From d3678a84a50fb78c46bb463e60f672c9b8e283f2 Mon Sep 17 00:00:00 2001
From: Luca Bernstein <luca.bernstein@sap.com>
Date: Wed, 1 Apr 2026 11:36:27 +0200
Subject: [PATCH 1/8] Fix outdated comment in components.yaml

---
 pkg/utils/componentvector/componentvector.go | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkg/utils/componentvector/componentvector.go b/pkg/utils/componentvector/componentvector.go
index f8476c8..3fe55d2 100644
--- a/pkg/utils/componentvector/componentvector.go
+++ b/pkg/utils/componentvector/componentvector.go
@@ -269,7 +269,7 @@ func WriteComponentVectorFile(fs afero.Afero, targetDirPath string, componentVec
 
 	header := []byte(strings.Join([]string{
 		"# This file is updated by the gardener-landscape-kit.",
-		"# If this file is specified in the gardener-landscape-kit configuration file, the component versions will be used as overrides.",
+		"# If this file is present in the root of a gardener-landscape-kit-managed repository, the component versions will be used as overrides.",
 		"# If custom component versions should be used, it is recommended to modify the specified versions here and run the `generate` command afterwards.",
 	}, "\n") + "\n")
 

From 399bd32c9b6c1caa4b72fb03846da4732451d5c1 Mon Sep 17 00:00:00 2001
From: Luca Bernstein <luca.bernstein@sap.com>
Date: Wed, 1 Apr 2026 11:47:36 +0200
Subject: [PATCH 2/8] Use general `WriteObjectsToFilesystem` for plain image
 vector resolution and writing

---
 pkg/cmd/resolve/plain/plain.go               | 34 +++++++++++---------
 pkg/utils/componentvector/componentvector.go | 15 +++++++++
 2 files changed, 33 insertions(+), 16 deletions(-)

diff --git a/pkg/cmd/resolve/plain/plain.go b/pkg/cmd/resolve/plain/plain.go
index 1329d14..88942fd 100644
--- a/pkg/cmd/resolve/plain/plain.go
+++ b/pkg/cmd/resolve/plain/plain.go
@@ -6,10 +6,7 @@ package plain
 
 import (
 	"context"
-	"errors"
 	"fmt"
-	"os"
-	"path"
 
 	"github.com/spf13/afero"
 	"github.com/spf13/cobra"
@@ -22,6 +19,7 @@ import (
 	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 	"github.com/gardener/gardener-landscape-kit/pkg/cmd"
 	utilscomponentvector "github.com/gardener/gardener-landscape-kit/pkg/utils/componentvector"
+	utilsfiles "github.com/gardener/gardener-landscape-kit/pkg/utils/files"
 )
 
 var configDecoder runtime.Decoder
@@ -122,21 +120,25 @@ func run(_ context.Context, opts *Options) error {
 		}
 	}
 
-	compVectorFile := path.Join(opts.TargetDirPath, utilscomponentvector.ComponentVectorFilename)
-	opts.Log.Info("Writing component vector file", "file", compVectorFile)
-
-	var customBytes []byte
-	var err error
-	if customBytes, err = opts.fs.ReadFile(compVectorFile); err != nil {
-		if !errors.Is(err, os.ErrNotExist) {
-			return fmt.Errorf("failed to read component vector override file: %w", err)
-		}
+	var (
+		err             error
+		newDefaultCV    utilscomponentvector.Interface
+		newDefaultBytes []byte
+	)
+	newDefaultCV, err = utilscomponentvector.NewWithOverride(componentvector.DefaultComponentsYAML)
+	if err != nil {
+		return fmt.Errorf("failed to build default component vector: %w", err)
 	}
-
-	componentVector, err := utilscomponentvector.NewWithOverride(componentvector.DefaultComponentsYAML, customBytes)
+	newDefaultBytes, err = utilscomponentvector.NameVersionBytes(newDefaultCV)
 	if err != nil {
-		return fmt.Errorf("failed to create component vector: %w", err)
+		return fmt.Errorf("failed to marshal default component vector: %w", err)
 	}
 
