnk push\033[0m to sync to remote\n")
+			printf(cmd, "   📝 Use \033[1mlnk push\033[0m to sync to remote\n")
 			return nil
 		},
 	}
-
-func init() {
-	rootCmd.AddCommand(addCmd)
 }

cmd/init.go

@@ -7,7 +7,8 @@ import (
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var initCmd = &cobra.Command{
+func newInitCmd() *cobra.Command {
+	cmd := &cobra.Command{
 		Use:          "init",
 		Short:        "🎯 Initialize a new lnk repository",
 		Long:         "Creates the lnk directory and initializes a Git repository for managing dotfiles.",
@@ -21,25 +22,24 @@ var initCmd = &cobra.Command{
 			}
 
 			if remote != "" {
-			fmt.Printf("🎯 \033[1mInitialized lnk repository\033[0m\n")
+				printf(cmd, "🎯 \033[1mInitialized lnk repository\033[0m\n")
-			fmt.Printf("   📦 Cloned from: \033[36m%s\033[0m\n", remote)
+				printf(cmd, "   📦 Cloned from: \033[36m%s\033[0m\n", remote)
-			fmt.Printf("   📁 Location: \033[90m~/.config/lnk\033[0m\n")
+				printf(cmd, "   📁 Location: \033[90m~/.config/lnk\033[0m\n")
-			fmt.Printf("\n💡 \033[33mNext steps:\033[0m\n")
+				printf(cmd, "\n💡 \033[33mNext steps:\033[0m\n")
-			fmt.Printf("   • Run \033[1mlnk pull\033[0m to restore symlinks\n")
+				printf(cmd, "   • Run \033[1mlnk pull\033[0m to restore symlinks\n")
-			fmt.Printf("   • Use \033[1mlnk add <file>\033[0m to manage new files\n")
+				printf(cmd, "   • Use \033[1mlnk add <file>\033[0m to manage new files\n")
 			} else {
-			fmt.Printf("🎯 \033[1mInitialized empty lnk repository\033[0m\n")
+				printf(cmd, "🎯 \033[1mInitialized empty lnk repository\033[0m\n")
-			fmt.Printf("   📁 Location: \033[90m~/.config/lnk\033[0m\n")
+				printf(cmd, "   📁 Location: \033[90m~/.config/lnk\033[0m\n")
-			fmt.Printf("\n💡 \033[33mNext steps:\033[0m\n")
+				printf(cmd, "\n💡 \033[33mNext steps:\033[0m\n")
-			fmt.Printf("   • Run \033[1mlnk add <file>\033[0m to start managing dotfiles\n")
+				printf(cmd, "   • Run \033[1mlnk add <file>\033[0m to start managing dotfiles\n")
-			fmt.Printf("   • Add a remote with: \033[1mgit remote add origin <url>\033[0m\n")
+				printf(cmd, "   • Add a remote with: \033[1mgit remote add origin <url>\033[0m\n")
 			}
 
 			return nil
 		},
 	}
 
-func init() {
+	cmd.Flags().StringP("remote", "r", "", "Clone from remote URL instead of creating empty repository")
-	initCmd.Flags().StringP("remote", "r", "", "Clone from remote URL instead of creating empty repository")
+	return cmd
-	rootCmd.AddCommand(initCmd)
 }

cmd/list.go

@@ -0,0 +1,43 @@
+package cmd
+
+import (
+	"fmt"
+
+	"github.com/spf13/cobra"
+	"github.com/yarlson/lnk/internal/core"
+)
+
+func newListCmd() *cobra.Command {
+	return &cobra.Command{
+		Use:          "list",
+		Short:        "📋 List files managed by lnk",
+		Long:         "Display all files and directories currently managed by lnk.",
+		SilenceUsage: true,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			lnk := core.NewLnk()
+			managedItems, err := lnk.List()
+			if err != nil {
+				return fmt.Errorf("failed to list managed items: %w", err)
+			}
+
+			if len(managedItems) == 0 {
+				printf(cmd, "📋 \033[1mNo files currently managed by lnk\033[0m\n")
+				printf(cmd, "   💡 Use \033[1mlnk add <file>\033[0m to start managing files\n")
+				return nil
+			}
+
+			printf(cmd, "📋 \033[1mFiles managed by lnk\033[0m (\033[36m%d item", len(managedItems))
+			if len(managedItems) > 1 {
+				printf(cmd, "s")
+			}
+			printf(cmd, "\033[0m):\n\n")
+
+			for _, item := range managedItems {
+				printf(cmd, "   🔗 \033[36m%s\033[0m\n", item)
+			}
+
+			printf(cmd, "\n💡 Use \033[1mlnk status\033[0m to check sync status\n")
+			return nil
+		},
+	}
+}

cmd/pull.go

@@ -7,7 +7,8 @@ import (
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var pullCmd = &cobra.Command{
+func newPullCmd() *cobra.Command {
+	return &cobra.Command{
 		Use:          "pull",
 		Short:        "⬇️ Pull changes from remote and restore symlinks",
 		Long:         "Fetches changes from remote repository and automatically restores symlinks for all managed files.",
@@ -20,26 +21,23 @@ var pullCmd = &cobra.Command{
 			}
 
 			if len(restored) > 0 {
-			fmt.Printf("⬇️  \033[1;32mSuccessfully pulled changes\033[0m\n")
+				printf(cmd, "⬇️  \033[1;32mSuccessfully pulled changes\033[0m\n")
-			fmt.Printf("   🔗 Restored \033[1m%d symlink", len(restored))
+				printf(cmd, "   🔗 Restored \033[1m%d symlink", len(restored))
 				if len(restored) > 1 {
-				fmt.Printf("s")
+					printf(cmd, "s")
 				}
-			fmt.Printf("\033[0m:\n")
+				printf(cmd, "\033[0m:\n")
 				for _, file := range restored {
-				fmt.Printf("      ✨ \033[36m%s\033[0m\n", file)
+					printf(cmd, "      ✨ \033[36m%s\033[0m\n", file)
 				}
-			fmt.Printf("\n   🎉 Your dotfiles are synced and ready!\n")
+				printf(cmd, "\n   🎉 Your dotfiles are synced and ready!\n")
 			} else {
-			fmt.Printf("⬇️  \033[1;32mSuccessfully pulled changes\033[0m\n")
+				printf(cmd, "⬇️  \033[1;32mSuccessfully pulled changes\033[0m\n")
-			fmt.Printf("   ✅ All symlinks already in place\n")
+				printf(cmd, "   ✅ All symlinks already in place\n")
-			fmt.Printf("   🎉 Everything is up to date!\n")
+				printf(cmd, "   🎉 Everything is up to date!\n")
 			}
 
 			return nil
 		},
 	}
-
-func init() {
-	rootCmd.AddCommand(pullCmd)
 }

cmd/push.go

@@ -7,7 +7,8 @@ import (
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var pushCmd = &cobra.Command{
+func newPushCmd() *cobra.Command {
+	return &cobra.Command{
 		Use:          "push [message]",
 		Short:        "🚀 Push local changes to remote repository",
 		Long:         "Stages all changes, creates a sync commit with the provided message, and pushes to remote.",
@@ -24,14 +25,11 @@ var pushCmd = &cobra.Command{
 				return fmt.Errorf("failed to push changes: %w", err)
 			}
 
-		fmt.Printf("🚀 \033[1;32mSuccessfully pushed changes\033[0m\n")
+			printf(cmd, "🚀 \033[1;32mSuccessfully pushed changes\033[0m\n")
-		fmt.Printf("   💾 Commit: \033[90m%s\033[0m\n", message)
+			printf(cmd, "   💾 Commit: \033[90m%s\033[0m\n", message)
-		fmt.Printf("   📡 Synced to remote\n")
+			printf(cmd, "   📡 Synced to remote\n")
-		fmt.Printf("   ✨ Your dotfiles are up to date!\n")
+			printf(cmd, "   ✨ Your dotfiles are up to date!\n")
 			return nil
 		},
 	}
-
-func init() {
-	rootCmd.AddCommand(pushCmd)
 }

cmd/rm.go

@@ -8,7 +8,8 @@ import (
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var rmCmd = &cobra.Command{
+func newRemoveCmd() *cobra.Command {
+	return &cobra.Command{
 		Use:          "rm <file>",
 		Short:        "🗑️ Remove a file from lnk management",
 		Long:         "Removes a symlink and restores the original file from the lnk repository.",
@@ -23,13 +24,10 @@ var rmCmd = &cobra.Command{
 			}
 
 			basename := filepath.Base(filePath)
-		fmt.Printf("🗑️  \033[1mRemoved %s from lnk\033[0m\n", basename)
+			printf(cmd, "🗑️  \033[1mRemoved %s from lnk\033[0m\n", basename)
-		fmt.Printf("   ↩️  \033[90m~/.config/lnk/%s\033[0m → \033[36m%s\033[0m\n", basename, filePath)
+			printf(cmd, "   ↩️  \033[90m~/.config/lnk/%s\033[0m → \033[36m%s\033[0m\n", basename, filePath)
-		fmt.Printf("   📄 Original file restored\n")
+			printf(cmd, "   📄 Original file restored\n")
 			return nil
 		},
 	}
-
-func init() {
-	rootCmd.AddCommand(rmCmd)
 }

cmd/root.go

@@ -12,7 +12,9 @@ var (
 	buildTime = "unknown"
 )
 
-var rootCmd = &cobra.Command{
+// NewRootCommand creates a new root command (testable)
+func NewRootCommand() *cobra.Command {
+	rootCmd := &cobra.Command{
 		Use:   "lnk",
 		Short: "🔗 Dotfiles, linked. No fluff.",
 		Long: `🔗 Lnk - Git-native dotfiles management that doesn't suck.
@@ -29,16 +31,29 @@ That's it.
 
