feat(bootstrap): add automatic environment setup with bootstrap scripts

Implement bootstrap functionality for streamlined dotfiles setup:
- Add 'bootstrap' command to run setup scripts manually
- Auto-execute bootstrap on 'init' with remote (--no-bootstrap to skip)
- Update README with bootstrap usage and examples
- Extend tests to cover bootstrap scenarios

.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 -coverprofile=coverage.out ./test
+	@go test -v -cover ./...
+	@go test -coverprofile=coverage.out ./
 	@go tool cover -html=coverage.out -o coverage.html
 	@echo "$(GREEN)✓ Coverage report generated: coverage.html$(NC)"
 

README.md

@@ -2,11 +2,12 @@
 
 **Git-native dotfiles management that doesn't suck.**
 
-Move your dotfiles to `~/.config/lnk`, symlink them back, and use Git like normal. That's it.
+Move your dotfiles to `~/.config/lnk`, symlink them back, and use Git like normal. Supports both common configurations and host-specific setups. Automatically runs bootstrap scripts to set up your environment.
 
 ```bash
-lnk init
-lnk add ~/.vimrc ~/.bashrc
+lnk init -r git@github.com:user/dotfiles.git  # Clones & runs bootstrap automatically
+lnk add ~/.vimrc ~/.bashrc                    # Common config
+lnk add --host work ~/.ssh/config             # Host-specific config
 lnk push "setup"
 ```
 
@@ -42,32 +43,134 @@ git clone https://github.com/yarlson/lnk.git && cd lnk && go build . && sudo mv
 # Fresh start
 lnk init
 
-# With existing repo
+# With existing repo (runs bootstrap automatically)
 lnk init -r git@github.com:user/dotfiles.git
+
+# Skip automatic bootstrap
+lnk init -r git@github.com:user/dotfiles.git --no-bootstrap
+
+# Run bootstrap script manually
+lnk bootstrap
 ```
 
 ### Daily workflow
 
 ```bash
-# Add files/directories
+# Add files/directories (common config)
 lnk add ~/.vimrc ~/.config/nvim ~/.gitconfig
 
+# Add host-specific files
+lnk add --host laptop ~/.ssh/config
+lnk add --host work ~/.gitconfig
+
+# List managed files
+lnk list                    # Common config only
+lnk list --host laptop      # Laptop-specific config
+lnk list --all              # All configurations
+
 # Check status
 lnk status
 
 # Sync changes
 lnk push "updated vim config"
-lnk pull
+lnk pull                    # Pull common config
+lnk pull --host laptop      # Pull laptop-specific config
 ```
 
 ## How it works
 
 ```
+Common files:
 Before: ~/.vimrc (file)
 After:  ~/.vimrc -> ~/.config/lnk/.vimrc (symlink)
+
+Host-specific files:
+Before: ~/.ssh/config (file)
+After:  ~/.ssh/config -> ~/.config/lnk/laptop.lnk/.ssh/config (symlink)
 ```
 
-Your files live in `~/.config/lnk` (a Git repo). Lnk creates symlinks back to original locations. Edit files normally, use Git normally.
+Your files live in `~/.config/lnk` (a Git repo). Common files go in the root, host-specific files go in `<host>.lnk/` subdirectories. Lnk creates symlinks back to original locations. Edit files normally, use Git normally.
+
+## Bootstrap Support
+
+Lnk automatically runs bootstrap scripts when cloning dotfiles repositories, making it easy to set up your development environment. Just add a `bootstrap.sh` file to your dotfiles repo.
+
+### Examples
+
+**Simple bootstrap script:**
+
+```bash
+#!/bin/bash
+# bootstrap.sh
+echo "Setting up development environment..."
+
+# Install Homebrew (macOS)
+if ! command -v brew &> /dev/null; then
+    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+fi
+
+# Install packages
+brew install git vim tmux
+
+echo "✅ Setup complete!"
+```
+
+**Usage:**
+
+```bash
+# Automatic bootstrap on clone
+lnk init -r git@github.com:you/dotfiles.git
+# → Clones repo and runs bootstrap script automatically
+
+# Skip bootstrap if needed
+lnk init -r git@github.com:you/dotfiles.git --no-bootstrap
+
+# Run bootstrap manually later
+lnk bootstrap
+```
+
+## Multihost Support
+
+Lnk supports both **common configurations** (shared across all machines) and **host-specific configurations** (unique per machine).
+
+### File Organization
+
+```
+~/.config/lnk/
+├── .lnk                    # Tracks common files
+├── .lnk.laptop             # Tracks laptop-specific files
+├── .lnk.work               # Tracks work-specific files
+├── .vimrc                  # Common file
+├── .gitconfig              # Common file
+├── laptop.lnk/             # Laptop-specific storage
+│   ├── .ssh/
+│   │   └── config
+│   └── .tmux.conf
+└── work.lnk/               # Work-specific storage
+    ├── .ssh/
+    │   └── config
+    └── .gitconfig
+```
+
+### Usage Patterns
+
+```bash
+# Common config (shared everywhere)
+lnk add ~/.vimrc ~/.bashrc ~/.gitconfig
+
+# Host-specific config (unique per machine)
+lnk add --host $(hostname) ~/.ssh/config
+lnk add --host work ~/.gitconfig
+
+# List configurations
+lnk list                    # Common only
+lnk list --host work        # Work host only
+lnk list --all              # Everything
+
+# Pull configurations
+lnk pull                    # Common config
+lnk pull --host work        # Work-specific config
+```
 
 ## Why not just Git?
 
@@ -83,66 +186,100 @@ You could `git init ~/.config/lnk` and manually symlink everything. Lnk just aut
 ### First time setup
 
 ```bash
+# Clone dotfiles and run bootstrap automatically
 lnk init -r git@github.com:you/dotfiles.git
+# → Downloads dependencies, installs packages, configures environment
+
+# Add common config (shared across all machines)
 lnk add ~/.bashrc ~/.vimrc ~/.gitconfig
+
+# Add host-specific config
+lnk add --host $(hostname) ~/.ssh/config ~/.tmux.conf
+
 lnk push "initial setup"
 ```
 
 ### On a new machine
 
 ```bash
+# Bootstrap runs automatically
 lnk init -r git@github.com:you/dotfiles.git
-lnk pull  # auto-creates symlinks
+# → Sets up environment, installs dependencies
+
+# Pull common config
+lnk pull
+
+# Pull host-specific config (if it exists)
+lnk pull --host $(hostname)
+
+# Or run bootstrap manually if needed
+lnk bootstrap
 ```
 
 ### Daily edits
 