-	return utilscomponentvector.WriteComponentVectorFile(opts.fs, opts.TargetDirPath, componentVector)
+	if err := utilsfiles.WriteObjectsToFilesystem(map[string][]byte{utilscomponentvector.ComponentVectorFilename: newDefaultBytes}, opts.TargetDirPath, "", opts.fs); err != nil {
+		return fmt.Errorf("failed to write updated component vector: %w", err)
+	}
+
+	//return utilscomponentvector.WriteComponentVectorFile(opts.fs, opts.TargetDirPath, componentVector)
+
+	return nil
 }
diff --git a/pkg/utils/componentvector/componentvector.go b/pkg/utils/componentvector/componentvector.go
index 3fe55d2..9800bf6 100644
--- a/pkg/utils/componentvector/componentvector.go
+++ b/pkg/utils/componentvector/componentvector.go
@@ -238,6 +238,21 @@ func stripDefaultVersionComments(data []byte) []byte {
 	return []byte(strings.Join(out, "\n"))
 }
 
+// NameVersionBytes marshals cv into a name+version-only Components YAML, stripping all other fields.
+// This compact format is used for the .glk/defaults/ snapshot and as the three-way merge baseline in plain.go.
+func NameVersionBytes(cv Interface) ([]byte, error) {
+	stripped := &Components{}
+	for _, name := range cv.ComponentNames() {
+		version, _ := cv.FindComponentVersion(name)
+		stripped.Components = append(stripped.Components, &ComponentVector{Name: name, Version: version})
+	}
+	data, err := yaml.Marshal(stripped)
+	if err != nil {
+		return nil, fmt.Errorf("failed to marshal component versions: %w", err)
+	}
+	return data, nil
+}
+
 // WriteComponentVectorFile writes the component vector file effectively used to the target directory if applicable.
 func WriteComponentVectorFile(fs afero.Afero, targetDirPath string, componentVector Interface) error {
 	var (

From 910a9fca1fa0311888b482b85dab63e2313b86fc Mon Sep 17 00:00:00 2001
From: Luca Bernstein <luca.bernstein@sap.com>
Date: Wed, 1 Apr 2026 11:52:28 +0200
Subject: [PATCH 3/8] Correctly support slices during three-way-merge and
 retain user modifications

---
 pkg/utils/meta/diff_test.go                       | 15 +++++++++++++++
 pkg/utils/meta/merge.go                           |  7 ++++++-
 .../meta/testdata/merge-slice-1-default.yaml      |  3 +++
 pkg/utils/meta/testdata/merge-slice-2-edited.yaml |  3 +++
 .../meta/testdata/merge-slice-3-new-default.yaml  |  3 +++
 .../merge-slice-4-expected-generated.yaml         |  3 +++
 6 files changed, 33 insertions(+), 1 deletion(-)
 create mode 100644 pkg/utils/meta/testdata/merge-slice-1-default.yaml
 create mode 100644 pkg/utils/meta/testdata/merge-slice-2-edited.yaml
 create mode 100644 pkg/utils/meta/testdata/merge-slice-3-new-default.yaml
 create mode 100644 pkg/utils/meta/testdata/merge-slice-4-expected-generated.yaml