 🎯 Simple, fast, and Git-native.`,
 		SilenceUsage: true,
+		Version:      fmt.Sprintf("%s (built %s)", version, buildTime),
+	}
+
+	// Add subcommands
+	rootCmd.AddCommand(newInitCmd())
+	rootCmd.AddCommand(newAddCmd())
+	rootCmd.AddCommand(newRemoveCmd())
+	rootCmd.AddCommand(newListCmd())
+	rootCmd.AddCommand(newStatusCmd())
+	rootCmd.AddCommand(newPushCmd())
+	rootCmd.AddCommand(newPullCmd())
+
+	return rootCmd
 }
 
 // SetVersion sets the version information for the CLI
 func SetVersion(v, bt string) {
 	version = v
 	buildTime = bt
-	rootCmd.Version = fmt.Sprintf("%s (built %s)", version, buildTime)
 }
 
 func Execute() {
+	rootCmd := NewRootCommand()
 	if err := rootCmd.Execute(); err != nil {
 		fmt.Fprintln(os.Stderr, err)
 		os.Exit(1)

cmd/root_test.go

@@ -0,0 +1,533 @@
+package cmd
+
+import (
+	"bytes"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"github.com/stretchr/testify/suite"
+)
+
+type CLITestSuite struct {
+	suite.Suite
+	tempDir     string
+	originalDir string
+	stdout      *bytes.Buffer
+	stderr      *bytes.Buffer
+}
+
+func (suite *CLITestSuite) SetupTest() {
+	// Create temp directory and change to it
+	tempDir, err := os.MkdirTemp("", "lnk-cli-test-*")
+	suite.Require().NoError(err)
+	suite.tempDir = tempDir
+
+	originalDir, err := os.Getwd()
+	suite.Require().NoError(err)
+	suite.originalDir = originalDir
+
+	err = os.Chdir(tempDir)
+	suite.Require().NoError(err)
+
+	// Set XDG_CONFIG_HOME to temp directory
+	suite.T().Setenv("XDG_CONFIG_HOME", tempDir)
+
+	// Capture output
+	suite.stdout = &bytes.Buffer{}
+	suite.stderr = &bytes.Buffer{}
+}
+
+func (suite *CLITestSuite) TearDownTest() {
+	err := os.Chdir(suite.originalDir)
+	suite.Require().NoError(err)
+	err = os.RemoveAll(suite.tempDir)
+	suite.Require().NoError(err)
+}
+
+func (suite *CLITestSuite) runCommand(args ...string) error {
+	rootCmd := NewRootCommand()
+	rootCmd.SetOut(suite.stdout)
+	rootCmd.SetErr(suite.stderr)
+	rootCmd.SetArgs(args)
+	return rootCmd.Execute()
+}
+
+func (suite *CLITestSuite) TestInitCommand() {
+	err := suite.runCommand("init")
+	suite.NoError(err)
+
+	// Check output
+	output := suite.stdout.String()
+	suite.Contains(output, "Initialized empty lnk repository")
+	suite.Contains(output, "Location:")
+	suite.Contains(output, "Next steps:")
+	suite.Contains(output, "lnk add <file>")
+
+	// Verify actual effect
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	suite.DirExists(lnkDir)
+
+	gitDir := filepath.Join(lnkDir, ".git")
+	suite.DirExists(gitDir)
+}
+
+func (suite *CLITestSuite) TestInitWithRemote() {
+	err := suite.runCommand("init", "-r", "https://github.com/user/dotfiles.git")
+	// This will fail because we don't have a real remote, but that's expected
+	suite.Error(err)
+	suite.Contains(err.Error(), "git clone failed")
+}
+
+func (suite *CLITestSuite) TestAddCommand() {
+	// Initialize first
+	err := suite.runCommand("init")
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Create test file
+	testFile := filepath.Join(suite.tempDir, ".bashrc")
+	err = os.WriteFile(testFile, []byte("export PATH=/usr/local/bin:$PATH"), 0644)
+	suite.Require().NoError(err)
+
+	// Test add command
+	err = suite.runCommand("add", testFile)
+	suite.NoError(err)
+
+	// Check output
+	output := suite.stdout.String()
+	suite.Contains(output, "Added .bashrc to lnk")
+	suite.Contains(output, "→")
+	suite.Contains(output, "sync to remote")
+
+	// Verify symlink was created
+	info, err := os.Lstat(testFile)
+	suite.NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	// Verify some file exists in repo with .bashrc in the name
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	entries, err := os.ReadDir(lnkDir)
+	suite.NoError(err)
+
+	found := false
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), ".bashrc") && entry.Name() != ".lnk" {
+			found = true
+			break
+		}
+	}
+	suite.True(found, "Repository should contain a file with .bashrc in the name")
+}
+
+func (suite *CLITestSuite) TestRemoveCommand() {
+	// Setup: init and add a file
+	_ = suite.runCommand("init")
+	testFile := filepath.Join(suite.tempDir, ".vimrc")
+	_ = os.WriteFile(testFile, []byte("set number"), 0644)
+	_ = suite.runCommand("add", testFile)
+	suite.stdout.Reset()
+
+	// Test remove command
+	err := suite.runCommand("rm", testFile)
+	suite.NoError(err)
+
+	// Check output
+	output := suite.stdout.String()
+	suite.Contains(output, "Removed .vimrc from lnk")
+	suite.Contains(output, "→")
+	suite.Contains(output, "Original file restored")
+
+	// Verify symlink is gone and regular file is restored
+	info, err := os.Lstat(testFile)
+	suite.NoError(err)
+	suite.Equal(os.FileMode(0), info.Mode()&os.ModeSymlink) // Not a symlink
+
+	// Verify content is preserved
+	content, err := os.ReadFile(testFile)
+	suite.NoError(err)
+	suite.Equal("set number", string(content))
+}
+
+func (suite *CLITestSuite) TestStatusCommand() {
+	// Initialize first
+	err := suite.runCommand("init")
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Test status without remote - should fail
+	err = suite.runCommand("status")
+	suite.Error(err)
+	suite.Contains(err.Error(), "no remote configured")
+}
+
+func (suite *CLITestSuite) TestListCommand() {
+	// Test list without init - should fail
+	err := suite.runCommand("list")
+	suite.Error(err)
+	suite.Contains(err.Error(), "Lnk repository not initialized")
+
+	// Initialize first
+	err = suite.runCommand("init")
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Test list with no managed files
+	err = suite.runCommand("list")
+	suite.NoError(err)
+	output := suite.stdout.String()
+	suite.Contains(output, "No files currently managed by lnk")
+	suite.Contains(output, "lnk add <file>")
+	suite.stdout.Reset()
+
+	// 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.runCommand("add", testFile)
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Test list with one managed file
+	err = suite.runCommand("list")
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Files managed by lnk")
+	suite.Contains(output, "1 item")
+	suite.Contains(output, ".bashrc")
+	suite.stdout.Reset()
+
+	// Add another file
+	testFile2 := filepath.Join(suite.tempDir, ".vimrc")
+	err = os.WriteFile(testFile2, []byte("set number"), 0644)
+	suite.Require().NoError(err)
+	err = suite.runCommand("add", testFile2)
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Test list with multiple managed files
+	err = suite.runCommand("list")
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Files managed by lnk")
+	suite.Contains(output, "2 items")
+	suite.Contains(output, ".bashrc")
+	suite.Contains(output, ".vimrc")
+}
+
+func (suite *CLITestSuite) TestErrorHandling() {
+	tests := []struct {
+		name        string
+		args        []string
+		wantErr     bool
+		errContains string
+		outContains string
+	}{
+		{
+			name:        "add nonexistent file",
+			args:        []string{"add", "/nonexistent/file"},
+			wantErr:     true,
+			errContains: "File does not exist",
+		},
+		{
+			name:        "status without init",
+			args:        []string{"status"},
+			wantErr:     true,
+			errContains: "Lnk repository not initialized",
+		},
+		{
+			name:        "help command",
+			args:        []string{"--help"},
+			wantErr:     false,
+			outContains: "Lnk - Git-native dotfiles management",
+		},
+		{
+			name:        "version command",
+			args:        []string{"--version"},
+			wantErr:     false,
+			outContains: "lnk version",
+		},
+		{
+			name:        "init help",
+			args:        []string{"init", "--help"},
+			wantErr:     false,
+			outContains: "Creates the lnk directory",
+		},
+		{
+			name:        "add help",
+			args:        []string{"add", "--help"},
+			wantErr:     false,
+			outContains: "Moves a file to the lnk repository",
+		},
+		{
+			name:        "list help",
+			args:        []string{"list", "--help"},
+			wantErr:     false,
+			outContains: "Display all files and directories",
+		},
+	}
+
+	for _, tt := range tests {
+		suite.Run(tt.name, func() {
+			suite.stdout.Reset()
+			suite.stderr.Reset()
+
+			err := suite.runCommand(tt.args...)
+
+			if tt.wantErr {
+				suite.Error(err, "Expected error for %s", tt.name)
+				if tt.errContains != "" {
+					suite.Contains(err.Error(), tt.errContains, "Wrong error message for %s", tt.name)
+				}
+			} else {
+				suite.NoError(err, "Unexpected error for %s", tt.name)
+			}
+
+			if tt.outContains != "" {
+				output := suite.stdout.String()
+				suite.Contains(output, tt.outContains, "Expected output not found for %s", tt.name)
+			}
+		})
+	}
+}
+
+func (suite *CLITestSuite) TestCompleteWorkflow() {
+	// Test realistic user workflow
+	steps := []struct {
+		name   string
+		args   []string
+		setup  func()
+		verify func(output string)
+	}{
+		{
+			name: "initialize repository",
+			args: []string{"init"},
+			verify: func(output string) {
+				suite.Contains(output, "Initialized empty lnk repository")
+			},
+		},
+		{
+			name: "add config file",
+			args: []string{"add", ".bashrc"},
+			setup: func() {
+				testFile := filepath.Join(suite.tempDir, ".bashrc")
+				_ = os.WriteFile(testFile, []byte("export PATH=/usr/local/bin:$PATH"), 0644)
+			},
+			verify: func(output string) {
+				suite.Contains(output, "Added .bashrc to lnk")
+			},
+		},
+		{
+			name: "add another file",
+			args: []string{"add", ".vimrc"},
+			setup: func() {
+				testFile := filepath.Join(suite.tempDir, ".vimrc")
+				_ = os.WriteFile(testFile, []byte("set number"), 0644)
+			},
+			verify: func(output string) {
+				suite.Contains(output, "Added .vimrc to lnk")
+			},
+		},
+		{
+			name: "remove file",
+			args: []string{"rm", ".vimrc"},
+			verify: func(output string) {
+				suite.Contains(output, "Removed .vimrc from lnk")
+			},
+		},
+	}
+
+	for _, step := range steps {
+		suite.Run(step.name, func() {
+			if step.setup != nil {
+				step.setup()
+			}
+
+			suite.stdout.Reset()
+			suite.stderr.Reset()
+
+			err := suite.runCommand(step.args...)
+			suite.NoError(err, "Step %s failed: %v", step.name, err)
+
+			output := suite.stdout.String()
+			if step.verify != nil {
+				step.verify(output)
+			}
+		})
+	}
+}
+
+func (suite *CLITestSuite) TestRemoveUnmanagedFile() {
+	// Initialize repository
+	_ = suite.runCommand("init")
+
+	// Create a regular file (not managed by lnk)
+	testFile := filepath.Join(suite.tempDir, ".regularfile")
+	_ = os.WriteFile(testFile, []byte("content"), 0644)
+
+	// Try to remove it
+	err := suite.runCommand("rm", testFile)
+	suite.Error(err)
+	suite.Contains(err.Error(), "File is not managed by lnk")
+}
+
+func (suite *CLITestSuite) TestAddDirectory() {
+	// Initialize repository
+	_ = suite.runCommand("init")
+	suite.stdout.Reset()
+
+	// Create a directory with files
+	testDir := filepath.Join(suite.tempDir, ".config")
+	_ = os.MkdirAll(testDir, 0755)
+	configFile := filepath.Join(testDir, "app.conf")
+	_ = os.WriteFile(configFile, []byte("setting=value"), 0644)
+
+	// Add the directory
+	err := suite.runCommand("add", testDir)
+	suite.NoError(err)
+
+	// Check output
+	output := suite.stdout.String()
+	suite.Contains(output, "Added .config to lnk")
+
+	// Verify directory is now a symlink
+	info, err := os.Lstat(testDir)
+	suite.NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	// Verify some directory exists in repo with .config in the name
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	entries, err := os.ReadDir(lnkDir)
+	suite.NoError(err)
+
+	found := false
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), ".config") && entry.Name() != ".lnk" {
+			found = true
+			break
+		}
+	}
+	suite.True(found, "Repository should contain a directory with .config in the name")
+}
+
+func (suite *CLITestSuite) TestSameBasenameFilesBug() {
+	// Initialize repository
+	err := suite.runCommand("init")
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Create two directories with files having the same basename
+	dirA := filepath.Join(suite.tempDir, "a")
+	dirB := filepath.Join(suite.tempDir, "b")
+	err = os.MkdirAll(dirA, 0755)
+	suite.Require().NoError(err)
+	err = os.MkdirAll(dirB, 0755)
+	suite.Require().NoError(err)
+
+	// Create files with same basename but different content
+	fileA := filepath.Join(dirA, "config.json")
+	fileB := filepath.Join(dirB, "config.json")
+	contentA := `{"name": "config_a"}`
+	contentB := `{"name": "config_b"}`
+
+	err = os.WriteFile(fileA, []byte(contentA), 0644)
+	suite.Require().NoError(err)
+	err = os.WriteFile(fileB, []byte(contentB), 0644)
+	suite.Require().NoError(err)
+
+	// Add first file
+	err = suite.runCommand("add", fileA)
+	suite.NoError(err)
+	suite.stdout.Reset()
+
+	// Verify first file content is preserved
+	content, err := os.ReadFile(fileA)
+	suite.NoError(err)
+	suite.Equal(contentA, string(content), "First file should preserve its original content")
+
+	// Add second file with same basename - this should work correctly
+	err = suite.runCommand("add", fileB)
+	suite.NoError(err, "Adding second file with same basename should work")
+
+	// CORRECT BEHAVIOR: Both files should preserve their original content
+	contentAfterAddA, err := os.ReadFile(fileA)
+	suite.NoError(err)
+	contentAfterAddB, err := os.ReadFile(fileB)
+	suite.NoError(err)
+
+	suite.Equal(contentA, string(contentAfterAddA), "First file should keep its original content")
+	suite.Equal(contentB, string(contentAfterAddB), "Second file should keep its original content")
+
+	// Both files should be removable independently
+	suite.stdout.Reset()
+	err = suite.runCommand("rm", fileA)
+	suite.NoError(err, "First file should be removable")
+
+	// Verify output shows removal
+	output := suite.stdout.String()
+	suite.Contains(output, "Removed config.json from lnk")
+
+	// Verify first file is restored with correct content
+	restoredContentA, err := os.ReadFile(fileA)
+	suite.NoError(err)
+	suite.Equal(contentA, string(restoredContentA), "Restored first file should have original content")
+
+	// Second file should still be removable without errors
+	suite.stdout.Reset()
+	err = suite.runCommand("rm", fileB)
+	suite.NoError(err, "Second file should also be removable without errors")
+
+	// Verify second file is restored with correct content
+	restoredContentB, err := os.ReadFile(fileB)
+	suite.NoError(err)
+	suite.Equal(contentB, string(restoredContentB), "Restored second file should have original content")
+}
+
+func (suite *CLITestSuite) TestStatusDirtyRepo() {
+	// Initialize repository
+	err := suite.runCommand("init")
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Add and commit a file
+	testFile := filepath.Join(suite.tempDir, "a")
+	err = os.WriteFile(testFile, []byte("abc"), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.runCommand("add", testFile)
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Add a remote so status works
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	cmd := exec.Command("git", "remote", "add", "origin", "https://github.com/test/dotfiles.git")
+	cmd.Dir = lnkDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	// Status should show clean but ahead
+	err = suite.runCommand("status")
+	suite.NoError(err)
+	output := suite.stdout.String()
+	suite.Contains(output, "1 commit ahead")
+	suite.NotContains(output, "uncommitted changes")
+	suite.stdout.Reset()
+
+	// Now edit the managed file (simulating the issue scenario)
+	err = os.WriteFile(testFile, []byte("def"), 0644)
+	suite.Require().NoError(err)
+
+	// Status should now detect dirty state and NOT say "up to date"
+	err = suite.runCommand("status")
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Repository has uncommitted changes")
+	suite.NotContains(output, "Repository is up to date")
+	suite.Contains(output, "lnk push")
+}
+
+func TestCLISuite(t *testing.T) {
+	suite.Run(t, new(CLITestSuite))
+}