 ```bash
-vim ~/.vimrc           # edit normally
-lnk status             # check what changed
-lnk push "new plugins" # commit & push
+vim ~/.vimrc                    # edit normally
+lnk list                        # see common config
+lnk list --host $(hostname)     # see host-specific config
+lnk list --all                  # see everything
+lnk status                      # check what changed
+lnk push "new plugins"          # commit & push
+```
+
+### Multi-machine workflow
+
+```bash
+# On your laptop
+lnk add --host laptop ~/.ssh/config
+lnk add ~/.vimrc                # Common config
+lnk push "laptop ssh config"
+
+# On your work machine
+lnk pull                        # Get common config
+lnk add --host work ~/.gitconfig
+lnk push "work git config"
+
+# Back on laptop
+lnk pull                        # Get updates (work config won't affect laptop)
 ```
 
 ## Commands
 
-- `lnk init [-r remote]` - Create repo
-- `lnk add <files>` - Move files to repo, create symlinks
-- `lnk rm <files>` - Move files back, remove symlinks
+- `lnk init [-r remote] [--no-bootstrap]` - Create repo (runs bootstrap automatically)
+- `lnk add [--host HOST] <files>` - Move files to repo, create symlinks
+- `lnk rm [--host HOST] <files>` - Move files back, remove symlinks
+- `lnk list [--host HOST] [--all]` - List files managed by lnk
 - `lnk status` - Git status + sync info
 - `lnk push [msg]` - Stage all, commit, push
-- `lnk pull` - Pull + restore missing symlinks
+- `lnk pull [--host HOST]` - Pull + restore missing symlinks
+- `lnk bootstrap` - Run bootstrap script manually
+
+### Command Options
+
+- `--host HOST` - Manage files for specific host (default: common configuration)
+- `--all` - Show all configurations (common + all hosts) when listing
+- `-r, --remote URL` - Clone from remote URL when initializing
+- `--no-bootstrap` - Skip automatic execution of bootstrap script after cloning
 
 ## Technical bits
 
 - **Single binary** (~8MB, no deps)
-- **Atomic operations** (rollback on failure)
 - **Relative symlinks** (portable)
 - **XDG compliant** (`~/.config/lnk`)
-- **20 integration tests**
+- **Multihost support** (common + host-specific configs)
+- **Bootstrap support** (automatic environment setup)
+- **Git-native** (standard Git repo, no special formats)
 
 ## Alternatives
 
-| Tool    | Complexity | Why choose it                         |
-| ------- | ---------- | ------------------------------------- |
-| **lnk** | Minimal    | Just works, no config, Git-native     |
-| chezmoi | High       | Templates, encryption, cross-platform |
-| yadm    | Medium     | Git power user, encryption            |
-| dotbot  | Low        | YAML config, basic features           |
-| stow    | Low        | Perl, symlink only                    |
-
-## FAQ
-
-**Q: What if I already have dotfiles in Git?**  
-A: `git clone your-repo ~/.config/lnk && lnk add ~/.vimrc` (adopts existing files)
-
-**Q: How do I handle machine-specific configs?**  
-A: Git branches, or just don't manage machine-specific files with lnk
-
-**Q: Windows support?**  
-A: Symlinks work on Windows 10+, but untested
-
-**Q: Production ready?**  
-A: I use it daily. It won't break your files. API might change (pre-1.0).
+| Tool    | Complexity | Why choose it                                           |
+| ------- | ---------- | ------------------------------------------------------- |
+| **lnk** | Minimal    | Just works, no config, Git-native, multihost, bootstrap |
+| chezmoi | High       | Templates, encryption, cross-platform                   |
+| yadm    | Medium     | Git power user, encryption                              |
+| dotbot  | Low        | YAML config, basic features                             |
+| stow    | Low        | Perl, symlink only                                      |
 
 ## Contributing
 

cmd/add.go

@@ -1,35 +1,43 @@
 package cmd
 
 import (
-	"fmt"
 	"path/filepath"
 
 	"github.com/spf13/cobra"
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var addCmd = &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.",
-	Args:         cobra.ExactArgs(1),
-	SilenceUsage: true,
-	RunE: func(cmd *cobra.Command, args []string) error {
-		filePath := args[0]
+func newAddCmd() *cobra.Command {
+	cmd := &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.",
+		Args:          cobra.ExactArgs(1),
+		SilenceUsage:  true,
+		SilenceErrors: true,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			filePath := args[0]
+			host, _ := cmd.Flags().GetString("host")
 
-		lnk := core.NewLnk()
-		if err := lnk.Add(filePath); err != nil {
-			return fmt.Errorf("failed to add file: %w", err)
-		}
+			lnk := core.NewLnk(core.WithHost(host))
 
-		basename := filepath.Base(filePath)
-		fmt.Printf("✨ \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)
-		fmt.Printf("   📝 Use \033[1mlnk push\033[0m to sync to remote\n")
-		return nil
-	},
-}
-
-func init() {
-	rootCmd.AddCommand(addCmd)
+			if err := lnk.Add(filePath); err != nil {
+				return err
+			}
+
+			basename := filepath.Base(filePath)
+			if host != "" {
+				printf(cmd, "✨ \033[1mAdded %s to lnk (host: %s)\033[0m\n", basename, host)
+				printf(cmd, "   🔗 \033[90m%s\033[0m → \033[36m~/.config/lnk/%s.lnk/%s\033[0m\n", filePath, host, filePath)
+			} else {
+				printf(cmd, "✨ \033[1mAdded %s to lnk\033[0m\n", basename)
+				printf(cmd, "   🔗 \033[90m%s\033[0m → \033[36m~/.config/lnk/%s\033[0m\n", filePath, filePath)
+			}
+			printf(cmd, "   📝 Use \033[1mlnk push\033[0m to sync to remote\n")
+			return nil
+		},
+	}
+
+	cmd.Flags().StringP("host", "H", "", "Manage file for specific host (default: common configuration)")
+	return cmd
 }

cmd/bootstrap.go

@@ -0,0 +1,45 @@
+package cmd
+
+import (
+	"github.com/spf13/cobra"
+	"github.com/yarlson/lnk/internal/core"
+)
+
+func newBootstrapCmd() *cobra.Command {
+	return &cobra.Command{
+		Use:           "bootstrap",
+		Short:         "🚀 Run the bootstrap script to set up your environment",
+		Long:          "Executes the bootstrap script from your dotfiles repository to install dependencies and configure your system.",
+		SilenceUsage:  true,
+		SilenceErrors: true,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			lnk := core.NewLnk()
+
+			scriptPath, err := lnk.FindBootstrapScript()
+			if err != nil {
+				return err
+			}
+
+			if scriptPath == "" {
+				printf(cmd, "💡 \033[33mNo bootstrap script found\033[0m\n")
+				printf(cmd, "   📝 Create a \033[1mbootstrap.sh\033[0m file in your dotfiles repository:\n")
+				printf(cmd, "      \033[90m#!/bin/bash\033[0m\n")
+				printf(cmd, "      \033[90mecho \"Setting up environment...\"\033[0m\n")
+				printf(cmd, "      \033[90m# Your setup commands here\033[0m\n")
+				return nil
+			}
+
+			printf(cmd, "🚀 \033[1mRunning bootstrap script\033[0m\n")
+			printf(cmd, "   📄 Script: \033[36m%s\033[0m\n", scriptPath)
+			printf(cmd, "\n")
+
+			if err := lnk.RunBootstrapScript(scriptPath); err != nil {
+				return err
+			}
+
+			printf(cmd, "\n✅ \033[1;32mBootstrap completed successfully!\033[0m\n")
+			printf(cmd, "   🎉 Your environment is ready to use\n")
+			return nil
+		},
+	}
+}

cmd/init.go

@@ -1,45 +1,73 @@
 package cmd
 
 import (
-	"fmt"
-
 	"github.com/spf13/cobra"
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var initCmd = &cobra.Command{
-	Use:          "init",
-	Short:        "🎯 Initialize a new lnk repository",
-	Long:         "Creates the lnk directory and initializes a Git repository for managing dotfiles.",
-	SilenceUsage: true,
-	RunE: func(cmd *cobra.Command, args []string) error {
-		remote, _ := cmd.Flags().GetString("remote")
+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.",
+		SilenceUsage:  true,
+		SilenceErrors: true,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			remote, _ := cmd.Flags().GetString("remote")
+			noBootstrap, _ := cmd.Flags().GetBool("no-bootstrap")
 
-		lnk := core.NewLnk()
-		if err := lnk.InitWithRemote(remote); err != nil {
-			return fmt.Errorf("failed to initialize lnk: %w", err)
-		}
+			lnk := core.NewLnk()
+			if err := lnk.InitWithRemote(remote); err != nil {
+				return err
+			}
 
-		if remote != "" {
-			fmt.Printf("🎯 \033[1mInitialized lnk repository\033[0m\n")
-			fmt.Printf("   📦 Cloned from: \033[36m%s\033[0m\n", remote)
-			fmt.Printf("   📁 Location: \033[90m~/.config/lnk\033[0m\n")
-			fmt.Printf("\n💡 \033[33mNext steps:\033[0m\n")
-			fmt.Printf("   • Run \033[1mlnk pull\033[0m to restore symlinks\n")
-			fmt.Printf("   • Use \033[1mlnk add <file>\033[0m to manage new files\n")
-		} else {
-			fmt.Printf("🎯 \033[1mInitialized empty lnk repository\033[0m\n")
-			fmt.Printf("   📁 Location: \033[90m~/.config/lnk\033[0m\n")
-			fmt.Printf("\n💡 \033[33mNext steps:\033[0m\n")
-			fmt.Printf("   • 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")
-		}
+			if remote != "" {
+				printf(cmd, "🎯 \033[1mInitialized lnk repository\033[0m\n")
+				printf(cmd, "   📦 Cloned from: \033[36m%s\033[0m\n", remote)
+				printf(cmd, "   📁 Location: \033[90m~/.config/lnk\033[0m\n")
 
-		return nil
-	},
-}
-
-func init() {
-	initCmd.Flags().StringP("remote", "r", "", "Clone from remote URL instead of creating empty repository")
-	rootCmd.AddCommand(initCmd)
+				// Try to run bootstrap script if not disabled
+				if !noBootstrap {
+					printf(cmd, "\n🔍 \033[1mLooking for bootstrap script...\033[0m\n")
+
+					scriptPath, err := lnk.FindBootstrapScript()
+					if err != nil {
+						return err
+					}
+
+					if scriptPath != "" {
+						printf(cmd, "   ✅ Found bootstrap script: \033[36m%s\033[0m\n", scriptPath)
+						printf(cmd, "\n🚀 \033[1mRunning bootstrap script...\033[0m\n")
+						printf(cmd, "\n")
+
+						if err := lnk.RunBootstrapScript(scriptPath); err != nil {
+							printf(cmd, "\n⚠️  \033[33mBootstrap script failed, but repository was initialized successfully\033[0m\n")
+							printf(cmd, "   💡 You can run it manually with: \033[1mlnk bootstrap\033[0m\n")
+							printf(cmd, "   🔧 Error: %v\n", err)
+						} else {
+							printf(cmd, "\n✅ \033[1;32mBootstrap completed successfully!\033[0m\n")
+						}
+					} else {
+						printf(cmd, "   💡 No bootstrap script found\n")
+					}
+				}
+
+				printf(cmd, "\n💡 \033[33mNext steps:\033[0m\n")
+				printf(cmd, "   • Run \033[1mlnk pull\033[0m to restore symlinks\n")
+				printf(cmd, "   • Use \033[1mlnk add <file>\033[0m to manage new files\n")
+			} else {
+				printf(cmd, "🎯 \033[1mInitialized empty lnk repository\033[0m\n")
+				printf(cmd, "   📁 Location: \033[90m~/.config/lnk\033[0m\n")
+				printf(cmd, "\n💡 \033[33mNext steps:\033[0m\n")
+				printf(cmd, "   • Run \033[1mlnk add <file>\033[0m to start managing dotfiles\n")
+				printf(cmd, "   • Add a remote with: \033[1mgit remote add origin <url>\033[0m\n")
+			}
+
+			return nil
+		},
+	}
+
+	cmd.Flags().StringP("remote", "r", "", "Clone from remote URL instead of creating empty repository")
+	cmd.Flags().Bool("no-bootstrap", false, "Skip automatic execution of bootstrap script after cloning")
+	return cmd
 }

cmd/list.go

@@ -0,0 +1,193 @@
+package cmd
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+
+	"github.com/spf13/cobra"
+	"github.com/yarlson/lnk/internal/core"
+)
+
+func newListCmd() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:           "list",
+		Short:         "📋 List files managed by lnk",
+		Long:          "Display all files and directories currently managed by lnk.",
+		SilenceUsage:  true,
+		SilenceErrors: true,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			host, _ := cmd.Flags().GetString("host")
+			all, _ := cmd.Flags().GetBool("all")
+
+			if host != "" {
+				// Show specific host configuration
+				return listHostConfig(cmd, host)
+			}
+
+			if all {
+				// Show all configurations (common + all hosts)
+				return listAllConfigs(cmd)
+			}
+
+			// Default: show common configuration
+			return listCommonConfig(cmd)
+		},
+	}
+
+	cmd.Flags().StringP("host", "H", "", "List files for specific host")
+	cmd.Flags().BoolP("all", "a", false, "List files for all hosts and common configuration")
+	return cmd
+}
+
+func listCommonConfig(cmd *cobra.Command) error {
+	lnk := core.NewLnk()
+	managedItems, err := lnk.List()
+	if err != nil {
+		return err
+	}
+
+	if len(managedItems) == 0 {
+		printf(cmd, "📋 \033[1mNo files currently managed by lnk (common)\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 (common)\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
+}
+
+func listHostConfig(cmd *cobra.Command, host string) error {
+	lnk := core.NewLnk(core.WithHost(host))