diff --git a/pkg/utils/meta/diff_test.go b/pkg/utils/meta/diff_test.go
index 7d626a2..c0aa175 100644
--- a/pkg/utils/meta/diff_test.go
+++ b/pkg/utils/meta/diff_test.go
@@ -229,5 +229,20 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(content)).To(Equal(string(expected)))
 		})
+
+		It("should retain user modifications in slices during a three-way-merge", func() {
+			oldDefault, err := testdata.ReadFile("testdata/merge-slice-1-default.yaml")
+			Expect(err).NotTo(HaveOccurred())
+			newDefault, err := testdata.ReadFile("testdata/merge-slice-3-new-default.yaml")
+			Expect(err).NotTo(HaveOccurred())
+			current, err := testdata.ReadFile("testdata/merge-slice-2-edited.yaml")
+			Expect(err).NotTo(HaveOccurred())
+			expected, err := testdata.ReadFile("testdata/merge-slice-4-expected-generated.yaml")
+			Expect(err).NotTo(HaveOccurred())
+
+			content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current)
+			Expect(err).NotTo(HaveOccurred())
+			Expect(string(content)).To(Equal(string(expected)))
+		})
 	})
 })
diff --git a/pkg/utils/meta/merge.go b/pkg/utils/meta/merge.go
index 805d28a..4ecab8d 100644
--- a/pkg/utils/meta/merge.go
+++ b/pkg/utils/meta/merge.go
@@ -103,13 +103,18 @@ func threeWayMerge(oldDefault, newDefault, current *yaml.Node) *yaml.Node {
 					oldValue = &yaml.Node{Kind: yaml.SequenceNode}
 				}
 				resultValue = threeWayMergeSequence(oldValue, newValueNode, currentValue)
-			case oldExists && !nodesEqual(oldValue, newValueNode, false):
+			case oldExists && !nodesEqual(oldValue, newValueNode, false) && nodesEqual(oldValue, currentValue, false):
+				// Default changed and current was not modified: take the new default.
 				resultValue = &yaml.Node{
 					Kind: newValueNode.Kind, Value: newValueNode.Value, Style: newValueNode.Style, Tag: newValueNode.Tag,
 					HeadComment: currentValue.HeadComment, LineComment: currentValue.LineComment, FootComment: currentValue.FootComment,
 					Content: newValueNode.Content,
 				}
 				mergeNodeComments(oldValue, newValueNode, resultValue)
+			case oldExists && !nodesEqual(oldValue, newValueNode, false):
+				// Both default and current changed: keep current (user's value wins).
+				resultValue = currentValue
+				mergeNodeComments(oldValue, newValueNode, resultValue)
 			default:
 				resultValue = currentValue
 				if oldExists {
diff --git a/pkg/utils/meta/testdata/merge-slice-1-default.yaml b/pkg/utils/meta/testdata/merge-slice-1-default.yaml
new file mode 100644
index 0000000..da79a13
--- /dev/null
+++ b/pkg/utils/meta/testdata/merge-slice-1-default.yaml
@@ -0,0 +1,3 @@
+components:
+- name: github.com/gardener/gardener
+  version: v1.139.0
diff --git a/pkg/utils/meta/testdata/merge-slice-2-edited.yaml b/pkg/utils/meta/testdata/merge-slice-2-edited.yaml
new file mode 100644
index 0000000..db6a125
--- /dev/null
+++ b/pkg/utils/meta/testdata/merge-slice-2-edited.yaml
@@ -0,0 +1,3 @@
+components:
+- name: github.com/gardener/gardener
+  version: v1.99.0
diff --git a/pkg/utils/meta/testdata/merge-slice-3-new-default.yaml b/pkg/utils/meta/testdata/merge-slice-3-new-default.yaml
new file mode 100644
index 0000000..8542ceb
--- /dev/null
+++ b/pkg/utils/meta/testdata/merge-slice-3-new-default.yaml
@@ -0,0 +1,3 @@
+components:
+- name: github.com/gardener/gardener
+  version: v1.139.1
diff --git a/pkg/utils/meta/testdata/merge-slice-4-expected-generated.yaml b/pkg/utils/meta/testdata/merge-slice-4-expected-generated.yaml
new file mode 100644
index 0000000..db6a125
--- /dev/null
+++ b/pkg/utils/meta/testdata/merge-slice-4-expected-generated.yaml
@@ -0,0 +1,3 @@
+components:
+- name: github.com/gardener/gardener
+  version: v1.99.0

From cee558aaea135a3994d0576278dec5694646803f Mon Sep 17 00:00:00 2001
From: Luca Bernstein <luca.bernstein@sap.com>
Date: Wed, 1 Apr 2026 12:04:52 +0200
Subject: [PATCH 4/8] Add `MergeMode` type and informative annotation logic to
 three-way merge

Introduces `MergeMode` (Silent/Informative) and threads it through
`threeWayMerge`, `threeWayMergeSection`, and `threeWayMergeSequence`.