cmd/status.go

@@ -7,10 +7,11 @@ import (
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var statusCmd = &cobra.Command{
+func newStatusCmd() *cobra.Command {
+	return &cobra.Command{
 		Use:          "status",
 		Short:        "📊 Show repository sync status",
-	Long:         "Display how many commits ahead/behind the local repository is relative to the remote.",
+		Long:         "Display how many commits ahead/behind the local repository is relative to the remote and check for uncommitted changes.",
 		SilenceUsage: true,
 		RunE: func(cmd *cobra.Command, args []string) error {
 			lnk := core.NewLnk()
@@ -19,40 +20,74 @@ var statusCmd = &cobra.Command{
 				return fmt.Errorf("failed to get status: %w", err)
 			}
 
+			if status.Dirty {
+				displayDirtyStatus(cmd, status)
+				return nil
+			}
+
 			if status.Ahead == 0 && status.Behind == 0 {
-			fmt.Printf("✅ \033[1;32mRepository is up to date\033[0m\n")
+				displayUpToDateStatus(cmd, status)
-			fmt.Printf("   📡 Synced with \033[36m%s\033[0m\n", status.Remote)
+				return nil
-		} else {
-			fmt.Printf("📊 \033[1mRepository Status\033[0m\n")
-			fmt.Printf("   📡 Remote: \033[36m%s\033[0m\n", status.Remote)
-			fmt.Printf("\n")
-
-			if status.Ahead > 0 {
-				commitText := "commit"
-				if status.Ahead > 1 {
-					commitText = "commits"
-				}
-				fmt.Printf("   ⬆️  \033[1;33m%d %s ahead\033[0m - ready to push\n", status.Ahead, commitText)
-			}
-			if status.Behind > 0 {
-				commitText := "commit"
-				if status.Behind > 1 {
-					commitText = "commits"
-				}
-				fmt.Printf("   ⬇️  \033[1;31m%d %s behind\033[0m - run \033[1mlnk pull\033[0m\n", status.Behind, commitText)
-			}
-
-			if status.Ahead > 0 && status.Behind == 0 {
-				fmt.Printf("\n💡 Run \033[1mlnk push\033[0m to sync your changes")
-			} else if status.Behind > 0 {
-				fmt.Printf("\n💡 Run \033[1mlnk pull\033[0m to get latest changes")
-			}
 			}
 
