fix: prevent file loss when multiple files have same basename

Fixes #2: https://github.com/yarlson/lnk/issues/2

Previously, files with the same basename (e.g., a/config.json and b/config.json)
would overwrite each other in the repository, causing data loss. The second file
would completely replace the first, and removing files would fail with 'no such
file or directory' errors.

Changes:
- Store files using unique names based on full relative paths (slashes → underscores)
- Track full relative paths in .lnk file instead of just basenames
- Generate repository names from relative paths to prevent collisions
- Update symlink restoration to work with new path-based system
- Add comprehensive tests for basename collision scenarios

This ensures each file maintains its unique content and can be managed
independently, eliminating the data loss issue.

cmd/root_test.go

@@ -4,6 +4,7 @@ import (
 	"bytes"
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
 
 	"github.com/stretchr/testify/suite"
@@ -105,9 +106,19 @@ func (suite *CLITestSuite) TestAddCommand() {
 	suite.NoError(err)
 	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
 
-	// Verify file exists in repo
-	repoFile := filepath.Join(suite.tempDir, "lnk", ".bashrc")
-	suite.FileExists(repoFile)
+	// Verify some file exists in repo with .bashrc in the name
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	entries, err := os.ReadDir(lnkDir)
+	suite.NoError(err)
+
+	found := false
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), ".bashrc") && entry.Name() != ".lnk" {
+			found = true
+			break
+		}
+	}
+	suite.True(found, "Repository should contain a file with .bashrc in the name")
 }
 
 func (suite *CLITestSuite) TestRemoveCommand() {
@@ -325,9 +336,92 @@ func (suite *CLITestSuite) TestAddDirectory() {
 	suite.NoError(err)
 	suite.Equal(os.ModeSymlink, info.Mode()&os.ModeSymlink)
 
-	// Verify directory exists in repo
-	repoDir := filepath.Join(suite.tempDir, "lnk", ".config")
-	suite.DirExists(repoDir)
+	// Verify some directory exists in repo with .config in the name
+	lnkDir := filepath.Join(suite.tempDir, "lnk")
+	entries, err := os.ReadDir(lnkDir)
+	suite.NoError(err)
+
+	found := false
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), ".config") && entry.Name() != ".lnk" {
+			found = true
+			break
+		}
+	}
+	suite.True(found, "Repository should contain a directory with .config in the name")
+}
+
+func (suite *CLITestSuite) TestSameBasenameFilesBug() {
+	// Initialize repository
+	err := suite.runCommand("init")
+	suite.Require().NoError(err)
+	suite.stdout.Reset()
+
+	// Create two directories with files having the same basename
+	dirA := filepath.Join(suite.tempDir, "a")
+	dirB := filepath.Join(suite.tempDir, "b")
+	err = os.MkdirAll(dirA, 0755)
+	suite.Require().NoError(err)
+	err = os.MkdirAll(dirB, 0755)
+	suite.Require().NoError(err)
+
+	// Create files with same basename but different content
+	fileA := filepath.Join(dirA, "config.json")
+	fileB := filepath.Join(dirB, "config.json")
+	contentA := `{"name": "config_a"}`
+	contentB := `{"name": "config_b"}`
+
+	err = os.WriteFile(fileA, []byte(contentA), 0644)
+	suite.Require().NoError(err)
+	err = os.WriteFile(fileB, []byte(contentB), 0644)
+	suite.Require().NoError(err)
+
+	// Add first file
+	err = suite.runCommand("add", fileA)
+	suite.NoError(err)
+	suite.stdout.Reset()
+
+	// Verify first file content is preserved
+	content, err := os.ReadFile(fileA)
+	suite.NoError(err)
+	suite.Equal(contentA, string(content), "First file should preserve its original content")
+
+	// Add second file with same basename - this should work correctly
+	err = suite.runCommand("add", fileB)
+	suite.NoError(err, "Adding second file with same basename should work")
+
+	// CORRECT BEHAVIOR: Both files should preserve their original content
+	contentAfterAddA, err := os.ReadFile(fileA)
+	suite.NoError(err)
+	contentAfterAddB, err := os.ReadFile(fileB)
+	suite.NoError(err)
+
+	suite.Equal(contentA, string(contentAfterAddA), "First file should keep its original content")
+	suite.Equal(contentB, string(contentAfterAddB), "Second file should keep its original content")
+
+	// Both files should be removable independently
+	suite.stdout.Reset()
+	err = suite.runCommand("rm", fileA)
+	suite.NoError(err, "First file should be removable")
+
+	// Verify output shows removal
+	output := suite.stdout.String()
+	suite.Contains(output, "Removed config.json from lnk")
+
+	// Verify first file is restored with correct content
+	restoredContentA, err := os.ReadFile(fileA)
+	suite.NoError(err)
+	suite.Equal(contentA, string(restoredContentA), "Restored first file should have original content")
+
+	// Second file should still be removable without errors
+	suite.stdout.Reset()
+	err = suite.runCommand("rm", fileB)
+	suite.NoError(err, "Second file should also be removable without errors")
+
+	// Verify second file is restored with correct content
+	restoredContentB, err := os.ReadFile(fileB)
+	suite.NoError(err)
+	suite.Equal(contentB, string(restoredContentB), "Restored second file should have original content")
 }
 
 func TestCLISuite(t *testing.T) {