In `MergeModeInformative`, when an operator-overridden scalar value
differs from the current GLK default, a `# glk default: <value>
# <-- glk-managed` line comment is appended to the value node.
For complex nodes (mappings/sequences), a head comment on the key
node signals the divergence.

`WriteComponentVectorFile`, `stripDefaultVersionComments`, and
`defaultVersionCommentMarker` are deleted. Their functionality is now
covered generically by `WriteObjectsToFilesystem(MergeModeInformative)``,
which plain.go already calls directly. The corresponding test describe
block is removed along with the now-unused imports.

Operator-comments are retained.
---
 pkg/apis/config/v1alpha1/types.go             |  29 +++++
 .../config/v1alpha1/validation/validation.go  |   4 +
 .../v1alpha1/validation/validation_test.go    |  37 ++++++
 .../config/v1alpha1/zz_generated.deepcopy.go  |   5 +
 pkg/cmd/resolve/plain/plain.go                |  12 +-
 pkg/components/types.go                       |  18 ++-
 pkg/utils/componentvector/componentvector.go  |  86 -------------
 .../componentvector/componentvector_test.go   | 116 ------------------
 pkg/utils/files/writer.go                     |  33 ++++-
 pkg/utils/files/writer_test.go                | 111 ++++++++++++++++-
 pkg/utils/meta/diff.go                        |   8 +-
 pkg/utils/meta/diff_test.go                   |  82 ++++++++++---
 pkg/utils/meta/merge.go                       |  68 ++++++++--
 pkg/utils/meta/preprocessing_test.go          |   5 +-
 14 files changed, 364 insertions(+), 250 deletions(-)

diff --git a/pkg/apis/config/v1alpha1/types.go b/pkg/apis/config/v1alpha1/types.go
index 7f893fa..1a79b16 100644
--- a/pkg/apis/config/v1alpha1/types.go
+++ b/pkg/apis/config/v1alpha1/types.go
@@ -26,6 +26,10 @@ type LandscapeKitConfiguration struct {
 	// VersionConfig is the configuration for versioning.
 	// +optional
 	VersionConfig *VersionConfiguration `json:"versionConfig,omitempty"`
+	// MergeMode controls how operator overrides conflicting with updated GLK defaults are handled during three-way merge.
+	// Possible values are "Informative" (default) and "Silent".
+	// +optional
+	MergeMode *MergeMode `json:"mergeMode,omitempty"`
 }
 
 // ComponentsConfiguration contains configuration for components.
@@ -119,3 +123,28 @@ type VersionConfiguration struct {
 	// +optional
 	DefaultVersionsUpdateStrategy *DefaultVersionsUpdateStrategy `json:"defaultVersionsUpdateStrategy,omitempty"`
 }
+
+// MergeMode controls how operator overrides are handled during three-way merge.
+type MergeMode string
+
+const (
+	// MergeModeInformative annotates operator-overridden values with a comment showing the current GLK default.
+	MergeModeInformative MergeMode = "Informative"
+	// MergeModeSilent retains operator overrides without annotation.
+	MergeModeSilent MergeMode = "Silent"
+)
+
+// AllowedMergeModes lists all allowed merge modes.
+var AllowedMergeModes = []string{
+	string(MergeModeInformative),
+	string(MergeModeSilent),
+}
+
+// GetMergeMode returns the configured MergeMode, defaulting to MergeModeInformative.
+// It is safe to call on a nil receiver.
+func (c *LandscapeKitConfiguration) GetMergeMode() MergeMode {
+	if c != nil && c.MergeMode != nil {
+		return *c.MergeMode
+	}
+	return MergeModeInformative
+}
diff --git a/pkg/apis/config/v1alpha1/validation/validation.go b/pkg/apis/config/v1alpha1/validation/validation.go
index 1144b81..c0567e9 100644
--- a/pkg/apis/config/v1alpha1/validation/validation.go
+++ b/pkg/apis/config/v1alpha1/validation/validation.go
@@ -36,6 +36,10 @@ func ValidateLandscapeKitConfiguration(conf *configv1alpha1.LandscapeKitConfigur
 		allErrs = append(allErrs, ValidateVersionConfig(conf.VersionConfig, field.NewPath("versionConfig"))...)
 	}
 