+			displaySyncStatus(cmd, status)
 			return nil
 		},
 	}
-
+}
-func init() {
+
-	rootCmd.AddCommand(statusCmd)
+func displayDirtyStatus(cmd *cobra.Command, status *core.StatusInfo) {
+	printf(cmd, "⚠️  \033[1;33mRepository has uncommitted changes\033[0m\n")
+	printf(cmd, "   📡 Remote: \033[36m%s\033[0m\n", status.Remote)
+
+	if status.Ahead == 0 && status.Behind == 0 {
+		printf(cmd, "\n💡 Run \033[1mgit add && git commit\033[0m in \033[36m~/.config/lnk\033[0m or \033[1mlnk push\033[0m to commit changes\n")
+		return
+	}
+
+	printf(cmd, "\n")
+	displayAheadBehindInfo(cmd, status, true)
+	printf(cmd, "\n💡 Run \033[1mgit add && git commit\033[0m in \033[36m~/.config/lnk\033[0m or \033[1mlnk push\033[0m to commit changes\n")
+}
+
+func displayUpToDateStatus(cmd *cobra.Command, status *core.StatusInfo) {
+	printf(cmd, "✅ \033[1;32mRepository is up to date\033[0m\n")
+	printf(cmd, "   📡 Synced with \033[36m%s\033[0m\n", status.Remote)
+}
+
+func displaySyncStatus(cmd *cobra.Command, status *core.StatusInfo) {
+	printf(cmd, "📊 \033[1mRepository Status\033[0m\n")
+	printf(cmd, "   📡 Remote: \033[36m%s\033[0m\n", status.Remote)
+	printf(cmd, "\n")
+
+	displayAheadBehindInfo(cmd, status, false)
+
+	if status.Ahead > 0 && status.Behind == 0 {
+		printf(cmd, "\n💡 Run \033[1mlnk push\033[0m to sync your changes\n")
+	} else if status.Behind > 0 {
+		printf(cmd, "\n💡 Run \033[1mlnk pull\033[0m to get latest changes\n")
+	}
+}
+
+func displayAheadBehindInfo(cmd *cobra.Command, status *core.StatusInfo, isDirty bool) {
+	if status.Ahead > 0 {
+		commitText := getCommitText(status.Ahead)
+		if isDirty {
+			printf(cmd, "   ⬆️ \033[1;33m%d %s ahead\033[0m (excluding uncommitted changes)\n", status.Ahead, commitText)
+		} else {
+			printf(cmd, "   ⬆️ \033[1;33m%d %s ahead\033[0m - ready to push\n", status.Ahead, commitText)
+		}
+	}
+
+	if status.Behind > 0 {
+		commitText := getCommitText(status.Behind)
+		printf(cmd, "   ⬇️ \033[1;31m%d %s behind\033[0m - run \033[1mlnk pull\033[0m\n", status.Behind, commitText)
+	}
+}
+
+func getCommitText(count int) string {
+	if count == 1 {
+		return "commit"
+	}
+	return "commits"
 }

cmd/utils.go

@@ -0,0 +1,12 @@
+package cmd
+
+import (
+	"fmt"
+
+	"github.com/spf13/cobra"
+)
+
+// printf is a helper function to simplify output formatting in commands
+func printf(cmd *cobra.Command, format string, args ...interface{}) {
+	_, _ = fmt.Fprintf(cmd.OutOrStdout(), format, args...)
+}

internal/core/lnk.go

@@ -43,6 +43,38 @@ func getRepoPath() string {
 	return filepath.Join(xdgConfig, "lnk")
 }
 
+// generateRepoName creates a unique repository filename from a relative path
+func generateRepoName(relativePath string) string {
+	// Replace slashes and backslashes with underscores to create valid filename
+	repoName := strings.ReplaceAll(relativePath, "/", "_")
+	repoName = strings.ReplaceAll(repoName, "\\", "_")
+	return repoName
+}
+
+// getRelativePath converts an absolute path to a relative path from home directory
+func getRelativePath(absPath string) (string, error) {
+	homeDir, err := os.UserHomeDir()
+	if err != nil {
+		return "", fmt.Errorf("failed to get home directory: %w", err)
+	}
+
+	// Check if the file is under home directory
+	relPath, err := filepath.Rel(homeDir, absPath)
+	if err != nil {
+		return "", fmt.Errorf("failed to get relative path: %w", err)
+	}
+
+	// If the relative path starts with "..", the file is outside home directory
+	// In this case, use the absolute path as relative (without the leading slash)
+	if strings.HasPrefix(relPath, "..") {
+		// Use absolute path but remove leading slash and drive letter (for cross-platform)
+		cleanPath := strings.TrimPrefix(absPath, "/")
+		return cleanPath, nil
+	}
+
+	return relPath, nil
+}
+
 // Init initializes the lnk repository
 func (l *Lnk) Init() error {
 	return l.InitWithRemote("")
@@ -109,9 +141,26 @@ func (l *Lnk) Add(filePath string) error {
 		return fmt.Errorf("failed to get absolute path: %w", err)
 	}
 
-	// Calculate destination path in repo
+	// Get relative path for tracking
-	basename := filepath.Base(absPath)
+	relativePath, err := getRelativePath(absPath)
-	destPath := filepath.Join(l.repoPath, basename)
+	if err != nil {
+		return fmt.Errorf("failed to get relative path: %w", err)
+	}
+
+	// Generate unique repository name from relative path
+	repoName := generateRepoName(relativePath)
+	destPath := filepath.Join(l.repoPath, repoName)
+
+	// Check if this relative path is already managed
+	managedItems, err := l.getManagedItems()
+	if err != nil {
+		return fmt.Errorf("failed to get managed items: %w", err)
+	}
+	for _, item := range managedItems {
+		if item == relativePath {
+			return fmt.Errorf("❌ File is already managed by lnk: \033[31m%s\033[0m", relativePath)
+		}
+	}
 
 	// Check if it's a directory or file
 	info, err := os.Stat(absPath)
@@ -141,8 +190,8 @@ func (l *Lnk) Add(filePath string) error {
 		return fmt.Errorf("failed to create symlink: %w", err)
 	}
 
-	// Add to .lnk tracking file
+	// Add to .lnk tracking file using relative path
-	if err := l.addManagedItem(absPath); err != nil {
+	if err := l.addManagedItem(relativePath); err != nil {
 		// Try to restore the original state if tracking fails
 		_ = os.Remove(absPath) // Ignore error in cleanup
 		if info.IsDir() {
@@ -154,10 +203,10 @@ func (l *Lnk) Add(filePath string) error {
 	}
 
 	// Add both the item and .lnk file to git in a single commit
-	if err := l.git.Add(basename); err != nil {
+	if err := l.git.Add(repoName); 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
+		_ = l.removeManagedItem(relativePath) // Ignore error in cleanup
 		if info.IsDir() {
 			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
 		} else {
@@ -170,7 +219,7 @@ func (l *Lnk) Add(filePath string) error {
 	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
+		_ = l.removeManagedItem(relativePath) // Ignore error in cleanup
 		if info.IsDir() {
 			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
 		} else {
@@ -180,10 +229,11 @@ func (l *Lnk) Add(filePath string) error {
 	}
 
 	// Commit both changes together
+	basename := filepath.Base(relativePath)
 	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
+		_ = l.removeManagedItem(relativePath) // Ignore error in cleanup
 		if info.IsDir() {
 			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
 		} else {
@@ -208,6 +258,29 @@ func (l *Lnk) Remove(filePath string) error {
 		return err
 	}
 
+	// Get relative path for tracking
+	relativePath, err := getRelativePath(absPath)
+	if err != nil {
+		return fmt.Errorf("failed to get relative path: %w", err)
+	}
+
+	// Check if this relative path is managed
+	managedItems, err := l.getManagedItems()
+	if err != nil {
+		return fmt.Errorf("failed to get managed items: %w", err)
+	}
+
+	found := false
+	for _, item := range managedItems {
+		if item == relativePath {
+			found = true
+			break
+		}
+	}
+	if !found {
+		return fmt.Errorf("❌ File is not managed by lnk: \033[31m%s\033[0m", relativePath)
+	}
+
 	// Get the target path in the repository
 	target, err := os.Readlink(absPath)
 	if err != nil {
@@ -219,7 +292,7 @@ func (l *Lnk) Remove(filePath string) error {
 		target = filepath.Join(filepath.Dir(absPath), target)
 	}
 
-	basename := filepath.Base(target)
+	repoName := filepath.Base(target)
 
 	// Check if target is a directory or file
 	info, err := os.Stat(target)
@@ -232,13 +305,13 @@ func (l *Lnk) Remove(filePath string) error {
 		return fmt.Errorf("failed to remove symlink: %w", err)
 	}
 
-	// Remove from .lnk tracking file
+	// Remove from .lnk tracking file using relative path
-	if err := l.removeManagedItem(absPath); err != nil {
+	if err := l.removeManagedItem(relativePath); 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 {
+	if err := l.git.Remove(repoName); err != nil {
 		return fmt.Errorf("failed to remove from git: %w", err)
 	}
 
@@ -248,6 +321,7 @@ func (l *Lnk) Remove(filePath string) error {
 	}
 
 	// Commit both changes together
+	basename := filepath.Base(relativePath)
 	if err := l.git.Commit(fmt.Sprintf("lnk: removed %s", basename)); err != nil {
 		return fmt.Errorf("failed to commit changes: %w", err)
 	}
@@ -276,6 +350,7 @@ type StatusInfo struct {
 	Ahead  int
 	Behind int
 	Remote string
+	Dirty  bool
 }
 
 // Status returns the repository sync status
@@ -294,6 +369,7 @@ func (l *Lnk) Status() (*StatusInfo, error) {
 		Ahead:  gitStatus.Ahead,
 		Behind: gitStatus.Behind,
 		Remote: gitStatus.Remote,
+		Dirty:  gitStatus.Dirty,
 	}, nil
 }
 
@@ -352,9 +428,12 @@ func (l *Lnk) Pull() ([]string, error) {
 	return restored, nil
 }
 
-// RestoreSymlinks finds all managed items from .lnk file and ensures they have proper symlinks
+// List returns the list of files and directories currently managed by lnk
-func (l *Lnk) RestoreSymlinks() ([]string, error) {
+func (l *Lnk) List() ([]string, error) {
-	var restored []string
+	// Check if repository is initialized
+	if !l.git.IsGitRepository() {
+		return nil, fmt.Errorf("❌ Lnk repository not initialized\n   💡 Run \033[1mlnk init\033[0m first")
+	}
 
 	// Get managed items from .lnk file
 	managedItems, err := l.getManagedItems()
@@ -362,28 +441,48 @@ func (l *Lnk) RestoreSymlinks() ([]string, error) {
 		return nil, fmt.Errorf("failed to get managed items: %w", err)
 	}
 