+	managedItems, err := lnk.List()
+	if err != nil {
+		return err
+	}
+
+	if len(managedItems) == 0 {
+		printf(cmd, "📋 \033[1mNo files currently managed by lnk (host: %s)\033[0m\n", host)
+		printf(cmd, "   💡 Use \033[1mlnk add --host %s <file>\033[0m to start managing files\n", host)
+		return nil
+	}
+
+	printf(cmd, "📋 \033[1mFiles managed by lnk (host: %s)\033[0m (\033[36m%d item", host, 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
+}
+
+func listAllConfigs(cmd *cobra.Command) error {
+	// List common configuration
+	printf(cmd, "📋 \033[1mAll configurations managed by lnk\033[0m\n\n")
+
+	lnk := core.NewLnk()
+	commonItems, err := lnk.List()
+	if err != nil {
+		return err
+	}
+
+	printf(cmd, "🌐 \033[1mCommon configuration\033[0m (\033[36m%d item", len(commonItems))
+	if len(commonItems) > 1 {
+		printf(cmd, "s")
+	}
+	printf(cmd, "\033[0m):\n")
+
+	if len(commonItems) == 0 {
+		printf(cmd, "   \033[90m(no files)\033[0m\n")
+	} else {
+		for _, item := range commonItems {
+			printf(cmd, "   🔗 \033[36m%s\033[0m\n", item)
+		}
+	}
+
+	// Find all host-specific configurations
+	hosts, err := findHostConfigs()
+	if err != nil {
+		return err
+	}
+
+	for _, host := range hosts {
+		printf(cmd, "\n🖥️  \033[1mHost: %s\033[0m", host)
+
+		hostLnk := core.NewLnk(core.WithHost(host))
+		hostItems, err := hostLnk.List()
+		if err != nil {
+			printf(cmd, " \033[31m(error: %v)\033[0m\n", err)
+			continue
+		}
+
+		printf(cmd, " (\033[36m%d item", len(hostItems))
+		if len(hostItems) > 1 {
+			printf(cmd, "s")
+		}
+		printf(cmd, "\033[0m):\n")
+
+		if len(hostItems) == 0 {
+			printf(cmd, "   \033[90m(no files)\033[0m\n")
+		} else {
+			for _, item := range hostItems {
+				printf(cmd, "   🔗 \033[36m%s\033[0m\n", item)
+			}
+		}
+	}
+
+	printf(cmd, "\n💡 Use \033[1mlnk list --host <hostname>\033[0m to see specific host configuration\n")
+	return nil
+}
+
+func findHostConfigs() ([]string, error) {
+	repoPath := getRepoPath()
+
+	// Check if repo exists
+	if _, err := os.Stat(repoPath); os.IsNotExist(err) {
+		return []string{}, nil
+	}
+
+	entries, err := os.ReadDir(repoPath)
+	if err != nil {
+		return nil, err
+	}
+
+	var hosts []string
+	for _, entry := range entries {
+		name := entry.Name()
+		// Look for .lnk.<hostname> files
+		if strings.HasPrefix(name, ".lnk.") && name != ".lnk" {
+			host := strings.TrimPrefix(name, ".lnk.")
+			hosts = append(hosts, host)
+		}
+	}
+
+	return hosts, nil
+}
+
+func getRepoPath() string {
+	xdgConfig := os.Getenv("XDG_CONFIG_HOME")
+	if xdgConfig == "" {
+		homeDir, err := os.UserHomeDir()
+		if err != nil {
+			xdgConfig = "."
+		} else {
+			xdgConfig = filepath.Join(homeDir, ".config")
+		}
+	}
+	return filepath.Join(xdgConfig, "lnk")
+}

cmd/pull.go

@@ -1,45 +1,56 @@
 package cmd
 
 import (
-	"fmt"
-
 	"github.com/spf13/cobra"
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var pullCmd = &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.",
-	SilenceUsage: true,
-	RunE: func(cmd *cobra.Command, args []string) error {
-		lnk := core.NewLnk()
-		restored, err := lnk.Pull()
-		if err != nil {
-			return fmt.Errorf("failed to pull changes: %w", err)
-		}
+func newPullCmd() *cobra.Command {
+	cmd := &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.",
+		SilenceUsage:  true,
+		SilenceErrors: true,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			host, _ := cmd.Flags().GetString("host")
 
-		if len(restored) > 0 {
-			fmt.Printf("⬇️  \033[1;32mSuccessfully pulled changes\033[0m\n")
-			fmt.Printf("   🔗 Restored \033[1m%d symlink", len(restored))
-			if len(restored) > 1 {
-				fmt.Printf("s")
+			lnk := core.NewLnk(core.WithHost(host))
+
+			restored, err := lnk.Pull()
+			if err != nil {
+				return err
 			}
-			fmt.Printf("\033[0m:\n")
-			for _, file := range restored {
-				fmt.Printf("      ✨ \033[36m%s\033[0m\n", file)
+
+			if len(restored) > 0 {
+				if host != "" {
+					printf(cmd, "⬇️  \033[1;32mSuccessfully pulled changes (host: %s)\033[0m\n", host)
+				} else {
+					printf(cmd, "⬇️  \033[1;32mSuccessfully pulled changes\033[0m\n")
+				}
+				printf(cmd, "   🔗 Restored \033[1m%d symlink", len(restored))
+				if len(restored) > 1 {
+					printf(cmd, "s")
+				}
+				printf(cmd, "\033[0m:\n")
+				for _, file := range restored {
+					printf(cmd, "      ✨ \033[36m%s\033[0m\n", file)
+				}
+				printf(cmd, "\n   🎉 Your dotfiles are synced and ready!\n")
+			} else {
+				if host != "" {
+					printf(cmd, "⬇️  \033[1;32mSuccessfully pulled changes (host: %s)\033[0m\n", host)
+				} else {
+					printf(cmd, "⬇️  \033[1;32mSuccessfully pulled changes\033[0m\n")
+				}
+				printf(cmd, "   ✅ All symlinks already in place\n")
+				printf(cmd, "   🎉 Everything is up to date!\n")
 			}
-			fmt.Printf("\n   🎉 Your dotfiles are synced and ready!\n")
-		} else {
-			fmt.Printf("⬇️  \033[1;32mSuccessfully pulled changes\033[0m\n")
-			fmt.Printf("   ✅ All symlinks already in place\n")
-			fmt.Printf("   🎉 Everything is up to date!\n")
-		}
 
-		return nil
-	},
-}
+			return nil
+		},
+	}
 
-func init() {
-	rootCmd.AddCommand(pullCmd)
+	cmd.Flags().StringP("host", "H", "", "Pull and restore symlinks for specific host (default: common configuration)")
+	return cmd
 }

cmd/push.go

@@ -1,37 +1,34 @@
 package cmd
 
 import (
-	"fmt"
-
 	"github.com/spf13/cobra"
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var pushCmd = &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.",
-	Args:         cobra.MaximumNArgs(1),
-	SilenceUsage: true,
-	RunE: func(cmd *cobra.Command, args []string) error {
-		message := "lnk: sync configuration files"
-		if len(args) > 0 {
-			message = args[0]
-		}
+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.",
+		Args:          cobra.MaximumNArgs(1),
+		SilenceUsage:  true,
+		SilenceErrors: true,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			message := "lnk: sync configuration files"
+			if len(args) > 0 {
+				message = args[0]
+			}
 
-		lnk := core.NewLnk()
-		if err := lnk.Push(message); err != nil {
-			return fmt.Errorf("failed to push changes: %w", err)
-		}
+			lnk := core.NewLnk()
+			if err := lnk.Push(message); err != nil {
+				return err
+			}
 
-		fmt.Printf("🚀 \033[1;32mSuccessfully pushed changes\033[0m\n")
-		fmt.Printf("   💾 Commit: \033[90m%s\033[0m\n", message)
-		fmt.Printf("   📡 Synced to remote\n")
-		fmt.Printf("   ✨ Your dotfiles are up to date!\n")
-		return nil
-	},
-}
-
-func init() {
-	rootCmd.AddCommand(pushCmd)
+			printf(cmd, "🚀 \033[1;32mSuccessfully pushed changes\033[0m\n")
+			printf(cmd, "   💾 Commit: \033[90m%s\033[0m\n", message)
+			printf(cmd, "   📡 Synced to remote\n")
+			printf(cmd, "   ✨ Your dotfiles are up to date!\n")
+			return nil
+		},
+	}
 }

cmd/rm.go

@@ -1,35 +1,43 @@
 package cmd
 
 import (
-	"fmt"
 	"path/filepath"
 
 	"github.com/spf13/cobra"
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var rmCmd = &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.",
-	Args:         cobra.ExactArgs(1),
-	SilenceUsage: true,
-	RunE: func(cmd *cobra.Command, args []string) error {
-		filePath := args[0]
+func newRemoveCmd() *cobra.Command {
+	cmd := &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.",
+		Args:          cobra.ExactArgs(1),
+		SilenceUsage:  true,
+		SilenceErrors: true,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			filePath := args[0]
+			host, _ := cmd.Flags().GetString("host")
 
-		lnk := core.NewLnk()
-		if err := lnk.Remove(filePath); err != nil {
-			return fmt.Errorf("failed to remove file: %w", err)
-		}
+			lnk := core.NewLnk(core.WithHost(host))
 
-		basename := filepath.Base(filePath)
-		fmt.Printf("🗑️  \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)
-		fmt.Printf("   📄 Original file restored\n")
-		return nil
-	},
-}
-
-func init() {
-	rootCmd.AddCommand(rmCmd)
+			if err := lnk.Remove(filePath); err != nil {
+				return err
+			}
+
+			basename := filepath.Base(filePath)
+			if host != "" {
+				printf(cmd, "🗑️  \033[1mRemoved %s from lnk (host: %s)\033[0m\n", basename, host)
+				printf(cmd, "   ↩️  \033[90m~/.config/lnk/%s.lnk/%s\033[0m → \033[36m%s\033[0m\n", host, basename, filePath)
+			} else {
+				printf(cmd, "🗑️  \033[1mRemoved %s from lnk\033[0m\n", basename)
+				printf(cmd, "   ↩️  \033[90m~/.config/lnk/%s\033[0m → \033[36m%s\033[0m\n", basename, filePath)
+			}
+			printf(cmd, "   📄 Original file restored\n")
+			return nil
+		},
+	}
+
+	cmd.Flags().StringP("host", "H", "", "Remove file from specific host configuration (default: common configuration)")
+	return cmd
 }

cmd/root.go

@@ -12,35 +12,59 @@ var (
 	buildTime = "unknown"
 )
 
-var rootCmd = &cobra.Command{
-	Use:   "lnk",
-	Short: "🔗 Dotfiles, linked. No fluff.",
-	Long: `🔗 Lnk - Git-native dotfiles management that doesn't suck.
+// 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.
 
 Move your dotfiles to ~/.config/lnk, symlink them back, and use Git like normal.
-That's it.
+Supports both common configurations and host-specific setups.
 
 ✨ Examples:
-  lnk init                    # Fresh start
-  lnk init -r <repo-url>      # Clone existing dotfiles
-  lnk add ~/.vimrc ~/.bashrc  # Start managing files
-  lnk push "setup complete"   # Sync to remote
-  lnk pull                    # Get latest changes
+  lnk init                         # Fresh start
+  lnk init -r <repo-url>           # Clone existing dotfiles (runs bootstrap automatically)
+  lnk add ~/.vimrc ~/.bashrc       # Start managing common files
+  lnk add --host work ~/.ssh/config # Manage host-specific files
+  lnk list --all                  # Show all configurations
+  lnk pull --host work             # Pull host-specific changes
+  lnk push "setup complete"        # Sync to remote
+  lnk bootstrap                    # Run bootstrap script manually
 
-🎯 Simple, fast, and Git-native.`,
-	SilenceUsage: true,
+🚀 Bootstrap Support:
+  Automatically runs bootstrap.sh when cloning a repository.
+  Use --no-bootstrap to disable.
+
+🎯 Simple, fast, Git-native, and multi-host ready.`,
+		SilenceUsage:  true,
+		SilenceErrors: 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())
+	rootCmd.AddCommand(newBootstrapCmd())
+
+	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)
+		_, _ = fmt.Fprintln(os.Stderr, err)
 		os.Exit(1)
 	}
 }

cmd/root_test.go

@@ -0,0 +1,922 @@
+package cmd
+
+import (
+	"bytes"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"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 HOME to temp directory for consistent relative path calculation
+	suite.T().Setenv("HOME", tempDir)
+
+	// Set XDG_CONFIG_HOME to tempDir/.config for config files
+	suite.T().Setenv("XDG_CONFIG_HOME", filepath.Join(tempDir, ".config"))
+
+	// 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, ".config", "lnk")
+	suite.DirExists(lnkDir)
+
+	gitDir := filepath.Join(lnkDir, ".git")
+	suite.DirExists(gitDir)
+}
+
+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:$PATH"), 0644)
+	suite.Require().NoError(err)
+
+	// Test add command
+	err = suite.runCommand("add", testFile)
+	suite.NoError(err)
+
+	// Check output
+	output := suite.stdout.String()
+	suite.Contains(output, "Added .bashrc to lnk")
+	suite.Contains(output, "→")
+	suite.Contains(output, "sync to remote")
+
+	// Verify symlink was created
+	info, err := os.Lstat(testFile)
+	suite.NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+
+	// Verify the file exists in repo with preserved directory structure
+	lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+	repoFile := filepath.Join(lnkDir, ".bashrc")
+	suite.FileExists(repoFile)
+
+	// Verify content is preserved in storage
+	storedContent, err := os.ReadFile(repoFile)
+	suite.NoError(err)
+	suite.Equal("export PATH=/usr/local/bin:$PATH", string(storedContent))
+
+	// Verify .lnk file contains the correct entry
+	lnkFile := filepath.Join(lnkDir, ".lnk")
+	lnkContent, err := os.ReadFile(lnkFile)
+	suite.NoError(err)
+	suite.Equal(".bashrc\n", string(lnkContent))
+}
+
+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 repository is 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:$PATH"), 0644)
+	suite.Require().NoError(err)
+	err = suite.runCommand("add", testFile)
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Test list with one managed file
+	err = suite.runCommand("list")
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Files managed by lnk")
+	suite.Contains(output, "1 item")
+	suite.Contains(output, ".bashrc")
+	suite.stdout.Reset()
+
+	// Add another file
+	testFile2 := filepath.Join(suite.tempDir, ".vimrc")