+	if conf.MergeMode != nil && !slices.Contains(configv1alpha1.AllowedMergeModes, string(*conf.MergeMode)) {
+		allErrs = append(allErrs, field.Invalid(field.NewPath("mergeMode"), *conf.MergeMode, "allowed values are: "+strings.Join(configv1alpha1.AllowedMergeModes, ", ")))
+	}
+
 	return allErrs
 }
 
diff --git a/pkg/apis/config/v1alpha1/validation/validation_test.go b/pkg/apis/config/v1alpha1/validation/validation_test.go
index 1d8614c..5ccd0e4 100644
--- a/pkg/apis/config/v1alpha1/validation/validation_test.go
+++ b/pkg/apis/config/v1alpha1/validation/validation_test.go
@@ -294,6 +294,43 @@ var _ = Describe("Validation", func() {
 				Expect(errList).To(BeEmpty())
 			})
 		})
+
+		Context("MergeMode Configuration", func() {
+			It("should pass with valid MergeMode values", func() {
+				for _, mode := range []v1alpha1.MergeMode{
+					v1alpha1.MergeModeInformative,
+					v1alpha1.MergeModeSilent,
+				} {
+					conf := &v1alpha1.LandscapeKitConfiguration{
+						MergeMode: &mode,
+					}
+					errList := validation.ValidateLandscapeKitConfiguration(conf)
+					Expect(errList).To(BeEmpty(), fmt.Sprintf("MergeMode %q should be valid", mode))
+				}
+			})
+
+			It("should pass when MergeMode is not set", func() {
+				conf := &v1alpha1.LandscapeKitConfiguration{}
+				errList := validation.ValidateLandscapeKitConfiguration(conf)
+				Expect(errList).To(BeEmpty())
+			})
+
+			It("should fail with an invalid MergeMode value", func() {
+				invalid := v1alpha1.MergeMode("Invalid")
+				conf := &v1alpha1.LandscapeKitConfiguration{
+					MergeMode: &invalid,
+				}
+
+				errList := validation.ValidateLandscapeKitConfiguration(conf)
+				Expect(errList).To(ConsistOf(
+					PointTo(MatchFields(IgnoreExtras, Fields{
+						"Type":     Equal(field.ErrorTypeInvalid),
+						"Field":    Equal("mergeMode"),
+						"BadValue": Equal(invalid),
+					})),
+				))
+			})
+		})
 	})
 })
 
diff --git a/pkg/apis/config/v1alpha1/zz_generated.deepcopy.go b/pkg/apis/config/v1alpha1/zz_generated.deepcopy.go
index 5d2b130..3ce6502 100644
--- a/pkg/apis/config/v1alpha1/zz_generated.deepcopy.go
+++ b/pkg/apis/config/v1alpha1/zz_generated.deepcopy.go
@@ -112,6 +112,11 @@ func (in *LandscapeKitConfiguration) DeepCopyInto(out *LandscapeKitConfiguration
 		*out = new(VersionConfiguration)
 		(*in).DeepCopyInto(*out)
 	}
+	if in.MergeMode != nil {
+		in, out := &in.MergeMode, &out.MergeMode
+		*out = new(MergeMode)
+		**out = **in
+	}
 	return
 }
 
diff --git a/pkg/cmd/resolve/plain/plain.go b/pkg/cmd/resolve/plain/plain.go
index 88942fd..6ac366d 100644
--- a/pkg/cmd/resolve/plain/plain.go
+++ b/pkg/cmd/resolve/plain/plain.go
@@ -7,6 +7,7 @@ package plain
 import (
 	"context"
 	"fmt"
+	"strings"
 