-	for _, itemName := range managedItems {
+	return managedItems, nil
-		repoItem := filepath.Join(l.repoPath, itemName)
+}
+
+// RestoreSymlinks finds all managed items from .lnk file and ensures they have proper symlinks
+func (l *Lnk) RestoreSymlinks() ([]string, error) {
+	var restored []string
+
+	// Get managed items from .lnk file (now containing relative paths)
+	managedItems, err := l.getManagedItems()
+	if err != nil {
+		return nil, fmt.Errorf("failed to get managed items: %w", err)
+	}
+
+	homeDir, err := os.UserHomeDir()
+	if err != nil {
+		return nil, fmt.Errorf("failed to get home directory: %w", err)
+	}
+
+	for _, relativePath := range managedItems {
+		// Generate repository name from relative path
+		repoName := generateRepoName(relativePath)
+		repoItem := filepath.Join(l.repoPath, repoName)
 
 		// Check if item exists in repository
 		if _, err := os.Stat(repoItem); os.IsNotExist(err) {
 			continue // Skip missing items
 		}
 
-		// Determine where the symlink should be
+		// Determine where the symlink should be created
-		// For config files, we'll place them in the user's home directory
+		symlinkPath := filepath.Join(homeDir, relativePath)
-		homeDir, err := os.UserHomeDir()
-		if err != nil {
-			return nil, fmt.Errorf("failed to get home directory: %w", err)
-		}
-
-		symlinkPath := filepath.Join(homeDir, itemName)
 
 		// Check if symlink already exists and is correct
 		if l.isValidSymlink(symlinkPath, repoItem) {
 			continue
 		}
 
+		// Ensure parent directory exists
+		symlinkDir := filepath.Dir(symlinkPath)
+		if err := os.MkdirAll(symlinkDir, 0755); err != nil {
+			return nil, fmt.Errorf("failed to create directory %s: %w", symlinkDir, err)
+		}
+
 		// Remove existing file/symlink if it exists
 		if _, err := os.Lstat(symlinkPath); err == nil {
 			if err := os.RemoveAll(symlinkPath); err != nil {
@@ -393,10 +492,10 @@ func (l *Lnk) RestoreSymlinks() ([]string, error) {
 
 		// Create symlink
 		if err := l.fs.CreateSymlink(repoItem, symlinkPath); err != nil {
-			return nil, fmt.Errorf("failed to create symlink for %s: %w", itemName, err)
+			return nil, fmt.Errorf("failed to create symlink for %s: %w", relativePath, err)
 		}
 
-		restored = append(restored, itemName)
+		restored = append(restored, relativePath)
 	}
 
 	return restored, nil
@@ -470,25 +569,22 @@ func (l *Lnk) getManagedItems() ([]string, error) {
 }
 
 // addManagedItem adds an item to the .lnk tracking file
-func (l *Lnk) addManagedItem(itemPath string) error {
+func (l *Lnk) addManagedItem(relativePath 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 {
+		if item == relativePath {
 			return nil // Already managed
 		}
 	}
 
-	// Add new item
+	// Add new item using relative path
-	items = append(items, basename)
+	items = append(items, relativePath)
 
 	// Sort for consistent ordering
 	sort.Strings(items)
@@ -497,20 +593,17 @@ func (l *Lnk) addManagedItem(itemPath string) error {
 }
 
 // removeManagedItem removes an item from the .lnk tracking file
-func (l *Lnk) removeManagedItem(itemPath string) error {
+func (l *Lnk) removeManagedItem(relativePath 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
+	// Remove item using relative path
-	basename := filepath.Base(itemPath)
-
-	// Remove item
 	var newItems []string
 	for _, item := range items {
-		if item != basename {
+		if item != relativePath {
 			newItems = append(newItems, item)
 		}
 	}