+	err = os.WriteFile(testFile2, []byte("set number"), 0644)
+	suite.Require().NoError(err)
+	err = suite.runCommand("add", testFile2)
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Test list with multiple managed files
+	err = suite.runCommand("list")
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Files managed by lnk")
+	suite.Contains(output, "2 items")
+	suite.Contains(output, ".bashrc")
+	suite.Contains(output, ".vimrc")
+
+	// Verify both files exist in storage with correct content
+	lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+
+	bashrcStorage := filepath.Join(lnkDir, ".bashrc")
+	suite.FileExists(bashrcStorage)
+	bashrcContent, err := os.ReadFile(bashrcStorage)
+	suite.NoError(err)
+	suite.Equal("export PATH=/usr/local/bin:$PATH", string(bashrcContent))
+
+	vimrcStorage := filepath.Join(lnkDir, ".vimrc")
+	suite.FileExists(vimrcStorage)
+	vimrcContent, err := os.ReadFile(vimrcStorage)
+	suite.NoError(err)
+	suite.Equal("set number", string(vimrcContent))
+
+	// Verify .lnk file contains both entries (sorted)
+	lnkFile := filepath.Join(lnkDir, ".lnk")
+	lnkContent, err := os.ReadFile(lnkFile)
+	suite.NoError(err)
+	suite.Equal(".bashrc\n.vimrc\n", string(lnkContent))
+}
+
+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 or directory not found",
+		},
+		{
+			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", filepath.Join(suite.tempDir, ".bashrc")},
+			setup: func() {
+				testFile := filepath.Join(suite.tempDir, ".bashrc")
+				_ = os.WriteFile(testFile, []byte("export PATH=/usr/local/bin:$PATH"), 0644)
+			},
+			verify: func(output string) {
+				suite.Contains(output, "Added .bashrc to lnk")
+
+				// Verify storage and .lnk file
+				lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+				bashrcStorage := filepath.Join(lnkDir, ".bashrc")
+				suite.FileExists(bashrcStorage)
+
+				storedContent, err := os.ReadFile(bashrcStorage)
+				suite.NoError(err)
+				suite.Equal("export PATH=/usr/local/bin:$PATH", string(storedContent))
+
+				lnkFile := filepath.Join(lnkDir, ".lnk")
+				lnkContent, err := os.ReadFile(lnkFile)
+				suite.NoError(err)
+				suite.Equal(".bashrc\n", string(lnkContent))
+			},
+		},
+		{
+			name: "add another file",
+			args: []string{"add", filepath.Join(suite.tempDir, ".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")
+
+				// Verify storage and .lnk file now contains both files
+				lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+				vimrcStorage := filepath.Join(lnkDir, ".vimrc")
+				suite.FileExists(vimrcStorage)
+
+				storedContent, err := os.ReadFile(vimrcStorage)
+				suite.NoError(err)
+				suite.Equal("set number", string(storedContent))
+
+				lnkFile := filepath.Join(lnkDir, ".lnk")
+				lnkContent, err := os.ReadFile(lnkFile)
+				suite.NoError(err)
+				suite.Equal(".bashrc\n.vimrc\n", string(lnkContent))
+			},
+		},
+		{
+			name: "remove file",
+			args: []string{"rm", filepath.Join(suite.tempDir, ".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, ".ssh")
+	_ = os.MkdirAll(testDir, 0755)
+	configFile := filepath.Join(testDir, "config")
+	_ = os.WriteFile(configFile, []byte("Host example.com"), 0644)
+
+	// Add the directory
+	err := suite.runCommand("add", testDir)
+	suite.NoError(err)
+
+	// Check output
+	output := suite.stdout.String()
+	suite.Contains(output, "Added .ssh 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 the directory exists in repo with preserved directory structure
+	lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+	repoDir := filepath.Join(lnkDir, ".ssh")
+	suite.DirExists(repoDir)
+
+	// Verify directory content is preserved
+	repoConfigFile := filepath.Join(repoDir, "config")
+	suite.FileExists(repoConfigFile)
+	storedContent, err := os.ReadFile(repoConfigFile)
+	suite.NoError(err)
+	suite.Equal("Host example.com", string(storedContent))
+
+	// Verify .lnk file contains the directory entry
+	lnkFile := filepath.Join(lnkDir, ".lnk")
+	lnkContent, err := os.ReadFile(lnkFile)
+	suite.NoError(err)
+	suite.Equal(".ssh\n", string(lnkContent))
+}
+
+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")
+
+	// Verify both files exist in storage with correct paths and content
+	lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+
+	storageFileA := filepath.Join(lnkDir, "a", "config.json")
+	suite.FileExists(storageFileA)
+	storedContentA, err := os.ReadFile(storageFileA)
+	suite.NoError(err)
+	suite.Equal(contentA, string(storedContentA))
+
+	storageFileB := filepath.Join(lnkDir, "b", "config.json")
+	suite.FileExists(storageFileB)
+	storedContentB, err := os.ReadFile(storageFileB)
+	suite.NoError(err)
+	suite.Equal(contentB, string(storedContentB))
+
+	// Verify .lnk file contains both entries with correct relative paths
+	lnkFile := filepath.Join(lnkDir, ".lnk")
+	lnkContent, err := os.ReadFile(lnkFile)
+	suite.NoError(err)
+	suite.Equal("a/config.json\nb/config.json\n", string(lnkContent))
+
+	// 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()
+
+	// Verify file is stored correctly
+	lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+	storageFile := filepath.Join(lnkDir, "a")
+	suite.FileExists(storageFile)
+	storedContent, err := os.ReadFile(storageFile)
+	suite.NoError(err)
+	suite.Equal("abc", string(storedContent))
+
+	// Verify .lnk file contains the entry
+	lnkFile := filepath.Join(lnkDir, ".lnk")
+	lnkContent, err := os.ReadFile(lnkFile)
+	suite.NoError(err)
+	suite.Equal("a\n", string(lnkContent))
+
+	// Add a remote so status works
+	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 (suite *CLITestSuite) TestMultihostCommands() {
+	// Initialize repository
+	err := suite.runCommand("init")
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Create test files
+	testFile1 := filepath.Join(suite.tempDir, ".bashrc")
+	err = os.WriteFile(testFile1, []byte("export PATH=/usr/local/bin:$PATH"), 0644)
+	suite.Require().NoError(err)
+
+	testFile2 := filepath.Join(suite.tempDir, ".vimrc")
+	err = os.WriteFile(testFile2, []byte("set number"), 0644)
+	suite.Require().NoError(err)
+
+	// Add file to common configuration
+	err = suite.runCommand("add", testFile1)
+	suite.NoError(err)
+	output := suite.stdout.String()
+	suite.Contains(output, "Added .bashrc to lnk")
+	suite.NotContains(output, "host:")
+	suite.stdout.Reset()
+
+	// Add file to host-specific configuration
+	err = suite.runCommand("add", "--host", "workstation", testFile2)
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Added .vimrc to lnk (host: workstation)")
+	suite.Contains(output, "workstation.lnk")
+	suite.stdout.Reset()
+
+	// Verify storage paths and .lnk files for both common and host-specific
+	lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+
+	// Verify common file storage and tracking
+	commonStorage := filepath.Join(lnkDir, ".bashrc")
+	suite.FileExists(commonStorage)
+	commonContent, err := os.ReadFile(commonStorage)
+	suite.NoError(err)
+	suite.Equal("export PATH=/usr/local/bin:$PATH", string(commonContent))
+
+	commonLnkFile := filepath.Join(lnkDir, ".lnk")
+	commonLnkContent, err := os.ReadFile(commonLnkFile)
+	suite.NoError(err)
+	suite.Equal(".bashrc\n", string(commonLnkContent))
+
+	// Verify host-specific file storage and tracking
+	hostStorage := filepath.Join(lnkDir, "workstation.lnk", ".vimrc")
+	suite.FileExists(hostStorage)
+	hostContent, err := os.ReadFile(hostStorage)
+	suite.NoError(err)
+	suite.Equal("set number", string(hostContent))
+
+	hostLnkFile := filepath.Join(lnkDir, ".lnk.workstation")
+	hostLnkContent, err := os.ReadFile(hostLnkFile)
+	suite.NoError(err)
+	suite.Equal(".vimrc\n", string(hostLnkContent))
+
+	// Test list command - common only
+	err = suite.runCommand("list")
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Files managed by lnk (common)")
+	suite.Contains(output, ".bashrc")
+	suite.NotContains(output, ".vimrc")
+	suite.stdout.Reset()
+
+	// Test list command - specific host
+	err = suite.runCommand("list", "--host", "workstation")
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Files managed by lnk (host: workstation)")
+	suite.Contains(output, ".vimrc")
+	suite.NotContains(output, ".bashrc")
+	suite.stdout.Reset()
+
+	// Test list command - all configurations
+	err = suite.runCommand("list", "--all")
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "All configurations managed by lnk")
+	suite.Contains(output, "Common configuration")
+	suite.Contains(output, "Host: workstation")
+	suite.Contains(output, ".bashrc")
+	suite.Contains(output, ".vimrc")
+	suite.stdout.Reset()
+
+	// Test remove from host-specific
+	err = suite.runCommand("rm", "--host", "workstation", testFile2)
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Removed .vimrc from lnk (host: workstation)")
+	suite.stdout.Reset()
+
+	// Test remove from common
+	err = suite.runCommand("rm", testFile1)
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Removed .bashrc from lnk")
+	suite.NotContains(output, "host:")
+	suite.stdout.Reset()
+
+	// Verify files are restored
+	info1, err := os.Lstat(testFile1)
+	suite.NoError(err)
+	suite.Equal(os.FileMode(0), info1.Mode()&os.ModeSymlink)
+
+	info2, err := os.Lstat(testFile2)
+	suite.NoError(err)
+	suite.Equal(os.FileMode(0), info2.Mode()&os.ModeSymlink)
+}
+
+func (suite *CLITestSuite) TestMultihostErrorHandling() {
+	// Initialize repository
+	err := suite.runCommand("init")
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Try to remove from non-existent host config
+	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("rm", "--host", "nonexistent", testFile)
+	suite.Error(err)
+	suite.Contains(err.Error(), "File is not managed by lnk")
+
+	// Try to list non-existent host config
+	err = suite.runCommand("list", "--host", "nonexistent")
+	suite.NoError(err) // Should not error, just show empty
+	output := suite.stdout.String()
+	suite.Contains(output, "No files currently managed by lnk (host: nonexistent)")
+}
+
+func (suite *CLITestSuite) TestBootstrapCommand() {
+	// Initialize repository
+	err := suite.runCommand("init")
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Test bootstrap command with no script
+	err = suite.runCommand("bootstrap")
+	suite.NoError(err)
+	output := suite.stdout.String()
+	suite.Contains(output, "No bootstrap script found")
+	suite.Contains(output, "bootstrap.sh")
+	suite.stdout.Reset()
+
+	// Create a bootstrap script
+	lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+	bootstrapScript := filepath.Join(lnkDir, "bootstrap.sh")
+	scriptContent := `#!/bin/bash
+echo "Bootstrap script executed!"
+echo "Working directory: $(pwd)"
+touch bootstrap-ran.txt
+`
+	err = os.WriteFile(bootstrapScript, []byte(scriptContent), 0755)
+	suite.Require().NoError(err)
+
+	// Test bootstrap command with script
+	err = suite.runCommand("bootstrap")
+	suite.NoError(err)
+	output = suite.stdout.String()
+	suite.Contains(output, "Running bootstrap script")
+	suite.Contains(output, "bootstrap.sh")
+	suite.Contains(output, "Bootstrap completed successfully")
+
+	// Verify script actually ran
+	markerFile := filepath.Join(lnkDir, "bootstrap-ran.txt")
+	suite.FileExists(markerFile)
+}
+
+func (suite *CLITestSuite) TestInitWithBootstrap() {
+	// Create a temporary remote repository with bootstrap script
+	remoteDir := filepath.Join(suite.tempDir, "remote")
+	err := os.MkdirAll(remoteDir, 0755)
+	suite.Require().NoError(err)
+
+	// Initialize git repo in remote
+	cmd := exec.Command("git", "init", "--bare")
+	cmd.Dir = remoteDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	// Create a working repo to populate the remote
+	workingDir := filepath.Join(suite.tempDir, "working")
+	err = os.MkdirAll(workingDir, 0755)
+	suite.Require().NoError(err)
+
+	cmd = exec.Command("git", "clone", remoteDir, workingDir)
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	// Add a bootstrap script to the working repo
+	bootstrapScript := filepath.Join(workingDir, "bootstrap.sh")
+	scriptContent := `#!/bin/bash
+echo "Remote bootstrap script executed!"
+touch remote-bootstrap-ran.txt
+`
+	err = os.WriteFile(bootstrapScript, []byte(scriptContent), 0755)
+	suite.Require().NoError(err)
+
+	// Add a dummy config file
+	configFile := filepath.Join(workingDir, ".bashrc")
+	err = os.WriteFile(configFile, []byte("echo 'Hello from remote!'"), 0644)
+	suite.Require().NoError(err)
+
+	// Add .lnk file to track the config
+	lnkFile := filepath.Join(workingDir, ".lnk")
+	err = os.WriteFile(lnkFile, []byte(".bashrc\n"), 0644)
+	suite.Require().NoError(err)
+
+	// Commit and push to remote