 	"github.com/spf13/afero"
 	"github.com/spf13/cobra"
@@ -134,11 +135,16 @@ func run(_ context.Context, opts *Options) error {
 		return fmt.Errorf("failed to marshal default component vector: %w", err)
 	}
 
-	if err := utilsfiles.WriteObjectsToFilesystem(map[string][]byte{utilscomponentvector.ComponentVectorFilename: newDefaultBytes}, opts.TargetDirPath, "", opts.fs); err != nil {
+	header := []byte(strings.Join([]string{
+		"# This file is updated by the gardener-landscape-kit.",
+		"# If this file is present in the root of a gardener-landscape-kit-managed repository, the component versions will be used as overrides.",
+		"# If custom component versions should be used, it is recommended to modify the specified versions here and run the `generate` command afterwards.",
+	}, "\n") + "\n")
+	newDefaultBytes = append(header, newDefaultBytes...)
+
+	if err := utilsfiles.WriteObjectsToFilesystem(map[string][]byte{utilscomponentvector.ComponentVectorFilename: newDefaultBytes}, opts.TargetDirPath, "", opts.fs, opts.Config.GetMergeMode()); err != nil {
 		return fmt.Errorf("failed to write updated component vector: %w", err)
 	}
 
-	//return utilscomponentvector.WriteComponentVectorFile(opts.fs, opts.TargetDirPath, componentVector)
-
 	return nil
 }
diff --git a/pkg/components/types.go b/pkg/components/types.go
index ca38214..0b0c22a 100644
--- a/pkg/components/types.go
+++ b/pkg/components/types.go
@@ -15,7 +15,7 @@ import (
 	"github.com/spf13/afero"
 
 	"github.com/gardener/gardener-landscape-kit/componentvector"
-	"github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
+	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 	generateoptions "github.com/gardener/gardener-landscape-kit/pkg/cmd/generate/options"
 	utilscomponentvector "github.com/gardener/gardener-landscape-kit/pkg/utils/componentvector"
 	"github.com/gardener/gardener-landscape-kit/pkg/utils/files"
@@ -36,6 +36,8 @@ type Options interface {
 	GetFilesystem() afero.Afero
 	// GetLogger returns the logger instance.
 	GetLogger() logr.Logger
+	// GetMergeMode returns the configured merge mode for three-way merges.
+	GetMergeMode() configv1alpha1.MergeMode
 }
 
 // LandscapeOptions is an interface for options passed to components for generating the landscape.
@@ -43,7 +45,7 @@ type LandscapeOptions interface {
 	Options
 
 	// GetGitRepository returns the git repository information.
-	GetGitRepository() *v1alpha1.GitRepository
+	GetGitRepository() *configv1alpha1.GitRepository
 	// GetRelativeBasePath returns the base directory that is relative to the target path.
 	GetRelativeBasePath() string
 	// GetRelativeLandscapePath returns the landscape directory that is relative to the target path.
@@ -65,6 +67,7 @@ type options struct {
 	targetPath      string
 	filesystem      afero.Afero
 	logger          logr.Logger
+	mergeMode       configv1alpha1.MergeMode
 }
 
 // GetComponentVector returns the component vector.
@@ -87,6 +90,11 @@ func (o *options) GetLogger() logr.Logger {
 	return o.logger
 }
 
+// GetMergeMode returns the configured merge mode for three-way merges.
+func (o *options) GetMergeMode() configv1alpha1.MergeMode {
+	return o.mergeMode
+}
+
 // NewOptions returns a new Options instance.
 func NewOptions(opts *generateoptions.Options, fs afero.Afero) (Options, error) {
 	var customComponentVectors [][]byte
@@ -113,11 +121,13 @@ func NewOptions(opts *generateoptions.Options, fs afero.Afero) (Options, error)
 	if err != nil {
 		return nil, fmt.Errorf("failed to create component vector: %w", err)
 	}
+
 	return &options{
 		componentVector: componentVector,
 		targetPath:      path.Clean(opts.TargetDirPath),
 		filesystem:      fs,
 		logger:          opts.Log,
+		mergeMode:       opts.Config.GetMergeMode(),
 	}, nil
 }
 