internal/core/lnk_test.go

@@ -0,0 +1,591 @@
+package core
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"github.com/stretchr/testify/suite"
+)
+
+type CoreTestSuite struct {
+	suite.Suite
+	tempDir     string
+	originalDir string
+	lnk         *Lnk
+}
+
+func (suite *CoreTestSuite) SetupTest() {
+	// Create temporary directory for each test
+	tempDir, err := os.MkdirTemp("", "lnk-test-*")
+	suite.Require().NoError(err)
+	suite.tempDir = tempDir
+
+	// Change to temp directory
+	originalDir, err := os.Getwd()
+	suite.Require().NoError(err)
+	suite.originalDir = originalDir
+
+	err = os.Chdir(tempDir)
+	suite.Require().NoError(err)
+
+	// Set XDG_CONFIG_HOME to temp directory
+	suite.T().Setenv("XDG_CONFIG_HOME", tempDir)
+
+	// Initialize Lnk instance
+	suite.lnk = NewLnk()
+}
+
+func (suite *CoreTestSuite) TearDownTest() {
+	// Return to original directory
+	err := os.Chdir(suite.originalDir)
+	suite.Require().NoError(err)
+
+	// Clean up temp directory
+	err = os.RemoveAll(suite.tempDir)
+	suite.Require().NoError(err)
+}
+
+// Test core initialization functionality
+func (suite *CoreTestSuite) TestCoreInit() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Check that the lnk directory was created
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	suite.DirExists(lnkDir)
+
+	// Check that Git repo was initialized
+	gitDir := filepath.Join(lnkDir, ".git")
+	suite.DirExists(gitDir)
+}
+
+// Test core add/remove functionality with files
+func (suite *CoreTestSuite) TestCoreFileOperations() {
+	// Initialize first
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create a test file
+	testFile := filepath.Join(suite.tempDir, ".bashrc")
+	content := "export PATH=$PATH:/usr/local/bin"
+	err = os.WriteFile(testFile, []byte(content), 0644)
+	suite.Require().NoError(err)
+
+	// Add the file
+	err = suite.lnk.Add(testFile)
+	suite.Require().NoError(err)
+
+	// Verify symlink and repo file
+	info, err := os.Lstat(testFile)
+	suite.Require().NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	// The repository file will have a generated name based on the relative path
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	entries, err := os.ReadDir(lnkDir)
+	suite.Require().NoError(err)
+
+	var repoFile string
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), ".bashrc") && entry.Name() != ".lnk" {
+			repoFile = filepath.Join(lnkDir, entry.Name())
+			break
+		}
+	}
+	suite.NotEmpty(repoFile, "Repository should contain a file with .bashrc in the name")
+	suite.FileExists(repoFile)
+
+	// Verify content is preserved
+	repoContent, err := os.ReadFile(repoFile)
+	suite.Require().NoError(err)
+	suite.Equal(content, string(repoContent))
+
+	// Test remove
+	err = suite.lnk.Remove(testFile)
+	suite.Require().NoError(err)
+
+	// Verify symlink is gone and regular file is restored
+	info, err = os.Lstat(testFile)
+	suite.Require().NoError(err)
+	suite.Equal(os.FileMode(0), info.Mode()&os.ModeSymlink) // Not a symlink
+
+	// Verify content is preserved
+	restoredContent, err := os.ReadFile(testFile)
+	suite.Require().NoError(err)
+	suite.Equal(content, string(restoredContent))
+}
+
+// Test core add/remove functionality with directories
+func (suite *CoreTestSuite) TestCoreDirectoryOperations() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create a directory with files
+	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)
+
+	// Add the directory
+	err = suite.lnk.Add(testDir)
+	suite.Require().NoError(err)
+
+	// Verify directory is now a symlink
+	info, err := os.Lstat(testDir)
+	suite.Require().NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	// Check that some repository directory exists with testdir in the name
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	entries, err := os.ReadDir(lnkDir)
+	suite.Require().NoError(err)
+
+	var repoDir string
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), "testdir") && entry.Name() != ".lnk" {
+			repoDir = filepath.Join(lnkDir, entry.Name())
+			break
+		}
+	}
+	suite.NotEmpty(repoDir, "Repository should contain a directory with testdir in the name")
+	suite.DirExists(repoDir)
+
+	// Remove the directory
+	err = suite.lnk.Remove(testDir)
+	suite.Require().NoError(err)
+
+	// Verify 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
+
+	// Verify content is preserved
+	restoredContent, err := os.ReadFile(testFile)
+	suite.Require().NoError(err)
+	suite.Equal(content, string(restoredContent))
+}
+
+// Test .lnk file tracking functionality
+func (suite *CoreTestSuite) TestLnkFileTracking() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Add multiple items
+	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)
+
+	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)
+
+	// The .lnk file now contains relative paths, not basenames
+	// Check that the content contains references to .bashrc and .ssh
+	content := string(lnkContent)
+	suite.Contains(content, ".bashrc", ".lnk file should contain reference to .bashrc")
+	suite.Contains(content, ".ssh", ".lnk file should contain reference to .ssh")
+
+	// Remove one item and verify tracking 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)
+
+	content = string(lnkContent)
+	suite.Contains(content, ".ssh", ".lnk file should still contain reference to .ssh")
+	suite.NotContains(content, ".bashrc", ".lnk file should not contain reference to .bashrc after removal")
+}
+
+// Test XDG_CONFIG_HOME fallback
+func (suite *CoreTestSuite) TestXDGConfigHomeFallback() {
+	// Test fallback to ~/.config/lnk when XDG_CONFIG_HOME is not set
+	suite.T().Setenv("XDG_CONFIG_HOME", "")
+
+	homeDir := filepath.Join(suite.tempDir, "home")
+	err := os.MkdirAll(homeDir, 0755)
+	suite.Require().NoError(err)
+	suite.T().Setenv("HOME", homeDir)
+
+	lnk := NewLnk()
+	err = lnk.Init()
+	suite.Require().NoError(err)
+
+	// Check that the lnk directory was created under ~/.config/lnk
+	expectedDir := filepath.Join(homeDir, ".config", "lnk")
+	suite.DirExists(expectedDir)
+}
+
+// Test symlink restoration (pull functionality)
+func (suite *CoreTestSuite) TestSymlinkRestoration() {
+	_ = suite.lnk.Init()
+
+	// Create a file in the repo directly (simulating a pull)
+	repoFile := filepath.Join(suite.tempDir, "lnk", ".bashrc")
+	content := "export PATH=$PATH:/usr/local/bin"
+	err := os.WriteFile(repoFile, []byte(content), 0644)
+	suite.Require().NoError(err)
+
+	// Create .lnk file to track it
+	lnkFile := filepath.Join(suite.tempDir, "lnk", ".lnk")
+	err = os.WriteFile(lnkFile, []byte(".bashrc\n"), 0644)
+	suite.Require().NoError(err)
+
+	// Get home directory for the test
+	homeDir, err := os.UserHomeDir()
+	suite.Require().NoError(err)
+
+	targetFile := filepath.Join(homeDir, ".bashrc")
+
+	// Clean up the test file after the test
+	defer func() {
+		_ = os.Remove(targetFile)
+	}()
+
+	// Test symlink restoration
+	restored, err := suite.lnk.RestoreSymlinks()
+	suite.Require().NoError(err)
+
+	// Should have restored the symlink
+	suite.Len(restored, 1)
+	suite.Equal(".bashrc", restored[0])
+
+	// Check that file is now a symlink
+	info, err := os.Lstat(targetFile)
+	suite.NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+}
+
+// Test error conditions
+func (suite *CoreTestSuite) TestErrorConditions() {
+	// Test add nonexistent file
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add("/nonexistent/file")
+	suite.Error(err)
+	suite.Contains(err.Error(), "File does not exist")
+
+	// Test remove unmanaged file
+	testFile := filepath.Join(suite.tempDir, ".regularfile")
+	err = os.WriteFile(testFile, []byte("content"), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Remove(testFile)
+	suite.Error(err)
+	suite.Contains(err.Error(), "File is not managed by lnk")
+
+	// Test status without remote
+	_, err = suite.lnk.Status()
+	suite.Error(err)
+	suite.Contains(err.Error(), "no remote configured")
+}
+
+// Test git operations
+func (suite *CoreTestSuite) TestGitOperations() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Add a file to create a commit
+	testFile := filepath.Join(suite.tempDir, ".bashrc")
+	content := "export PATH=$PATH:/usr/local/bin"
+	err = os.WriteFile(testFile, []byte(content), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add(testFile)
+	suite.Require().NoError(err)
+
+	// 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 .bashrc")
+
+	// Test add remote
+	err = suite.lnk.AddRemote("origin", "https://github.com/test/dotfiles.git")
+	suite.Require().NoError(err)
+
+	// Test status with remote
+	status, err := suite.lnk.Status()
+	suite.Require().NoError(err)
+	suite.Equal(1, status.Ahead)
+	suite.Equal(0, status.Behind)
+}
+
+// Test edge case: files with same basename from different directories should be handled properly
+func (suite *CoreTestSuite) TestSameBasenameFilesOverwrite() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create two directories with files having the same basename
+	dirA := filepath.Join(suite.tempDir, "a")
+	dirB := filepath.Join(suite.tempDir, "b")
+	err = os.MkdirAll(dirA, 0755)
+	suite.Require().NoError(err)
+	err = os.MkdirAll(dirB, 0755)
+	suite.Require().NoError(err)
+
+	// Create files with same basename but different content
+	fileA := filepath.Join(dirA, "config.json")
+	fileB := filepath.Join(dirB, "config.json")
+	contentA := `{"name": "config_a"}`
+	contentB := `{"name": "config_b"}`
+
+	err = os.WriteFile(fileA, []byte(contentA), 0644)
+	suite.Require().NoError(err)
+	err = os.WriteFile(fileB, []byte(contentB), 0644)
+	suite.Require().NoError(err)
+
+	// Add first file
+	err = suite.lnk.Add(fileA)
+	suite.Require().NoError(err)
+
+	// Verify first file is managed correctly and preserves content
+	info, err := os.Lstat(fileA)
+	suite.Require().NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	symlinkContentA, err := os.ReadFile(fileA)
+	suite.Require().NoError(err)
+	suite.Equal(contentA, string(symlinkContentA), "First file should preserve its original content")
+
+	// Add second file - this should work without overwriting the first
+	err = suite.lnk.Add(fileB)
+	suite.Require().NoError(err)
+
+	// Verify second file is managed
+	info, err = os.Lstat(fileB)
+	suite.Require().NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	// CORRECT BEHAVIOR: Both files should preserve their original content
+	symlinkContentA, err = os.ReadFile(fileA)
+	suite.Require().NoError(err)
+	symlinkContentB, err := os.ReadFile(fileB)
+	suite.Require().NoError(err)
+
+	suite.Equal(contentA, string(symlinkContentA), "First file should keep its original content")
+	suite.Equal(contentB, string(symlinkContentB), "Second file should keep its original content")
+
+	// Both files should be removable independently
+	err = suite.lnk.Remove(fileA)
+	suite.Require().NoError(err, "First file should be removable")
+
+	// First file should be restored with correct content
+	info, err = os.Lstat(fileA)
+	suite.Require().NoError(err)
+	suite.Equal(os.FileMode(0), info.Mode()&os.ModeSymlink) // Not a symlink anymore
+
+	restoredContentA, err := os.ReadFile(fileA)
+	suite.Require().NoError(err)
+	suite.Equal(contentA, string(restoredContentA), "Restored file should have original content")
+
+	// Second file should still be manageable and removable
+	err = suite.lnk.Remove(fileB)
+	suite.Require().NoError(err, "Second file should also be removable without errors")
+
+	// Second file should be restored with correct content
+	info, err = os.Lstat(fileB)
+	suite.Require().NoError(err)
+	suite.Equal(os.FileMode(0), info.Mode()&os.ModeSymlink) // Not a symlink anymore
+
+	restoredContentB, err := os.ReadFile(fileB)
+	suite.Require().NoError(err)
+	suite.Equal(contentB, string(restoredContentB), "Second restored file should have original content")
+}
+
+// Test another variant: adding files with same basename should work correctly
+func (suite *CoreTestSuite) TestSameBasenameSequentialAdd() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create subdirectories in different locations
+	configDir := filepath.Join(suite.tempDir, "config")
+	backupDir := filepath.Join(suite.tempDir, "backup")
+	err = os.MkdirAll(configDir, 0755)
+	suite.Require().NoError(err)
+	err = os.MkdirAll(backupDir, 0755)
+	suite.Require().NoError(err)
+
+	// Create files with same basename (.bashrc)
+	configBashrc := filepath.Join(configDir, ".bashrc")
+	backupBashrc := filepath.Join(backupDir, ".bashrc")
+
+	originalContent := "export PATH=/usr/local/bin:$PATH"
+	backupContent := "export PATH=/opt/bin:$PATH"
+
+	err = os.WriteFile(configBashrc, []byte(originalContent), 0644)
+	suite.Require().NoError(err)
+	err = os.WriteFile(backupBashrc, []byte(backupContent), 0644)
+	suite.Require().NoError(err)
+
+	// Add first .bashrc
+	err = suite.lnk.Add(configBashrc)
+	suite.Require().NoError(err)
+
+	// Add second .bashrc - should work without overwriting the first
+	err = suite.lnk.Add(backupBashrc)
+	suite.Require().NoError(err)
+
+	// Check .lnk tracking file should track both properly
+	lnkFile := filepath.Join(suite.tempDir, "lnk", ".lnk")
+	lnkContent, err := os.ReadFile(lnkFile)
+	suite.Require().NoError(err)
+
+	// Both entries should be tracked and distinguishable
+	content := string(lnkContent)
+	suite.Contains(content, ".bashrc", "Both .bashrc files should be tracked")
+
+	// Both files should maintain their distinct content
+	content1, err := os.ReadFile(configBashrc)
+	suite.Require().NoError(err)
+	content2, err := os.ReadFile(backupBashrc)
+	suite.Require().NoError(err)
+
+	suite.Equal(originalContent, string(content1), "First file should keep original content")
+	suite.Equal(backupContent, string(content2), "Second file should keep its distinct content")
+
+	// Both should be removable independently
+	err = suite.lnk.Remove(configBashrc)
+	suite.Require().NoError(err, "First .bashrc should be removable")
+
+	err = suite.lnk.Remove(backupBashrc)
+	suite.Require().NoError(err, "Second .bashrc should be removable")
+}
+
+// Test dirty repository status detection
+func (suite *CoreTestSuite) TestStatusDetectsDirtyRepo() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Add and commit a file
+	testFile := filepath.Join(suite.tempDir, "a")
+	err = os.WriteFile(testFile, []byte("abc"), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add(testFile)
+	suite.Require().NoError(err)
+
+	// Add a remote so status works
+	err = suite.lnk.AddRemote("origin", "https://github.com/test/dotfiles.git")
+	suite.Require().NoError(err)
+
+	// Check status - should be clean but ahead of remote
+	status, err := suite.lnk.Status()
+	suite.Require().NoError(err)
+	suite.Equal(1, status.Ahead)
+	suite.Equal(0, status.Behind)
+	suite.False(status.Dirty, "Repository should not be dirty after commit")
+
+	// Now edit the managed file (simulating the issue scenario)
+	err = os.WriteFile(testFile, []byte("def"), 0644)
+	suite.Require().NoError(err)
+
+	// Check status again - should detect dirty state
+	status, err = suite.lnk.Status()
+	suite.Require().NoError(err)
+	suite.Equal(1, status.Ahead)
+	suite.Equal(0, status.Behind)
+	suite.True(status.Dirty, "Repository should be dirty after editing managed file")
+}
+
+// Test list functionality
+func (suite *CoreTestSuite) TestListManagedItems() {
+	// Test list without init - should fail
+	_, err := suite.lnk.List()
+	suite.Error(err)
+	suite.Contains(err.Error(), "Lnk repository not initialized")
+
+	// Initialize repository
+	err = suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Test list with no managed files
+	items, err := suite.lnk.List()
+	suite.Require().NoError(err)
+	suite.Empty(items)
+
+	// Add a file
+	testFile := filepath.Join(suite.tempDir, ".bashrc")
+	content := "export PATH=$PATH:/usr/local/bin"
+	err = os.WriteFile(testFile, []byte(content), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add(testFile)
+	suite.Require().NoError(err)
+
+	// Test list with one managed file
+	items, err = suite.lnk.List()
+	suite.Require().NoError(err)
+	suite.Len(items, 1)
+	suite.Contains(items[0], ".bashrc")
+
+	// Add a directory
+	testDir := filepath.Join(suite.tempDir, ".config")
+	err = os.MkdirAll(testDir, 0755)
+	suite.Require().NoError(err)
+	configFile := filepath.Join(testDir, "app.conf")
+	err = os.WriteFile(configFile, []byte("setting=value"), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add(testDir)
+	suite.Require().NoError(err)
+
+	// Test list with multiple managed items
+	items, err = suite.lnk.List()
+	suite.Require().NoError(err)
+	suite.Len(items, 2)
+
+	// Check that both items are present
+	found := make(map[string]bool)
+	for _, item := range items {
+		if strings.Contains(item, ".bashrc") {
+			found[".bashrc"] = true
+		}
+		if strings.Contains(item, ".config") {
+			found[".config"] = true
+		}
+	}
+	suite.True(found[".bashrc"], "Should contain .bashrc")
+	suite.True(found[".config"], "Should contain .config")
+
+	// Remove one item and verify list is updated
+	err = suite.lnk.Remove(testFile)
+	suite.Require().NoError(err)
+
+	items, err = suite.lnk.List()
+	suite.Require().NoError(err)
+	suite.Len(items, 1)
+	suite.Contains(items[0], ".config")
+}
+
+func TestCoreSuite(t *testing.T) {
+	suite.Run(t, new(CoreTestSuite))
+}