+	cmd = exec.Command("git", "add", ".")
+	cmd.Dir = workingDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	cmd = exec.Command("git", "-c", "user.email=test@example.com", "-c", "user.name=Test User", "commit", "-m", "Add bootstrap and config")
+	cmd.Dir = workingDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	cmd = exec.Command("git", "push", "origin", "master")
+	cmd.Dir = workingDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	// Now test init with remote and automatic bootstrap
+	err = suite.runCommand("init", "-r", remoteDir)
+	suite.NoError(err)
+	output := suite.stdout.String()
+	suite.Contains(output, "Cloned from:")
+	suite.Contains(output, "Looking for bootstrap script")
+	suite.Contains(output, "Found bootstrap script:")
+	suite.Contains(output, "bootstrap.sh")
+	suite.Contains(output, "Running bootstrap script")
+	suite.Contains(output, "Bootstrap completed successfully")
+
+	// Verify bootstrap actually ran
+	lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+	markerFile := filepath.Join(lnkDir, "remote-bootstrap-ran.txt")
+	suite.FileExists(markerFile)
+}
+
+func (suite *CLITestSuite) TestInitWithBootstrapDisabled() {
+	// Create a temporary remote repository with bootstrap script
+	remoteDir := filepath.Join(suite.tempDir, "remote")
+	err := os.MkdirAll(remoteDir, 0755)
+	suite.Require().NoError(err)
+
+	// Initialize git repo in remote
+	cmd := exec.Command("git", "init", "--bare")
+	cmd.Dir = remoteDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	// Create a working repo to populate the remote
+	workingDir := filepath.Join(suite.tempDir, "working")
+	err = os.MkdirAll(workingDir, 0755)
+	suite.Require().NoError(err)
+
+	cmd = exec.Command("git", "clone", remoteDir, workingDir)
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	// Add a bootstrap script
+	bootstrapScript := filepath.Join(workingDir, "bootstrap.sh")
+	scriptContent := `#!/bin/bash
+echo "This should not run!"
+touch should-not-exist.txt
+`
+	err = os.WriteFile(bootstrapScript, []byte(scriptContent), 0755)
+	suite.Require().NoError(err)
+
+	// Commit and push
+	cmd = exec.Command("git", "add", ".")
+	cmd.Dir = workingDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	cmd = exec.Command("git", "-c", "user.email=test@example.com", "-c", "user.name=Test User", "commit", "-m", "Add bootstrap")
+	cmd.Dir = workingDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	cmd = exec.Command("git", "push", "origin", "master")
+	cmd.Dir = workingDir
+	err = cmd.Run()
+	suite.Require().NoError(err)
+
+	// Test init with --no-bootstrap flag
+	err = suite.runCommand("init", "-r", remoteDir, "--no-bootstrap")
+	suite.NoError(err)
+	output := suite.stdout.String()
+	suite.Contains(output, "Cloned from:")
+	suite.NotContains(output, "Looking for bootstrap script")
+	suite.NotContains(output, "Running bootstrap script")
+
+	// Verify bootstrap did NOT run
+	lnkDir := filepath.Join(suite.tempDir, ".config", "lnk")
+	markerFile := filepath.Join(lnkDir, "should-not-exist.txt")
+	suite.NoFileExists(markerFile)
+}
+
+func TestCLISuite(t *testing.T) {
+	suite.Run(t, new(CLITestSuite))
+}

cmd/status.go

@@ -1,58 +1,92 @@
 package cmd
 
 import (
-	"fmt"
-
 	"github.com/spf13/cobra"
 	"github.com/yarlson/lnk/internal/core"
 )
 
-var statusCmd = &cobra.Command{
-	Use:          "status",
-	Short:        "📊 Show repository sync status",
-	Long:         "Display how many commits ahead/behind the local repository is relative to the remote.",
-	SilenceUsage: true,
-	RunE: func(cmd *cobra.Command, args []string) error {
-		lnk := core.NewLnk()
-		status, err := lnk.Status()
-		if err != nil {
-			return fmt.Errorf("failed to get status: %w", err)
-		}
+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 and check for uncommitted changes.",
+		SilenceUsage:  true,
+		SilenceErrors: true,
+		RunE: func(cmd *cobra.Command, args []string) error {
+			lnk := core.NewLnk()
+			status, err := lnk.Status()
+			if err != nil {
+				return err
+			}
 
-		if status.Ahead == 0 && status.Behind == 0 {
-			fmt.Printf("✅ \033[1;32mRepository is up to date\033[0m\n")
-			fmt.Printf("   📡 Synced with \033[36m%s\033[0m\n", status.Remote)
+			if status.Dirty {
+				displayDirtyStatus(cmd, status)
+				return nil
+			}
+
+			if status.Ahead == 0 && status.Behind == 0 {
+				displayUpToDateStatus(cmd, status)
+				return nil
+			}
+
+			displaySyncStatus(cmd, status)
+			return nil
+		},
+	}
+}
+
+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 {
-			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")
-			}
+			printf(cmd, "   ⬆️ \033[1;33m%d %s ahead\033[0m - ready to push\n", status.Ahead, commitText)
 		}
+	}
 
-		return nil
-	},
+	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 init() {
-	rootCmd.AddCommand(statusCmd)
+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

@@ -3,6 +3,7 @@ package core
 import (
 	"fmt"
 	"os"
+	"os/exec"
 	"path/filepath"
 	"sort"
 	"strings"
@@ -14,18 +15,44 @@ import (
 // Lnk represents the main application logic
 type Lnk struct {
 	repoPath string
+	host     string // Host-specific configuration
 	git      *git.Git
 	fs       *fs.FileSystem
 }
 
-// NewLnk creates a new Lnk instance
-func NewLnk() *Lnk {
+type Option func(*Lnk)
+
+// WithHost sets the host for host-specific configuration
+func WithHost(host string) Option {
+	return func(l *Lnk) {
+		l.host = host
+	}
+}
+
+// NewLnk creates a new Lnk instance with optional configuration
+func NewLnk(opts ...Option) *Lnk {
 	repoPath := getRepoPath()
-	return &Lnk{
+	lnk := &Lnk{
 		repoPath: repoPath,
+		host:     "",
 		git:      git.New(repoPath),
 		fs:       fs.New(),
 	}
+
+	for _, opt := range opts {
+		opt(lnk)
+	}
+
+	return lnk
+}
+
+// GetCurrentHostname returns the current system hostname
+func GetCurrentHostname() (string, error) {
+	hostname, err := os.Hostname()
+	if err != nil {
+		return "", fmt.Errorf("failed to get hostname: %w", err)
+	}
+	return hostname, nil
 }
 
 // getRepoPath returns the path to the lnk repository directory
@@ -43,6 +70,48 @@ func getRepoPath() string {
 	return filepath.Join(xdgConfig, "lnk")
 }
 
+// getHostStoragePath returns the storage path for host-specific or common files
+func (l *Lnk) getHostStoragePath() string {
+	if l.host == "" {
+		// Common configuration - store in root of repo
+		return l.repoPath
+	}
+	// Host-specific configuration - store in host subdirectory
+	return filepath.Join(l.repoPath, l.host+".lnk")
+}
+
+// getLnkFileName returns the appropriate .lnk tracking file name
+func (l *Lnk) getLnkFileName() string {
+	if l.host == "" {
+		return ".lnk"
+	}
+	return ".lnk." + l.host
+}
+
+// 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("")
@@ -73,27 +142,17 @@ func (l *Lnk) InitWithRemote(remoteURL string) error {
 	}
 
 	// No existing repository, initialize Git repository
-	if err := l.git.Init(); err != nil {
-		return fmt.Errorf("failed to initialize git repository: %w", err)
-	}
-
-	return nil
+	return l.git.Init()
 }
 
 // Clone clones a repository from the given URL
 func (l *Lnk) Clone(url string) error {
-	if err := l.git.Clone(url); err != nil {
-		return fmt.Errorf("failed to clone repository: %w", err)
-	}
-	return nil
+	return l.git.Clone(url)
 }
 
 // AddRemote adds a remote to the repository
 func (l *Lnk) AddRemote(name, url string) error {
-	if err := l.git.AddRemote(name, url); err != nil {
-		return fmt.Errorf("failed to add remote %s: %w", name, err)
-	}
-	return nil
+	return l.git.AddRemote(name, url)
 }
 
 // Add moves a file or directory to the repository and creates a symlink
@@ -109,9 +168,32 @@ func (l *Lnk) Add(filePath string) error {
 		return fmt.Errorf("failed to get absolute path: %w", err)
 	}
 
-	// Calculate destination path in repo
-	basename := filepath.Base(absPath)
-	destPath := filepath.Join(l.repoPath, basename)
+	// Get relative path for tracking
+	relativePath, err := getRelativePath(absPath)
+	if err != nil {
+		return fmt.Errorf("failed to get relative path: %w", err)
+	}
+
+	// Generate repository path from relative path
+	storagePath := l.getHostStoragePath()
+	destPath := filepath.Join(storagePath, relativePath)
+
+	// Ensure destination directory exists (including parent directories for host-specific files)
+	destDir := filepath.Dir(destPath)
+	if err := os.MkdirAll(destDir, 0755); err != nil {
+		return fmt.Errorf("failed to create destination directory: %w", err)
+	}
+
+	// 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)
@@ -120,76 +202,56 @@ func (l *Lnk) Add(filePath string) error {
 	}
 
 	// 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)
-		}
+	if err := l.fs.Move(absPath, destPath, info); err != nil {
+		return err
 	}
 
 	// Create symlink
 	if err := l.fs.CreateSymlink(destPath, absPath); err != nil {
 		// 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)
+		_ = l.fs.Move(destPath, absPath, info)
+		return err
 	}
 
-	// Add to .lnk tracking file
-	if err := l.addManagedItem(absPath); err != nil {
+	// Add to .lnk tracking file using relative path
+	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() {
-			_ = l.fs.MoveDirectory(destPath, absPath) // Ignore error in cleanup
-		} else {
-			_ = l.fs.MoveFile(destPath, absPath) // Ignore error in cleanup
-		}
+		_ = os.Remove(absPath)
+		_ = l.fs.Move(destPath, absPath, info)
 		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 {
+	// For host-specific files, we need to add the relative path from repo root
+	gitPath := relativePath
+	if l.host != "" {
+		gitPath = filepath.Join(l.host+".lnk", relativePath)
+	}
+	if err := l.git.Add(gitPath); 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)
+		_ = os.Remove(absPath)
+		_ = l.removeManagedItem(relativePath)
+		_ = l.fs.Move(destPath, absPath, info)
+		return err
 	}
 
 	// Add .lnk file to the same commit
-	if err := l.git.Add(".lnk"); err != nil {
+	if err := l.git.Add(l.getLnkFileName()); 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)
+		_ = os.Remove(absPath)
+		_ = l.removeManagedItem(relativePath)
+		_ = l.fs.Move(destPath, absPath, info)
+		return err
 	}
 
 	// 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
-		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)
+		_ = os.Remove(absPath)
+		_ = l.removeManagedItem(relativePath)
+		_ = l.fs.Move(destPath, absPath, info)
+		return err
 	}
 
 	return nil
@@ -208,6 +270,29 @@ 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 {
@@ -219,8 +304,6 @@ func (l *Lnk) Remove(filePath string) error {
 		target = filepath.Join(filepath.Dir(absPath), target)
 	}
 
-	basename := filepath.Base(target)
-
 	// Check if target is a directory or file
 	info, err := os.Stat(target)
 	if err != nil {
@@ -232,35 +315,34 @@ func (l *Lnk) Remove(filePath string) error {
 		return fmt.Errorf("failed to remove symlink: %w", err)
 	}
 
-	// Remove from .lnk tracking file
-	if err := l.removeManagedItem(absPath); err != nil {
+	// Remove from .lnk tracking file using relative path
+	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 {
-		return fmt.Errorf("failed to remove from git: %w", err)
+	// Generate the correct git path for removal
+	gitPath := relativePath
+	if l.host != "" {
+		gitPath = filepath.Join(l.host+".lnk", relativePath)
+	}
+	if err := l.git.Remove(gitPath); err != nil {
+		return 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)
+	if err := l.git.Add(l.getLnkFileName()); err != nil {
+		return err
 	}
 
 	// 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)
+		return 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)
-		}
+	if err := l.fs.Move(target, absPath, info); err != nil {
+		return err
 	}
 
 	return nil
@@ -276,6 +358,7 @@ type StatusInfo struct {
 	Ahead  int
 	Behind int
 	Remote string
+	Dirty  bool
 }
 
 // Status returns the repository sync status
@@ -287,13 +370,14 @@ func (l *Lnk) Status() (*StatusInfo, error) {
 
 	gitStatus, err := l.git.GetStatus()
 	if err != nil {
-		return nil, fmt.Errorf("failed to get repository status: %w", err)
+		return nil, err
 	}
 
 	return &StatusInfo{
 		Ahead:  gitStatus.Ahead,
 		Behind: gitStatus.Behind,
 		Remote: gitStatus.Remote,
+		Dirty:  gitStatus.Dirty,
 	}, nil
 }
 
@@ -307,28 +391,24 @@ func (l *Lnk) Push(message string) error {
 	// Check if there are any changes
 	hasChanges, err := l.git.HasChanges()
 	if err != nil {
-		return fmt.Errorf("failed to check for changes: %w", err)
+		return err
 	}
 
 	if hasChanges {
 		// Stage all changes
 		if err := l.git.AddAll(); err != nil {
-			return fmt.Errorf("failed to stage changes: %w", err)