@@ -134,11 +144,11 @@ func readCustomComponentsFile(opts *generateoptions.Options, fs afero.Afero, fil
 type landscapeOptions struct {
 	Options
 
-	gitRepository *v1alpha1.GitRepository
+	gitRepository *configv1alpha1.GitRepository
 }
 
 // GetGitRepository returns the git repository information.
-func (l *landscapeOptions) GetGitRepository() *v1alpha1.GitRepository {
+func (l *landscapeOptions) GetGitRepository() *configv1alpha1.GitRepository {
 	return l.gitRepository
 }
 
diff --git a/pkg/utils/componentvector/componentvector.go b/pkg/utils/componentvector/componentvector.go
index 9800bf6..9b24e6c 100644
--- a/pkg/utils/componentvector/componentvector.go
+++ b/pkg/utils/componentvector/componentvector.go
@@ -7,18 +7,12 @@ package componentvector
 import (
 	"fmt"
 	"maps"
-	"path/filepath"
 	"reflect"
 	"slices"
-	"strings"
 
-	"github.com/spf13/afero"
 	"k8s.io/apimachinery/pkg/util/validation/field"
 	"k8s.io/utils/ptr"
 	"sigs.k8s.io/yaml"
-
-	"github.com/gardener/gardener-landscape-kit/componentvector"
-	"github.com/gardener/gardener-landscape-kit/pkg/utils/files"
 )
 
 const (
@@ -220,24 +214,6 @@ func resourcesToUnstructuredMap(resources map[string]ResourceData) (map[string]a
 	return unstructuredMap, nil
 }
 