internal/git/git.go

@@ -305,6 +305,7 @@ type StatusInfo struct {
 	Ahead  int
 	Behind int
 	Remote string
+	Dirty  bool
 }
 
 // GetStatus returns the repository status relative to remote
@@ -315,6 +316,12 @@ func (g *Git) GetStatus() (*StatusInfo, error) {
 		return nil, err
 	}
 
+	// Check for uncommitted changes
+	dirty, err := g.HasChanges()
+	if err != nil {
+		return nil, fmt.Errorf("failed to check for uncommitted changes: %w", err)
+	}
+
 	// Get the remote tracking branch
 	cmd := exec.Command("git", "rev-parse", "--abbrev-ref", "--symbolic-full-name", "@{u}")
 	cmd.Dir = g.repoPath
@@ -327,6 +334,7 @@ func (g *Git) GetStatus() (*StatusInfo, error) {
 			Ahead:  g.getAheadCount(remoteBranch),
 			Behind: 0, // Can't be behind if no upstream
 			Remote: remoteBranch,
+			Dirty:  dirty,
 		}, nil
 	}
 
@@ -336,6 +344,7 @@ func (g *Git) GetStatus() (*StatusInfo, error) {
 		Ahead:  g.getAheadCount(remoteBranch),
 		Behind: g.getBehindCount(remoteBranch),
 		Remote: remoteBranch,
+		Dirty:  dirty,
 	}, nil
 }
 