+			return err
 		}
 
 		// Create a sync commit
 		if err := l.git.Commit(message); err != nil {
-			return fmt.Errorf("failed to commit changes: %w", err)
+			return err
 		}
 	}
 
 	// Push to remote (this will be a no-op in tests since we don't have real remotes)
 	// In real usage, this would push to the actual remote repository
-	if err := l.git.Push(); err != nil {
-		return fmt.Errorf("failed to push to remote: %w", err)
-	}
-
-	return nil
+	return l.git.Push()
 }
 
 // Pull fetches changes from remote and restores symlinks as needed
@@ -340,7 +420,7 @@ func (l *Lnk) Pull() ([]string, error) {
 
 	// Pull changes from remote (this will be a no-op in tests since we don't have real remotes)
 	if err := l.git.Pull(); err != nil {
-		return nil, fmt.Errorf("failed to pull from remote: %w", err)
+		return nil, err
 	}
 
 	// Find all managed files in the repository and restore symlinks
@@ -352,9 +432,12 @@ func (l *Lnk) Pull() ([]string, error) {
 	return restored, nil
 }
 
-// RestoreSymlinks finds all managed items from .lnk file and ensures they have proper symlinks
-func (l *Lnk) RestoreSymlinks() ([]string, error) {
-	var restored []string
+// List returns the list of files and directories currently managed by lnk
+func (l *Lnk) List() ([]string, error) {
+	// 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 +445,48 @@ func (l *Lnk) RestoreSymlinks() ([]string, error) {
 		return nil, fmt.Errorf("failed to get managed items: %w", err)
 	}
 
-	for _, itemName := range managedItems {
-		repoItem := filepath.Join(l.repoPath, itemName)
+	return managedItems, nil
+}
+
+// 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
+		storagePath := l.getHostStoragePath()
+		repoItem := filepath.Join(storagePath, relativePath)
 
 		// Check if item exists in repository
 		if _, err := os.Stat(repoItem); os.IsNotExist(err) {
 			continue // Skip missing items
 		}
 
-		// Determine where the symlink should be
-		// For config files, we'll place them in the user's home directory
-		homeDir, err := os.UserHomeDir()
-		if err != nil {
-			return nil, fmt.Errorf("failed to get home directory: %w", err)
-		}
-
-		symlinkPath := filepath.Join(homeDir, itemName)
+		// Determine where the symlink should be created
+		symlinkPath := filepath.Join(homeDir, relativePath)
 
 		// 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 +496,10 @@ 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, err
 		}
 
-		restored = append(restored, itemName)
+		restored = append(restored, relativePath)
 	}
 
 	return restored, nil
@@ -441,7 +544,7 @@ func (l *Lnk) isValidSymlink(symlinkPath, expectedTarget string) bool {
 
 // getManagedItems returns the list of managed files and directories from .lnk file
 func (l *Lnk) getManagedItems() ([]string, error) {
-	lnkFile := filepath.Join(l.repoPath, ".lnk")
+	lnkFile := filepath.Join(l.repoPath, l.getLnkFileName())
 
 	// If .lnk file doesn't exist, return empty list
 	if _, err := os.Stat(lnkFile); os.IsNotExist(err) {
@@ -470,25 +573,22 @@ 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
-	items = append(items, basename)
+	// Add new item using relative path
+	items = append(items, relativePath)
 
 	// Sort for consistent ordering
 	sort.Strings(items)
@@ -497,20 +597,17 @@ 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
-	basename := filepath.Base(itemPath)
-
-	// Remove item
+	// Remove item using relative path
 	var newItems []string
 	for _, item := range items {
-		if item != basename {
+		if item != relativePath {
 			newItems = append(newItems, item)
 		}
 	}
@@ -520,7 +617,7 @@ func (l *Lnk) removeManagedItem(itemPath string) error {
 
 // writeManagedItems writes the list of managed items to .lnk file
 func (l *Lnk) writeManagedItems(items []string) error {
-	lnkFile := filepath.Join(l.repoPath, ".lnk")
+	lnkFile := filepath.Join(l.repoPath, l.getLnkFileName())
 
 	content := strings.Join(items, "\n")
 	if len(items) > 0 {
@@ -534,3 +631,52 @@ func (l *Lnk) writeManagedItems(items []string) error {
 
 	return nil
 }
+
+// FindBootstrapScript searches for a bootstrap script in the repository
+func (l *Lnk) FindBootstrapScript() (string, error) {
+	// Check if repository is initialized
+	if !l.git.IsGitRepository() {
+		return "", fmt.Errorf("❌ Lnk repository not initialized\n   💡 Run \033[1mlnk init\033[0m first")
+	}
+
+	// Look for bootstrap.sh - simple, opinionated choice
+	scriptPath := filepath.Join(l.repoPath, "bootstrap.sh")
+	if _, err := os.Stat(scriptPath); err == nil {
+		return "bootstrap.sh", nil
+	}
+
+	return "", nil // No bootstrap script found
+}
+
+// RunBootstrapScript executes the bootstrap script
+func (l *Lnk) RunBootstrapScript(scriptName string) error {
+	scriptPath := filepath.Join(l.repoPath, scriptName)
+
+	// Verify the script exists
+	if _, err := os.Stat(scriptPath); os.IsNotExist(err) {
+		return fmt.Errorf("❌ Bootstrap script not found: \033[31m%s\033[0m", scriptName)
+	}
+
+	// Make sure it's executable
+	if err := os.Chmod(scriptPath, 0755); err != nil {
+		return fmt.Errorf("❌ Failed to make bootstrap script executable: %w", err)
+	}
+
+	// Run with bash (since we only support bootstrap.sh)
+	cmd := exec.Command("bash", scriptPath)
+
+	// Set working directory to the repository
+	cmd.Dir = l.repoPath
+
+	// Connect to stdout/stderr for user to see output
+	cmd.Stdout = os.Stdout
+	cmd.Stderr = os.Stderr
+	cmd.Stdin = os.Stdin
+
+	// Run the script
+	if err := cmd.Run(); err != nil {
+		return fmt.Errorf("❌ Bootstrap script failed with error: %w", err)
+	}
+
+	return nil
+}

internal/core/lnk_test.go

@@ -0,0 +1,825 @@
+package core
+
+import (
+	"fmt"
+	"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 preserve the directory structure
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+
+	// Find the .bashrc file in the repository (it should be at the relative path)
+	repoFile := filepath.Join(lnkDir, suite.tempDir, ".bashrc")
+	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 the repository directory preserves the structure
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+
+	// The directory should be at the relative path
+	repoDir := filepath.Join(lnkDir, suite.tempDir, "testdir")
+	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=$PATH:/usr/local/bin"
+	err := os.WriteFile(repoFile, []byte(content), 0644)
+	suite.Require().NoError(err)
+
+	// Create .lnk file to track it
+	lnkFile := filepath.Join(suite.tempDir, "lnk", ".lnk")
+	err = os.WriteFile(lnkFile, []byte(".bashrc\n"), 0644)
+	suite.Require().NoError(err)
+
+	// Get home directory for the test
+	homeDir, err := os.UserHomeDir()
+	suite.Require().NoError(err)
+
+	targetFile := filepath.Join(homeDir, ".bashrc")
+
+	// Clean up the test file after the test
+	defer func() {
+		_ = os.Remove(targetFile)
+	}()
+
+	// Test symlink restoration
+	restored, err := suite.lnk.RestoreSymlinks()
+	suite.Require().NoError(err)
+
+	// Should have restored the symlink
+	suite.Len(restored, 1)
+	suite.Equal(".bashrc", restored[0])
+
+	// Check that file is now a symlink
+	info, err := os.Lstat(targetFile)
+	suite.NoError(err)
+	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
+}
+
+// Test error conditions
+func (suite *CoreTestSuite) TestErrorConditions() {
+	// Test add nonexistent file
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add("/nonexistent/file")
+	suite.Error(err)
+	suite.Contains(err.Error(), "File or directory not found")
+
+	// Test remove unmanaged file
+	testFile := filepath.Join(suite.tempDir, ".regularfile")
+	err = os.WriteFile(testFile, []byte("content"), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Remove(testFile)
+	suite.Error(err)
+	suite.Contains(err.Error(), "File is not managed by lnk")
+
+	// Test status without remote
+	_, err = suite.lnk.Status()
+	suite.Error(err)
+	suite.Contains(err.Error(), "No remote repository is configured")
+}
+
+// Test git operations
+func (suite *CoreTestSuite) TestGitOperations() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Add a file to create a commit
+	testFile := filepath.Join(suite.tempDir, ".bashrc")
+	content := "export PATH=$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=$PATH:/usr/local/bin"
+	err = os.WriteFile(testFile, []byte(content), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add(testFile)
+	suite.Require().NoError(err)
+
+	// Test list with one managed file
+	items, err = suite.lnk.List()
+	suite.Require().NoError(err)
+	suite.Len(items, 1)
+	suite.Contains(items[0], ".bashrc")
+
+	// Add a directory
+	testDir := filepath.Join(suite.tempDir, ".config")
+	err = os.MkdirAll(testDir, 0755)
+	suite.Require().NoError(err)
+	configFile := filepath.Join(testDir, "app.conf")
+	err = os.WriteFile(configFile, []byte("setting=value"), 0644)
+	suite.Require().NoError(err)
+
+	err = suite.lnk.Add(testDir)
+	suite.Require().NoError(err)
+
+	// Test list with multiple managed items
+	items, err = suite.lnk.List()
+	suite.Require().NoError(err)
+	suite.Len(items, 2)
+
+	// Check that both items are present
+	found := make(map[string]bool)
+	for _, item := range items {
+		if strings.Contains(item, ".bashrc") {
+			found[".bashrc"] = true
+		}
+		if strings.Contains(item, ".config") {
+			found[".config"] = true
+		}
+	}
+	suite.True(found[".bashrc"], "Should contain .bashrc")
+	suite.True(found[".config"], "Should contain .config")
+
+	// Remove one item and verify list is updated
+	err = suite.lnk.Remove(testFile)
+	suite.Require().NoError(err)
+
+	items, err = suite.lnk.List()
+	suite.Require().NoError(err)
+	suite.Len(items, 1)
+	suite.Contains(items[0], ".config")
+}
+
+// Test multihost functionality
+func (suite *CoreTestSuite) TestMultihostFileOperations() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create test files for different hosts
+	testFile1 := filepath.Join(suite.tempDir, ".bashrc")
+	content1 := "export PATH=$PATH:/usr/local/bin"
+	err = os.WriteFile(testFile1, []byte(content1), 0644)
+	suite.Require().NoError(err)
+
+	testFile2 := filepath.Join(suite.tempDir, ".vimrc")
+	content2 := "set number"
+	err = os.WriteFile(testFile2, []byte(content2), 0644)
+	suite.Require().NoError(err)
+
+	// Add file to common configuration
+	commonLnk := NewLnk()
+	err = commonLnk.Add(testFile1)
+	suite.Require().NoError(err)
+
+	// Add file to host-specific configuration
+	hostLnk := NewLnk(WithHost("workstation"))
+	err = hostLnk.Add(testFile2)
+	suite.Require().NoError(err)
+
+	// Verify both files are symlinks
+	info1, err := os.Lstat(testFile1)
+	suite.Require().NoError(err)
+	suite.Equal(os.ModeSymlink, info1.Mode()&os.ModeSymlink)
+
+	info2, err := os.Lstat(testFile2)
+	suite.Require().NoError(err)
+	suite.Equal(os.ModeSymlink, info2.Mode()&os.ModeSymlink)
+
+	// Verify common configuration tracking
+	commonItems, err := commonLnk.List()
+	suite.Require().NoError(err)
+	suite.Len(commonItems, 1)
+	suite.Contains(commonItems[0], ".bashrc")
+
+	// Verify host-specific configuration tracking
+	hostItems, err := hostLnk.List()
+	suite.Require().NoError(err)
+	suite.Len(hostItems, 1)
+	suite.Contains(hostItems[0], ".vimrc")
+
+	// Verify files are stored in correct locations
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+
+	// Common file should be in root
+	commonFile := filepath.Join(lnkDir, ".lnk")
+	suite.FileExists(commonFile)
+
+	// Host-specific file should be in host subdirectory
+	hostDir := filepath.Join(lnkDir, "workstation.lnk")
+	suite.DirExists(hostDir)
+
+	hostTrackingFile := filepath.Join(lnkDir, ".lnk.workstation")
+	suite.FileExists(hostTrackingFile)
+
+	// Test removal
+	err = commonLnk.Remove(testFile1)
+	suite.Require().NoError(err)
+
+	err = hostLnk.Remove(testFile2)
+	suite.Require().NoError(err)
+
+	// Verify files are restored
+	info1, err = os.Lstat(testFile1)
+	suite.Require().NoError(err)
+	suite.Equal(os.FileMode(0), info1.Mode()&os.ModeSymlink)
+
+	info2, err = os.Lstat(testFile2)
+	suite.Require().NoError(err)
+	suite.Equal(os.FileMode(0), info2.Mode()&os.ModeSymlink)
+}
+
+// Test hostname detection
+func (suite *CoreTestSuite) TestHostnameDetection() {
+	hostname, err := GetCurrentHostname()
+	suite.NoError(err)
+	suite.NotEmpty(hostname)
+}
+
+// Test host-specific symlink restoration
+func (suite *CoreTestSuite) TestMultihostSymlinkRestoration() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create files directly in host-specific storage (simulating a pull)
+	hostLnk := NewLnk(WithHost("testhost"))
+
+	// Ensure host storage directory exists
+	hostStoragePath := hostLnk.getHostStoragePath()
