diff --git a/.github/workflows/build.yml b/.github/workflows/tests.yml
similarity index 54%
rename from .github/workflows/build.yml
rename to .github/workflows/tests.yml
index 8929183..35692f0 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/tests.yml
@@ -1,4 +1,4 @@
-name: build
+name: tests
 
 on:
   pull_request:
@@ -8,7 +8,7 @@ permissions:
   contents: read
 
 jobs:
-  build:
+  unit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -17,3 +17,13 @@ jobs:
           go-version: 1.21
           cache: true
       - run: go test -v ./...
+
+  e2e:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-go@v4
+        with:
+          go-version: 1.21
+          cache: true
+      - run: ./test-e2e.sh
diff --git a/example/klone.yaml b/example/klone.yaml
index a50991e..9b53b61 100644
--- a/example/klone.yaml
+++ b/example/klone.yaml
@@ -3,12 +3,12 @@
 targets:
   projects:
     - folder_name: kube_apis
-      repo_url: git@github.com:kubernetes/kubernetes.git
+      repo_url: https://github.com/kubernetes/kubernetes.git
       repo_ref: master
       repo_hash: 56d7898510f2a973f92fda13c2ba3a5e756d9621
       repo_path: api
     - folder_name: kube_changelog
-      repo_url: git@github.com:kubernetes/kubernetes.git
+      repo_url: https://github.com/kubernetes/kubernetes.git
       repo_ref: master
       repo_hash: 56d7898510f2a973f92fda13c2ba3a5e756d9621
       repo_path: CHANGELOG
diff --git a/pkg/mod/index.go b/pkg/mod/index.go
index 903a03d..248521f 100644
--- a/pkg/mod/index.go
+++ b/pkg/mod/index.go
@@ -73,6 +73,9 @@ func (w WorkDir) editKloneFile(fn func(*kloneFile) error) error {
 		reader := bufio.NewReader(file)
 		for {
 			line, isPrefix, err := reader.ReadLine()
+			if err == io.EOF {
+				break
+			}
 			if err != nil {
 				return err
 			}
diff --git a/pkg/mod/index_test.go b/pkg/mod/index_test.go
index ea8fad3..9ad6380 100644
--- a/pkg/mod/index_test.go
+++ b/pkg/mod/index_test.go
@@ -1,6 +1,8 @@
 package mod
 
 import (
+	"os"
+	"path"
 	"sort"
 	"testing"
 )
@@ -26,3 +28,94 @@ func TestKloneItemSorting(t *testing.T) {
 		}
 	}
 }
+
+func Test_editKloneFile(t *testing.T) {
+	tests := []struct {
+		name      string
+		initial   string
+		modifyFn  func(*kloneFile) error
+		expected  string
+		expectErr bool
+	}{
+		{
+			name: "Preserve comments",
+			initial: `# Test comment1
+# Test comment2
+targets:
+  target1:
+    - folder_name: Folder A
+      repo_url: https://github.com/repo1
+      repo_ref: main
+      repo_hash: abc123
+      repo_path: path/to/repo1
+`,
+			modifyFn: func(kf *kloneFile) error {
+				return nil
+			},
+			expected: `# Test comment1
+# Test comment2
+targets:
+  target1:
+    - folder_name: Folder A
+      repo_url: https://github.com/repo1
+      repo_ref: main
+      repo_hash: abc123
+      repo_path: path/to/repo1
+`,
+			expectErr: false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			tempDirPath := t.TempDir()
+
+			// Create the file and write the initial contents
+			{
+				tempFile, err := os.Create(path.Join(tempDirPath, kloneFileName))
+				if err != nil {
+					t.Fatalf("Failed to create temporary file: %v", err)
+				}
+
+				// Write the initial content to the temporary file
+				_, err = tempFile.WriteString(tt.initial)
+				if err != nil {
+					t.Fatalf("Failed to write initial content to temporary file: %v", err)
+				}
+
+				// Close the temporary file
+				err = tempFile.Close()
+				if err != nil {
+					t.Fatalf("Failed to close temporary file: %v", err)
+				}
+			}
+
+			// Create a WorkDir instance with the path to the temporary file
+			workDir := WorkDir(tempDirPath)
+
+			// Call the editKloneFile function with the modifyFn
+			err := workDir.editKloneFile(tt.modifyFn)
+
+			// Check if an error is expected
+			if tt.expectErr && err == nil {
+				t.Errorf("Expected an error, but got nil")
+			} else if !tt.expectErr && err != nil {
+				t.Errorf("Expected no error, but got: %v", err)
+			}
+
+			// Read the new file contents and compare with the expected contents
+			{
+				// Read the content of the modified file
+				modifiedContent, err := os.ReadFile(path.Join(tempDirPath, kloneFileName))
+				if err != nil {
+					t.Fatalf("Failed to read modified content: %v", err)
+				}
+
+				// Compare the modified content with the expected content
+				if string(modifiedContent) != tt.expected {
+					t.Errorf("Expected modified content:\n%s\n\nBut got:\n%s", tt.expected, modifiedContent)
+				}
+			}
+		})
+	}
+}
diff --git a/test-e2e.sh b/test-e2e.sh
new file mode 100755
index 0000000..060a93e
--- /dev/null
+++ b/test-e2e.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+set -e
+
+go build -o ./dist/klone_test .
+klone_binary=$(realpath ./dist/klone_test)
+
+# Test that the sync command works for the example directory
+pushd ./example
+"$klone_binary" sync
+popd
+
+# Create a temp directory and test that the init, add, and sync commands work
+temp_dir=$(mktemp -d)
+trap '{ rm -rf "$temp_dir"; echo "> Deleted temp dir $temp_dir"; }' EXIT
+pushd "$temp_dir"
+"$klone_binary" init
+mkdir -p a/b
+touch a/SHOULD_NOT_BE_DELETED
+touch a/b/SHOULD_BE_DELETED
+"$klone_binary" add a/b c/d https://github.com/cert-manager/community.git main logo
+"$klone_binary" sync
+tree -a
+popd
diff --git a/test.sh b/test.sh
deleted file mode 100755
index ae1522d..0000000
--- a/test.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/bash
-
-set -e
-
-go build -o ./dist/klone_test .
-
-cd ./example && ../dist/klone_test sync