test/integration_test.go

@@ -1,718 +0,0 @@
-package test
-
-import (
-	"os"
-	"os/exec"
-	"path/filepath"
-	"strings"
-	"testing"
-
-	"github.com/stretchr/testify/suite"
-	"github.com/yarlson/lnk/internal/core"
-)
-
-type LnkIntegrationTestSuite struct {
-	suite.Suite
-	tempDir     string
-	originalDir string
-	lnk         *core.Lnk
-}
-
-func (suite *LnkIntegrationTestSuite) SetupTest() {
-	// Create temporary directory for each test
-	tempDir, err := os.MkdirTemp("", "lnk-test-*")
-	suite.Require().NoError(err)
-	suite.tempDir = tempDir
-
-	// Change to temp directory
-	originalDir, err := os.Getwd()
-	suite.Require().NoError(err)
-	suite.originalDir = originalDir
-
-	err = os.Chdir(tempDir)
-	suite.Require().NoError(err)
-
-	// Set XDG_CONFIG_HOME to temp directory
-	suite.T().Setenv("XDG_CONFIG_HOME", tempDir)
-
-	// Initialize Lnk instance
-	suite.lnk = core.NewLnk()
-}
-
-func (suite *LnkIntegrationTestSuite) TearDownTest() {
-	// Return to original directory
-	err := os.Chdir(suite.originalDir)
-	suite.Require().NoError(err)
-
-	// Clean up temp directory
-	err = os.RemoveAll(suite.tempDir)
-	suite.Require().NoError(err)
-}
-
-func (suite *LnkIntegrationTestSuite) TestInit() {
-	// Test that init creates the directory and Git repo
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	// Check that the lnk directory was created
-	lnkDir := filepath.Join(suite.tempDir, "lnk")
-	suite.DirExists(lnkDir)
-
-	// Check that Git repo was initialized
-	gitDir := filepath.Join(lnkDir, ".git")
-	suite.DirExists(gitDir)
-
-	// Verify it's a non-bare repo
-	configPath := filepath.Join(gitDir, "config")
-	suite.FileExists(configPath)
-
-	// Verify the default branch is set to 'main'
-	cmd := exec.Command("git", "symbolic-ref", "HEAD")
-	cmd.Dir = lnkDir
-	output, err := cmd.Output()
-	suite.Require().NoError(err)
-	suite.Equal("refs/heads/main", strings.TrimSpace(string(output)))
-}
-
-func (suite *LnkIntegrationTestSuite) TestAddFile() {
-	// Initialize first
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	// Create a test file
-	testFile := filepath.Join(suite.tempDir, ".bashrc")
-	content := "export PATH=$PATH:/usr/local/bin"
-	err = os.WriteFile(testFile, []byte(content), 0644)
-	suite.Require().NoError(err)
-
-	// Add the file
-	err = suite.lnk.Add(testFile)
-	suite.Require().NoError(err)
-
-	// Check that the original file is now a symlink
-	info, err := os.Lstat(testFile)
-	suite.Require().NoError(err)
-	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
-
-	// Check that the file exists in the repo
-	repoFile := filepath.Join(suite.tempDir, "lnk", ".bashrc")
-	suite.FileExists(repoFile)
-
-	// Check that the content is preserved
-	repoContent, err := os.ReadFile(repoFile)
-	suite.Require().NoError(err)
-	suite.Equal(content, string(repoContent))
-
-	// Check that symlink points to the correct location
-	linkTarget, err := os.Readlink(testFile)
-	suite.Require().NoError(err)
-	expectedTarget, err := filepath.Rel(filepath.Dir(testFile), repoFile)
-	suite.Require().NoError(err)
-	suite.Equal(expectedTarget, linkTarget)
-
-	// 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 .bashrc")
-}
-
-func (suite *LnkIntegrationTestSuite) TestRemoveFile() {
-	// Initialize and add a file first
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	testFile := filepath.Join(suite.tempDir, ".vimrc")
-	content := "set number"
-	err = os.WriteFile(testFile, []byte(content), 0644)
-	suite.Require().NoError(err)
-
-	err = suite.lnk.Add(testFile)
-	suite.Require().NoError(err)
-
-	// Now remove the file
-	err = suite.lnk.Remove(testFile)
-	suite.Require().NoError(err)
-
-	// Check that the symlink is gone and regular file is restored
-	info, err := os.Lstat(testFile)
-	suite.Require().NoError(err)
-	suite.Equal(os.FileMode(0), info.Mode()&os.ModeSymlink) // Not a symlink
-
-	// Check that content is preserved
-	restoredContent, err := os.ReadFile(testFile)
-	suite.Require().NoError(err)
-	suite.Equal(content, string(restoredContent))
-
-	// Check that file is removed from repo
-	repoFile := filepath.Join(suite.tempDir, "lnk", ".vimrc")
-	suite.NoFileExists(repoFile)
-
-	// 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 .vimrc")
-	suite.Contains(commits[1], "lnk: added .vimrc")
-}
-
-func (suite *LnkIntegrationTestSuite) TestAddNonexistentFile() {
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	err = suite.lnk.Add("/nonexistent/file")
-	suite.Error(err)
-	suite.Contains(err.Error(), "File does not exist")
-}
-
-func (suite *LnkIntegrationTestSuite) TestAddDirectory() {
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	// 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.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() {
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	// Create a regular file (not managed by lnk)
-	testFile := filepath.Join(suite.tempDir, ".regularfile")
-	err = os.WriteFile(testFile, []byte("content"), 0644)
-	suite.Require().NoError(err)
-
-	err = suite.lnk.Remove(testFile)
-	suite.Error(err)
-	suite.Contains(err.Error(), "File is not managed by lnk")
-}
-
-func (suite *LnkIntegrationTestSuite) TestXDGConfigHomeFallback() {
-	// Test fallback to ~/.config/lnk when XDG_CONFIG_HOME is not set
-	suite.T().Setenv("XDG_CONFIG_HOME", "")
-
-	homeDir := filepath.Join(suite.tempDir, "home")
-	err := os.MkdirAll(homeDir, 0755)
-	suite.Require().NoError(err)
-	suite.T().Setenv("HOME", homeDir)
-
-	lnk := core.NewLnk()
-	err = lnk.Init()
-	suite.Require().NoError(err)
-
-	// Check that the lnk directory was created under ~/.config/lnk
-	expectedDir := filepath.Join(homeDir, ".config", "lnk")
-	suite.DirExists(expectedDir)
-}
-
-func (suite *LnkIntegrationTestSuite) TestInitWithRemote() {
-	// Test that init with remote adds the origin remote
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	remoteURL := "https://github.com/user/dotfiles.git"
-	err = suite.lnk.AddRemote("origin", remoteURL)
-	suite.Require().NoError(err)
-
-	// Verify the remote was added by checking git config
-	lnkDir := filepath.Join(suite.tempDir, "lnk")
-	cmd := exec.Command("git", "remote", "get-url", "origin")
-	cmd.Dir = lnkDir
-
-	output, err := cmd.Output()
-	suite.Require().NoError(err)
-	suite.Equal(remoteURL, strings.TrimSpace(string(output)))
-}
-
-func (suite *LnkIntegrationTestSuite) TestInitIdempotent() {
-	// Test that running init multiple times is safe
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	lnkDir := filepath.Join(suite.tempDir, "lnk")
-
-	// Add a file to the repo to ensure it's not lost
-	testFile := filepath.Join(lnkDir, "test.txt")
-	err = os.WriteFile(testFile, []byte("test content"), 0644)
-	suite.Require().NoError(err)
-
-	// Run init again - should be idempotent
-	err = suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	// File should still exist
-	suite.FileExists(testFile)
-	content, err := os.ReadFile(testFile)
-	suite.Require().NoError(err)
-	suite.Equal("test content", string(content))
-}
-
-func (suite *LnkIntegrationTestSuite) TestInitWithExistingRemote() {
-	// Test init with remote when remote already exists (same URL)
-	remoteURL := "https://github.com/user/dotfiles.git"
-
-	// First init with remote
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-	err = suite.lnk.AddRemote("origin", remoteURL)
-	suite.Require().NoError(err)
-
-	// Init again with same remote should be idempotent
-	err = suite.lnk.Init()
-	suite.Require().NoError(err)
-	err = suite.lnk.AddRemote("origin", remoteURL)
-	suite.Require().NoError(err)
-
-	// Verify remote is still correct
-	lnkDir := filepath.Join(suite.tempDir, "lnk")
-	cmd := exec.Command("git", "remote", "get-url", "origin")
-	cmd.Dir = lnkDir
-	output, err := cmd.Output()
-	suite.Require().NoError(err)
-	suite.Equal(remoteURL, strings.TrimSpace(string(output)))
-}
-
-func (suite *LnkIntegrationTestSuite) TestInitWithDifferentRemote() {
-	// Test init with different remote when remote already exists
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	// Add first remote
-	err = suite.lnk.AddRemote("origin", "https://github.com/user/dotfiles.git")
-	suite.Require().NoError(err)
-
-	// Try to add different remote - should error
-	err = suite.lnk.AddRemote("origin", "https://github.com/user/other-repo.git")
-	suite.Error(err)
-	suite.Contains(err.Error(), "already exists with different URL")
-}
-
-func (suite *LnkIntegrationTestSuite) TestInitWithNonLnkRepo() {
-	// Test init when directory contains a non-lnk Git repository
-	lnkDir := filepath.Join(suite.tempDir, "lnk")
-	err := os.MkdirAll(lnkDir, 0755)
-	suite.Require().NoError(err)
-
-	// Create a non-lnk git repo in the lnk directory
-	cmd := exec.Command("git", "init")
-	cmd.Dir = lnkDir
-	err = cmd.Run()
-	suite.Require().NoError(err)
-
-	// Add some content to make it look like a real repo
-	testFile := filepath.Join(lnkDir, "important-file.txt")
-	err = os.WriteFile(testFile, []byte("important data"), 0644)
-	suite.Require().NoError(err)
-
-	// Configure git and commit
-	cmd = exec.Command("git", "config", "user.name", "Test User")
-	cmd.Dir = lnkDir
-	err = cmd.Run()
-	suite.Require().NoError(err)
-
-	cmd = exec.Command("git", "config", "user.email", "test@example.com")
-	cmd.Dir = lnkDir
-	err = cmd.Run()
-	suite.Require().NoError(err)
-
-	cmd = exec.Command("git", "add", "important-file.txt")
-	cmd.Dir = lnkDir
-	err = cmd.Run()
-	suite.Require().NoError(err)
-
-	cmd = exec.Command("git", "commit", "-m", "important commit")
-	cmd.Dir = lnkDir
-	err = cmd.Run()
-	suite.Require().NoError(err)
-
-	// Now try to init lnk - should error to protect existing repo
-	err = suite.lnk.Init()
-	suite.Error(err)
-	suite.Contains(err.Error(), "contains an existing Git repository")
-
-	// Verify the original file is still there
-	suite.FileExists(testFile)
-}
-
-// TestSyncStatus tests the status command functionality
-func (suite *LnkIntegrationTestSuite) TestSyncStatus() {
-	// Initialize repo with remote
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	err = suite.lnk.AddRemote("origin", "https://github.com/test/dotfiles.git")
-	suite.Require().NoError(err)
-
-	// Add a file to create some local changes
-	testFile := filepath.Join(suite.tempDir, ".bashrc")
-	content := "export PATH=$PATH:/usr/local/bin"
-	err = os.WriteFile(testFile, []byte(content), 0644)
-	suite.Require().NoError(err)
-
-	err = suite.lnk.Add(testFile)
-	suite.Require().NoError(err)
-
-	// Get status - should show 1 commit ahead
-	status, err := suite.lnk.Status()
-	suite.Require().NoError(err)
-	suite.Equal(1, status.Ahead)
-	suite.Equal(0, status.Behind)
-	suite.Equal("origin/main", status.Remote)
-}
-
-// TestSyncPush tests the push command functionality
-func (suite *LnkIntegrationTestSuite) TestSyncPush() {
-	// Initialize repo
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	// Add remote for push to work
-	err = suite.lnk.AddRemote("origin", "https://github.com/test/dotfiles.git")
-	suite.Require().NoError(err)
-
-	// Add a file
-	testFile := filepath.Join(suite.tempDir, ".vimrc")
-	content := "set number"
-	err = os.WriteFile(testFile, []byte(content), 0644)
-	suite.Require().NoError(err)
-
-	err = suite.lnk.Add(testFile)
-	suite.Require().NoError(err)
-
-	// Add another file for a second commit
-	testFile2 := filepath.Join(suite.tempDir, ".gitconfig")
-	content2 := "[user]\n    name = Test User"
-	err = os.WriteFile(testFile2, []byte(content2), 0644)
-	suite.Require().NoError(err)
-
-	err = suite.lnk.Add(testFile2)
-	suite.Require().NoError(err)
-
-	// Modify one of the files to create uncommitted changes
-	repoFile := filepath.Join(suite.tempDir, "lnk", ".vimrc")
-	modifiedContent := "set number\nset relativenumber"
-	err = os.WriteFile(repoFile, []byte(modifiedContent), 0644)
-	suite.Require().NoError(err)
-
-	// Push should stage all changes and create a sync commit
-	message := "Updated configuration files"
-	err = suite.lnk.Push(message)
-	// In tests, push will fail because we don't have real remotes, but that's expected
-	// The important part is that it stages and commits changes
-	if err != nil {
-		suite.Contains(err.Error(), "git push failed")
-	}
-
-	// Check that a sync commit was made (even if push failed)
-	commits, err := suite.lnk.GetCommits()
-	suite.Require().NoError(err)
-	suite.GreaterOrEqual(len(commits), 3) // at least 2 add commits + 1 sync commit
-	suite.Contains(commits[0], message)   // Latest commit should contain our message
-}
-
-// TestSyncPull tests the pull command functionality
-func (suite *LnkIntegrationTestSuite) TestSyncPull() {
-	// 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)
-
-	// Pull should attempt to pull from remote (will fail in tests but that's expected)
-	_, err = suite.lnk.Pull()
-	// In tests, pull will fail because we don't have real remotes, but that's expected
-	suite.Error(err)
-	suite.Contains(err.Error(), "git pull failed")
-
-	// Test RestoreSymlinks functionality separately
-	// Create a file in the repo directly
-	repoFile := filepath.Join(suite.tempDir, "lnk", ".bashrc")
-	content := "export PATH=$PATH:/usr/local/bin"
-	err = os.WriteFile(repoFile, []byte(content), 0644)
-	suite.Require().NoError(err)
-
-	// Test that RestoreSymlinks can be called (even if it doesn't restore anything in this test setup)
-	restored, err := suite.lnk.RestoreSymlinks()
-	suite.Require().NoError(err)
-	// In this test setup, it might not restore anything, and that's okay for Phase 1
-	suite.GreaterOrEqual(len(restored), 0)
-}
-
-// TestSyncStatusNoRemote tests status when no remote is configured
-func (suite *LnkIntegrationTestSuite) TestSyncStatusNoRemote() {
-	// Initialize repo without remote
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	// Status should indicate no remote
-	_, err = suite.lnk.Status()
-	suite.Error(err)
-	suite.Contains(err.Error(), "no remote configured")
-}
-
-// TestSyncPushWithModifiedFiles tests push when files are modified
-func (suite *LnkIntegrationTestSuite) TestSyncPushWithModifiedFiles() {
-	// Initialize repo and add a file
-	err := suite.lnk.Init()
-	suite.Require().NoError(err)
-
-	// Add remote for push to work
-	err = suite.lnk.AddRemote("origin", "https://github.com/test/dotfiles.git")
-	suite.Require().NoError(err)
-
-	testFile := filepath.Join(suite.tempDir, ".bashrc")
-	content := "export PATH=$PATH:/usr/local/bin"
-	err = os.WriteFile(testFile, []byte(content), 0644)
-	suite.Require().NoError(err)
-
-	err = suite.lnk.Add(testFile)
-	suite.Require().NoError(err)
-
-	// Modify the file in the repo (simulate editing managed file)
-	repoFile := filepath.Join(suite.tempDir, "lnk", ".bashrc")
-	modifiedContent := "export PATH=$PATH:/usr/local/bin\nexport EDITOR=vim"
-	err = os.WriteFile(repoFile, []byte(modifiedContent), 0644)
-	suite.Require().NoError(err)
-
-	// Push should detect and commit the changes
-	message := "Updated bashrc with editor setting"
-	err = suite.lnk.Push(message)
-	// In tests, push will fail because we don't have real remotes, but that's expected
-	if err != nil {
-		suite.Contains(err.Error(), "git push failed")
-	}
-
-	// Check that changes were committed (even if push failed)
-	commits, err := suite.lnk.GetCommits()
-	suite.Require().NoError(err)
-	suite.GreaterOrEqual(len(commits), 2) // add commit + sync commit
-	suite.Contains(commits[0], message)
-}
-
-func TestLnkIntegrationSuite(t *testing.T) {
-	suite.Run(t, new(LnkIntegrationTestSuite))
-}