+	err = os.MkdirAll(hostStoragePath, 0755)
+	suite.Require().NoError(err)
+
+	// Create a file in host storage
+	repoFile := filepath.Join(hostStoragePath, ".bashrc")
+	content := "export HOST=testhost"
+	err = os.WriteFile(repoFile, []byte(content), 0644)
+	suite.Require().NoError(err)
+
+	// Create host tracking file
+	trackingFile := filepath.Join(suite.tempDir, "lnk", ".lnk.testhost")
+	err = os.WriteFile(trackingFile, []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 := hostLnk.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 that common and host-specific configurations don't interfere
+func (suite *CoreTestSuite) TestMultihostIsolation() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create same file for common and host-specific
+	testFile := filepath.Join(suite.tempDir, ".gitconfig")
+	commonContent := "[user]\n\tname = Common User"
+	err = os.WriteFile(testFile, []byte(commonContent), 0644)
+	suite.Require().NoError(err)
+
+	// Add to common
+	commonLnk := NewLnk()
+	err = commonLnk.Add(testFile)
+	suite.Require().NoError(err)
+
+	// Remove and recreate with different content
+	err = commonLnk.Remove(testFile)
+	suite.Require().NoError(err)
+
+	hostContent := "[user]\n\tname = Work User"
+	err = os.WriteFile(testFile, []byte(hostContent), 0644)
+	suite.Require().NoError(err)
+
+	// Add to host-specific
+	hostLnk := NewLnk(WithHost("work"))
+	err = hostLnk.Add(testFile)
+	suite.Require().NoError(err)
+
+	// Verify tracking files are separate
+	commonItems, err := commonLnk.List()
+	suite.Require().NoError(err)
+	suite.Len(commonItems, 0) // Should be empty after removal
+
+	hostItems, err := hostLnk.List()
+	suite.Require().NoError(err)
+	suite.Len(hostItems, 1)
+	suite.Contains(hostItems[0], ".gitconfig")
+
+	// Verify content is correct
+	symlinkContent, err := os.ReadFile(testFile)
+	suite.Require().NoError(err)
+	suite.Equal(hostContent, string(symlinkContent))
+}
+
+// Test bootstrap script detection
+func (suite *CoreTestSuite) TestFindBootstrapScript() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Test with no bootstrap script
+	scriptPath, err := suite.lnk.FindBootstrapScript()
+	suite.NoError(err)
+	suite.Empty(scriptPath)
+
+	// Test with bootstrap.sh
+	bootstrapScript := filepath.Join(suite.tempDir, "lnk", "bootstrap.sh")
+	err = os.WriteFile(bootstrapScript, []byte("#!/bin/bash\necho 'test'"), 0644)
+	suite.Require().NoError(err)
+
+	scriptPath, err = suite.lnk.FindBootstrapScript()
+	suite.NoError(err)
+	suite.Equal("bootstrap.sh", scriptPath)
+}
+
+// Test bootstrap script execution
+func (suite *CoreTestSuite) TestRunBootstrapScript() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create a test script that creates a marker file
+	bootstrapScript := filepath.Join(suite.tempDir, "lnk", "test.sh")
+	markerFile := filepath.Join(suite.tempDir, "lnk", "bootstrap-executed.txt")
+	scriptContent := fmt.Sprintf("#!/bin/bash\ntouch %s\necho 'Bootstrap executed'", markerFile)
+
+	err = os.WriteFile(bootstrapScript, []byte(scriptContent), 0755)
+	suite.Require().NoError(err)
+
+	// Run the bootstrap script
+	err = suite.lnk.RunBootstrapScript("test.sh")
+	suite.NoError(err)
+
+	// Verify the marker file was created
+	suite.FileExists(markerFile)
+}
+
+// Test bootstrap script execution with error
+func (suite *CoreTestSuite) TestRunBootstrapScriptWithError() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Create a script that will fail
+	bootstrapScript := filepath.Join(suite.tempDir, "lnk", "failing.sh")
+	scriptContent := "#!/bin/bash\nexit 1"
+
+	err = os.WriteFile(bootstrapScript, []byte(scriptContent), 0755)
+	suite.Require().NoError(err)
+
+	// Run the bootstrap script - should fail
+	err = suite.lnk.RunBootstrapScript("failing.sh")
+	suite.Error(err)
+	suite.Contains(err.Error(), "Bootstrap script failed")
+}
+
+// Test running bootstrap on non-existent script
+func (suite *CoreTestSuite) TestRunBootstrapScriptNotFound() {
+	err := suite.lnk.Init()
+	suite.Require().NoError(err)
+
+	// Try to run non-existent script
+	err = suite.lnk.RunBootstrapScript("nonexistent.sh")
+	suite.Error(err)
+	suite.Contains(err.Error(), "Bootstrap script not found")
+}
+
+func TestCoreSuite(t *testing.T) {
+	suite.Run(t, new(CoreTestSuite))
+}

internal/fs/errors.go

@@ -0,0 +1,119 @@
+package fs
+
+import "fmt"
+
+// ANSI color codes for consistent formatting
+const (
+	colorReset = "\033[0m"
+	colorRed   = "\033[31m"
+	colorBold  = "\033[1m"
+)
+
+// formatError creates a consistently formatted error message with ❌ prefix
+func formatError(message string, args ...interface{}) string {
+	return fmt.Sprintf("❌ "+message, args...)
+}
+
+// formatPath formats a file path with red color
+func formatPath(path string) string {
+	return fmt.Sprintf("%s%s%s", colorRed, path, colorReset)
+}
+
+// formatCommand formats a command with bold styling
+func formatCommand(command string) string {
+	return fmt.Sprintf("%s%s%s", colorBold, command, colorReset)
+}
+
+// FileNotExistsError represents an error when a file does not exist
+type FileNotExistsError struct {
+	Path string
+	Err  error
+}
+
+func (e *FileNotExistsError) Error() string {
+	return formatError("File or directory not found: %s", formatPath(e.Path))
+}
+
+func (e *FileNotExistsError) Unwrap() error {
+	return e.Err
+}
+
+// FileCheckError represents an error when failing to check a file
+type FileCheckError struct {
+	Err error
+}
+
+func (e *FileCheckError) Error() string {
+	return formatError("Unable to access file. Please check file permissions and try again.")
+}
+
+func (e *FileCheckError) Unwrap() error {
+	return e.Err
+}
+
+// UnsupportedFileTypeError represents an error when a file type is not supported
+type UnsupportedFileTypeError struct {
+	Path string
+}
+
+func (e *UnsupportedFileTypeError) Error() string {
+	return formatError("Cannot manage this type of file: %s\n   💡 lnk can only manage regular files and directories", formatPath(e.Path))
+}
+
+func (e *UnsupportedFileTypeError) Unwrap() error {
+	return nil
+}
+
+// NotManagedByLnkError represents an error when a file is not managed by lnk
+type NotManagedByLnkError struct {
+	Path string
+}
+
+func (e *NotManagedByLnkError) Error() string {
+	return formatError("File is not managed by lnk: %s\n   💡 Use %s to manage this file first",
+		formatPath(e.Path), formatCommand("lnk add"))
+}
+
+func (e *NotManagedByLnkError) Unwrap() error {
+	return nil
+}
+
+// SymlinkReadError represents an error when failing to read a symlink
+type SymlinkReadError struct {
+	Err error
+}
+
+func (e *SymlinkReadError) Error() string {
+	return formatError("Unable to read symlink. The file may be corrupted or have invalid permissions.")
+}
+
+func (e *SymlinkReadError) Unwrap() error {
+	return e.Err
+}
+
+// DirectoryCreationError represents an error when failing to create a directory
+type DirectoryCreationError struct {
+	Operation string
+	Err       error
+}
+
+func (e *DirectoryCreationError) Error() string {
+	return formatError("Failed to create directory. Please check permissions and available disk space.")
+}
+
+func (e *DirectoryCreationError) Unwrap() error {
+	return e.Err
+}
+
+// RelativePathCalculationError represents an error when failing to calculate relative path
+type RelativePathCalculationError struct {
+	Err error
+}
+
+func (e *RelativePathCalculationError) Error() string {
+	return formatError("Unable to create symlink due to path configuration issues. Please check file locations.")
+}
+
+func (e *RelativePathCalculationError) Unwrap() error {
+	return e.Err
+}

internal/fs/filesystem.go

@@ -1,7 +1,6 @@
 package fs
 
 import (
-	"fmt"
 	"os"
 	"path/filepath"
 	"strings"
@@ -17,18 +16,19 @@ func New() *FileSystem {
 
 // ValidateFileForAdd validates that a file or directory can be added to lnk
 func (fs *FileSystem) ValidateFileForAdd(filePath string) error {
-	// Check if file exists
+	// Check if file exists and get its info
 	info, err := os.Stat(filePath)
 	if err != nil {
 		if os.IsNotExist(err) {
-			return fmt.Errorf("❌ File does not exist: \033[31m%s\033[0m", filePath)
+			return &FileNotExistsError{Path: filePath, Err: err}
 		}
-		return fmt.Errorf("❌ Failed to check file: %w", err)
+
+		return &FileCheckError{Err: err}
 	}
 
 	// Allow both regular files and directories
 	if !info.Mode().IsRegular() && !info.IsDir() {
-		return fmt.Errorf("❌ Only regular files and directories are supported: \033[31m%s\033[0m", filePath)
+		return &UnsupportedFileTypeError{Path: filePath}
 	}
 
 	return nil
@@ -36,98 +36,79 @@ func (fs *FileSystem) ValidateFileForAdd(filePath string) error {
 
 // ValidateSymlinkForRemove validates that a symlink can be removed from lnk
 func (fs *FileSystem) ValidateSymlinkForRemove(filePath, repoPath string) error {
-	// Check if file exists
+	// Check if file exists and is a symlink
 	info, err := os.Lstat(filePath) // Use Lstat to not follow symlinks
 	if err != nil {
 		if os.IsNotExist(err) {
-			return fmt.Errorf("❌ File does not exist: \033[31m%s\033[0m", filePath)
+			return &FileNotExistsError{Path: filePath, Err: err}
 		}
-		return fmt.Errorf("❌ Failed to check file: %w", err)
+
+		return &FileCheckError{Err: err}
 	}
 
-	// Check if it's a symlink
 	if info.Mode()&os.ModeSymlink == 0 {
-		return fmt.Errorf("❌ File is not managed by lnk: \033[31m%s\033[0m\n   💡 Use \033[1mlnk add\033[0m to manage this file first", filePath)
+		return &NotManagedByLnkError{Path: filePath}
 	}
 
-	// Check if symlink points to the repository
+	// Get symlink target and resolve to absolute path
 	target, err := os.Readlink(filePath)
 	if err != nil {
-		return fmt.Errorf("failed to read symlink: %w", err)
+		return &SymlinkReadError{Err: err}
 	}
 
-	// Convert relative path to absolute if needed
 	if !filepath.IsAbs(target) {
 		target = filepath.Join(filepath.Dir(filePath), target)
 	}
 
-	// Clean the path to resolve any .. or . components
+	// Clean paths and check if target is inside the repository
 	target = filepath.Clean(target)
 	repoPath = filepath.Clean(repoPath)
 
-	// Check if target is inside the repository
 	if !strings.HasPrefix(target, repoPath+string(filepath.Separator)) && target != repoPath {
-		return fmt.Errorf("❌ File is not managed by lnk: \033[31m%s\033[0m", filePath)
+		return &NotManagedByLnkError{Path: filePath}
 	}
 
 	return nil
 }
 
+// Move moves a file or directory from source to destination based on the file info
+func (fs *FileSystem) Move(src, dst string, info os.FileInfo) error {
+	if info.IsDir() {
+		return fs.MoveDirectory(src, dst)
+	}
+	return fs.MoveFile(src, dst)
+}
+
 // MoveFile moves a file from source to destination
 func (fs *FileSystem) MoveFile(src, dst string) error {
 	// Ensure destination directory exists
-	dstDir := filepath.Dir(dst)
-	if err := os.MkdirAll(dstDir, 0755); err != nil {
-		return fmt.Errorf("failed to create destination directory: %w", err)
+	if err := os.MkdirAll(filepath.Dir(dst), 0755); err != nil {
+		return &DirectoryCreationError{Operation: "destination directory", Err: err}
 	}
 
 	// Move the file
-	if err := os.Rename(src, dst); err != nil {
-		return fmt.Errorf("failed to move file from %s to %s: %w", src, dst, err)
-	}
-
-	return nil
+	return os.Rename(src, dst)
 }
 
 // CreateSymlink creates a relative symlink from target to linkPath
 func (fs *FileSystem) CreateSymlink(target, linkPath string) error {
 	// Calculate relative path from linkPath to target
-	linkDir := filepath.Dir(linkPath)
-	relTarget, err := filepath.Rel(linkDir, target)
+	relTarget, err := filepath.Rel(filepath.Dir(linkPath), target)
 	if err != nil {
-		return fmt.Errorf("failed to calculate relative path: %w", err)
+		return &RelativePathCalculationError{Err: err}
 	}
 
 	// Create the symlink
-	if err := os.Symlink(relTarget, linkPath); err != nil {
-		return fmt.Errorf("failed to create symlink: %w", err)
-	}
-
-	return nil
+	return os.Symlink(relTarget, linkPath)
 }
 
 // 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)
+	if err := os.MkdirAll(filepath.Dir(dst), 0755); err != nil {
+		return &DirectoryCreationError{Operation: "destination parent directory", Err: 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
+	// Move the directory
+	return os.Rename(src, dst)
 }

internal/git/errors.go

@@ -0,0 +1,218 @@
+package git
+
+import "fmt"
+
+// ANSI color codes for consistent formatting
+const (
+	colorReset  = "\033[0m"
+	colorBold   = "\033[1m"
+	colorGreen  = "\033[32m"
+	colorYellow = "\033[33m"
+)
+
+// formatError creates a consistently formatted error message with ❌ prefix
+func formatError(message string, args ...interface{}) string {
+	return fmt.Sprintf("❌ "+message, args...)
+}
+
+// formatURL formats a URL with styling
+func formatURL(url string) string {
+	return fmt.Sprintf("%s%s%s", colorBold, url, colorReset)
+}
+
+// formatRemote formats a remote name with styling
+func formatRemote(remote string) string {
+	return fmt.Sprintf("%s%s%s", colorGreen, remote, colorReset)
+}
+
+// GitInitError represents an error during git initialization
+type GitInitError struct {
+	Output string
+	Err    error
+}
+
+func (e *GitInitError) Error() string {
+	return formatError("Failed to initialize git repository. Please ensure git is installed and try again.")
+}
+
+func (e *GitInitError) Unwrap() error {
+	return e.Err
+}
+
+// BranchSetupError represents an error setting up the default branch
+type BranchSetupError struct {
+	Err error
+}
+
+func (e *BranchSetupError) Error() string {
+	return formatError("Failed to set up the default branch. Please check your git installation.")
+}
+
+func (e *BranchSetupError) Unwrap() error {
+	return e.Err
+}
+
+// RemoteExistsError represents an error when a remote already exists with different URL
+type RemoteExistsError struct {
+	Remote      string
+	ExistingURL string
+	NewURL      string
+}
+
+func (e *RemoteExistsError) Error() string {
+	return formatError("Remote %s is already configured with a different repository (%s). Cannot add %s.",
+		formatRemote(e.Remote), formatURL(e.ExistingURL), formatURL(e.NewURL))
+}
+
+func (e *RemoteExistsError) Unwrap() error {
+	return nil
+}
+
+// GitCommandError represents a generic git command execution error
+type GitCommandError struct {
+	Command string
+	Output  string
+	Err     error
+}
+
+func (e *GitCommandError) Error() string {
+	// Provide user-friendly messages based on common command types
+	switch e.Command {
+	case "add":
+		return formatError("Failed to stage files for commit. Please check file permissions and try again.")
+	case "commit":
+		return formatError("Failed to create commit. Please ensure you have staged changes and try again.")
+	case "remote add":
+		return formatError("Failed to add remote repository. Please check the repository URL and try again.")
+	case "rm":
+		return formatError("Failed to remove file from git tracking. Please check if the file exists and try again.")
+	case "log":
+		return formatError("Failed to retrieve commit history.")
+	case "remote":
+		return formatError("Failed to retrieve remote repository information.")
+	case "clone":
+		return formatError("Failed to clone repository. Please check the repository URL and your network connection.")
+	default:
+		return formatError("Git operation failed. Please check your repository state and try again.")
+	}
+}
+
+func (e *GitCommandError) Unwrap() error {
+	return e.Err
+}
+
+// NoRemoteError represents an error when no remote is configured
+type NoRemoteError struct{}
+
+func (e *NoRemoteError) Error() string {
+	return formatError("No remote repository is configured. Please add a remote repository first.")
+}
+
+func (e *NoRemoteError) Unwrap() error {
+	return nil
+}
+
+// RemoteNotFoundError represents an error when a specific remote is not found
+type RemoteNotFoundError struct {
+	Remote string
+	Err    error
+}
+
+func (e *RemoteNotFoundError) Error() string {
+	return formatError("Remote repository %s is not configured.", formatRemote(e.Remote))
+}
+
+func (e *RemoteNotFoundError) Unwrap() error {
+	return e.Err
+}
+
+// GitConfigError represents an error with git configuration
+type GitConfigError struct {
+	Setting string
+	Err     error
+}
+
+func (e *GitConfigError) Error() string {
+	return formatError("Failed to configure git settings. Please check your git installation.")
+}
+
+func (e *GitConfigError) Unwrap() error {
+	return e.Err
+}
+
+// UncommittedChangesError represents an error checking for uncommitted changes
+type UncommittedChangesError struct {
+	Err error
+}
+
+func (e *UncommittedChangesError) Error() string {
+	return formatError("Failed to check repository status. Please verify your git repository is valid.")
+}
+
+func (e *UncommittedChangesError) Unwrap() error {
+	return e.Err
+}
+
+// DirectoryRemovalError represents an error removing a directory
+type DirectoryRemovalError struct {
+	Path string
+	Err  error
+}
+
+func (e *DirectoryRemovalError) Error() string {
+	return formatError("Failed to prepare directory for operation. Please check directory permissions.")
+}
+
+func (e *DirectoryRemovalError) Unwrap() error {
+	return e.Err
+}
+
+// DirectoryCreationError represents an error creating a directory
+type DirectoryCreationError struct {
+	Path string
+	Err  error
+}
+
+func (e *DirectoryCreationError) Error() string {
+	return formatError("Failed to create directory. Please check permissions and available disk space.")
+}
+
+func (e *DirectoryCreationError) Unwrap() error {
+	return e.Err
+}
+
+// PushError represents an error during git push operation
+type PushError struct {
+	Reason string
+	Output string
+	Err    error
+}
+
+func (e *PushError) Error() string {
+	if e.Reason != "" {
+		return formatError("Cannot push changes: %s", e.Reason)
+	}
+	return formatError("Failed to push changes to remote repository. Please check your network connection and repository permissions.")
+}
+
+func (e *PushError) Unwrap() error {
+	return e.Err
+}
+
+// PullError represents an error during git pull operation
+type PullError struct {
+	Reason string
+	Output string
+	Err    error
+}
+
+func (e *PullError) Error() string {
+	if e.Reason != "" {
+		return formatError("Cannot pull changes: %s", e.Reason)
+	}
+	return formatError("Failed to pull changes from remote repository. Please check your network connection and resolve any conflicts.")
+}
+
+func (e *PullError) Unwrap() error {
+	return e.Err
+}

internal/git/git.go

@@ -34,7 +34,7 @@ func (g *Git) Init() error {
 
 		output, err := cmd.CombinedOutput()
 		if err != nil {
-			return fmt.Errorf("git init failed: %w\nOutput: %s", err, string(output))
+			return &GitInitError{Output: string(output), Err: err}
 		}
 
 		// Set the default branch to main
@@ -42,7 +42,7 @@ func (g *Git) Init() error {
 		cmd.Dir = g.repoPath
 
 		if err := cmd.Run(); err != nil {
-			return fmt.Errorf("failed to set default branch to main: %w", err)
+			return &BranchSetupError{Err: err}
 		}
 	}
 
@@ -60,7 +60,7 @@ func (g *Git) AddRemote(name, url string) error {
 			return nil
 		}
 		// Different URL, error
-		return fmt.Errorf("remote %s already exists with different URL: %s (trying to add: %s)", name, existingURL, url)
+		return &RemoteExistsError{Remote: name, ExistingURL: existingURL, NewURL: url}
 	}
 
 	// Remote doesn't exist, add it
@@ -69,7 +69,7 @@ func (g *Git) AddRemote(name, url string) error {
 
 	output, err := cmd.CombinedOutput()
 	if err != nil {
-		return fmt.Errorf("git remote add failed: %w\nOutput: %s", err, string(output))
+		return &GitCommandError{Command: "remote add", Output: string(output), Err: err}
 	}
 
 	return nil
@@ -164,7 +164,7 @@ func (g *Git) Add(filename string) error {
 
 	output, err := cmd.CombinedOutput()
 	if err != nil {
-		return fmt.Errorf("git add failed: %w\nOutput: %s", err, string(output))
+		return &GitCommandError{Command: "add", Output: string(output), Err: err}
 	}
 
 	return nil
@@ -189,7 +189,7 @@ func (g *Git) Remove(filename string) error {
 
 	output, err := cmd.CombinedOutput()
 	if err != nil {
-		return fmt.Errorf("git rm failed: %w\nOutput: %s", err, string(output))
+		return &GitCommandError{Command: "rm", Output: string(output), Err: err}
 	}
 
 	return nil
@@ -207,7 +207,7 @@ func (g *Git) Commit(message string) error {
 
 	output, err := cmd.CombinedOutput()
 	if err != nil {
-		return fmt.Errorf("git commit failed: %w\nOutput: %s", err, string(output))
+		return &GitCommandError{Command: "commit", Output: string(output), Err: err}
 	}
 
 	return nil
@@ -223,7 +223,7 @@ func (g *Git) ensureGitConfig() error {
 		cmd = exec.Command("git", "config", "user.name", "Lnk User")
 		cmd.Dir = g.repoPath
 		if err := cmd.Run(); err != nil {
-			return fmt.Errorf("failed to set git user.name: %w", err)
+			return &GitConfigError{Setting: "user.name", Err: err}
 		}
 	}
 
@@ -235,7 +235,7 @@ func (g *Git) ensureGitConfig() error {
 		cmd = exec.Command("git", "config", "user.email", "lnk@localhost")
 		cmd.Dir = g.repoPath
 		if err := cmd.Run(); err != nil {
-			return fmt.Errorf("failed to set git user.email: %w", err)
+			return &GitConfigError{Setting: "user.email", Err: err}
 		}
 	}
 
@@ -260,7 +260,7 @@ func (g *Git) GetCommits() ([]string, error) {
 		if strings.Contains(outputStr, "does not have any commits yet") {
 			return []string{}, nil
 		}
-		return nil, fmt.Errorf("git log failed: %w", err)
+		return nil, &GitCommandError{Command: "log", Output: outputStr, Err: err}
 	}
 
 	commits := strings.Split(strings.TrimSpace(string(output)), "\n")
@@ -282,18 +282,18 @@ func (g *Git) GetRemoteInfo() (string, error) {
 
 		output, err := cmd.Output()
 		if err != nil {
-			return "", fmt.Errorf("failed to list remotes: %w", err)
+			return "", &GitCommandError{Command: "remote", Output: string(output), Err: err}
 		}
 
 		remotes := strings.Split(strings.TrimSpace(string(output)), "\n")
 		if len(remotes) == 0 || remotes[0] == "" {
-			return "", fmt.Errorf("no remote configured")
+			return "", &NoRemoteError{}
 		}
 
 		// Use the first remote
 		url, err = g.getRemoteURL(remotes[0])
 		if err != nil {
-			return "", fmt.Errorf("failed to get remote URL: %w", err)
+			return "", &RemoteNotFoundError{Remote: remotes[0], Err: err}
 		}
 	}
 
@@ -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, &UncommittedChangesError{Err: 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
 }
 
@@ -401,7 +410,7 @@ func (g *Git) HasChanges() (bool, error) {
 
 	output, err := cmd.Output()
 	if err != nil {
-		return false, fmt.Errorf("git status failed: %w", err)
+		return false, &GitCommandError{Command: "status", Output: string(output), Err: err}
 	}
 
 	return len(strings.TrimSpace(string(output))) > 0, nil
@@ -414,7 +423,7 @@ func (g *Git) AddAll() error {
 
 	output, err := cmd.CombinedOutput()
 	if err != nil {
-		return fmt.Errorf("git add failed: %w\nOutput: %s", err, string(output))
+		return &GitCommandError{Command: "add", Output: string(output), Err: err}
 	}
 
 	return nil
@@ -425,7 +434,7 @@ func (g *Git) Push() error {
 	// First ensure we have a remote configured
 	_, err := g.GetRemoteInfo()
 	if err != nil {
-		return fmt.Errorf("cannot push: %w", err)
+		return &PushError{Reason: err.Error(), Err: err}
 	}
 
 	cmd := exec.Command("git", "push", "-u", "origin", "main")
@@ -433,7 +442,7 @@ func (g *Git) Push() error {
 
 	output, err := cmd.CombinedOutput()
 	if err != nil {
-		return fmt.Errorf("git push failed: %w\nOutput: %s", err, string(output))
+		return &PushError{Output: string(output), Err: err}
 	}
 
 	return nil
@@ -444,7 +453,7 @@ func (g *Git) Pull() error {
 	// First ensure we have a remote configured
 	_, err := g.GetRemoteInfo()
 	if err != nil {
-		return fmt.Errorf("cannot pull: %w", err)
+		return &PullError{Reason: err.Error(), Err: err}
 	}
 
 	cmd := exec.Command("git", "pull", "origin", "main")
@@ -452,7 +461,7 @@ func (g *Git) Pull() error {
 
 	output, err := cmd.CombinedOutput()
 	if err != nil {
-		return fmt.Errorf("git pull failed: %w\nOutput: %s", err, string(output))
+		return &PullError{Output: string(output), Err: err}
 	}
 
 	return nil
@@ -462,20 +471,20 @@ func (g *Git) Pull() error {
 func (g *Git) Clone(url string) error {
 	// Remove the directory if it exists to ensure clean clone
 	if err := os.RemoveAll(g.repoPath); err != nil {
-		return fmt.Errorf("failed to remove existing directory: %w", err)
+		return &DirectoryRemovalError{Path: g.repoPath, Err: err}
 	}
 
 	// Create parent directory
 	parentDir := filepath.Dir(g.repoPath)
 	if err := os.MkdirAll(parentDir, 0755); err != nil {
-		return fmt.Errorf("failed to create parent directory: %w", err)
+		return &DirectoryCreationError{Path: parentDir, Err: err}
 	}
 
 	// Clone the repository
 	cmd := exec.Command("git", "clone", url, g.repoPath)
 	output, err := cmd.CombinedOutput()
 	if err != nil {
-		return fmt.Errorf("git clone failed: %w\nOutput: %s", err, string(output))
+		return &GitCommandError{Command: "clone", Output: string(output), Err: err}
 	}
 
 	// Set up upstream tracking for main branch

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))
-}