-const (
-	defaultVersionCommentMarker = "# <-- gardener-landscape-kit version default"
-)
-
-// stripDefaultVersionComments removes GLK-managed default-version comment lines from a components.yaml file.
-// A line is considered GLK-managed when it contains the unique GLK marker suffix.
-// Stripping them before the three-way merge ensures the canonical comment is always (re-)written on the next run, even when the user has edited the comment text.
-func stripDefaultVersionComments(data []byte) []byte {
-	lines := strings.Split(string(data), "\n")
-	out := make([]string, 0, len(lines))
-	for _, line := range lines {
-		if !strings.Contains(line, defaultVersionCommentMarker) {
-			out = append(out, line)
-		}
-	}
-	return []byte(strings.Join(out, "\n"))
-}
-
 // NameVersionBytes marshals cv into a name+version-only Components YAML, stripping all other fields.
 // This compact format is used for the .glk/defaults/ snapshot and as the three-way merge baseline in plain.go.
 func NameVersionBytes(cv Interface) ([]byte, error) {
@@ -252,65 +228,3 @@ func NameVersionBytes(cv Interface) ([]byte, error) {
 	}
 	return data, nil
 }
-
-// WriteComponentVectorFile writes the component vector file effectively used to the target directory if applicable.
-func WriteComponentVectorFile(fs afero.Afero, targetDirPath string, componentVector Interface) error {
-	var (
-		comp                                 = &Components{}
-		postGenerateDefaultVersionCommentFns []func(string) string
-	)
-	cvDefault, err := NewWithOverride(componentvector.DefaultComponentsYAML)
-	if err != nil {
-		return fmt.Errorf("failed to build default component vector: %w", err)
-	}
-	for _, componentName := range componentVector.ComponentNames() {
-		componentVersion, _ := componentVector.FindComponentVersion(componentName)
-		comp.Components = append(comp.Components, &ComponentVector{
-			Name:    componentName,
-			Version: componentVersion,
-		})
-		defaultVersion, found := cvDefault.FindComponentVersion(componentName)
-		if found && componentVersion != defaultVersion {
-			defaultVersionComment := "# version: " + defaultVersion + " " + defaultVersionCommentMarker
-			postGenerateDefaultVersionCommentFns = append(postGenerateDefaultVersionCommentFns, func(data string) string {
-				return strings.ReplaceAll(data, componentName+"\n", componentName+"\n"+defaultVersionComment+"\n")
-			})
-		}
-	}
-	data, err := yaml.Marshal(comp)
-	if err != nil {
-		return fmt.Errorf("failed to marshal component vector: %w", err)
-	}
-
-	header := []byte(strings.Join([]string{
-		"# This file is updated by the gardener-landscape-kit.",
-		"# If this file is present in the root of a gardener-landscape-kit-managed repository, the component versions will be used as overrides.",
-		"# If custom component versions should be used, it is recommended to modify the specified versions here and run the `generate` command afterwards.",
-	}, "\n") + "\n")
-
-	// Before writing, strip any GLK-managed default-version comment lines from the on-disk file.
-	// This resets GLK-owned annotations so the canonical comment is always (re-)applied below, even when the user has edited or removed the comment line.
-	filePath := filepath.Join(targetDirPath, ComponentVectorFilename)
-	if existing, readErr := fs.ReadFile(filePath); readErr == nil {
-		if stripped := stripDefaultVersionComments(existing); string(stripped) != string(existing) {
-			if writeErr := fs.WriteFile(filePath, stripped, 0600); writeErr != nil {
-				return writeErr
-			}
-		}
-	}
-
-	// Pass 1: write without default-version comments so the three-way merge operates on
-	// comment-free content. This establishes a clean baseline in the .glk/defaults/ snapshot.
-	dataWithoutComments := append(header, data...)
-	if err := files.WriteObjectsToFilesystem(map[string][]byte{ComponentVectorFilename: dataWithoutComments}, targetDirPath, "", fs); err != nil {
-		return err
-	}
-
-	// Pass 2: inject default-version comments and write again. Because the .glk/defaults/ snapshot from Pass 1 has no comments,
-	// the comments are always treated as "new" by the three-way merge and are therefore reliably written into the output file.
-	for _, fn := range postGenerateDefaultVersionCommentFns {
-		data = []byte(fn(string(data)))
-	}
-	dataWithComments := append(header, data...)
-	return files.WriteObjectsToFilesystem(map[string][]byte{ComponentVectorFilename: dataWithComments}, targetDirPath, "", fs)
-}
diff --git a/pkg/utils/componentvector/componentvector_test.go b/pkg/utils/componentvector/componentvector_test.go
index 753d556..8836547 100644
--- a/pkg/utils/componentvector/componentvector_test.go
+++ b/pkg/utils/componentvector/componentvector_test.go
@@ -5,14 +5,9 @@
 package componentvector_test
 
 import (
-	"strings"
-
 	. "github.com/onsi/ginkgo/v2"
 	. "github.com/onsi/gomega"
-	"github.com/spf13/afero"
-	"sigs.k8s.io/yaml"
 
-	"github.com/gardener/gardener-landscape-kit/componentvector"
 	. "github.com/gardener/gardener-landscape-kit/pkg/utils/componentvector"
 )
 
@@ -683,115 +678,4 @@ components:
 		})
 	})
 
-	Describe("#WriteComponentVectorFile", func() {
-		const outputDir = "/output"
-
-		// componentNames parses the written components.yaml and returns the list of component names.
-		componentNames := func(fs afero.Afero) []string {
-			data, err := fs.ReadFile(outputDir + "/components.yaml")
-			ExpectWithOffset(1, err).NotTo(HaveOccurred())
-			var comps struct {
-				Components []struct {
-					Name string `json:"name"`
-				} `json:"components"`
-			}
-			ExpectWithOffset(1, yaml.Unmarshal(data, &comps)).NotTo(HaveOccurred())
-			names := make([]string, 0, len(comps.Components))
-			for _, c := range comps.Components {
-				names = append(names, c.Name)
-			}
-			return names
-		}
-
-		cv := func(contents []byte) Interface {
-			cv, err := NewWithOverride(contents)
-			ExpectWithOffset(1, err).NotTo(HaveOccurred())
-			return cv
-		}
-
-		BeforeEach(func() {
-			componentvector.DefaultComponentsYAML = []byte(`components:
-- name: github.com/gardener/gardener
-  sourceRepository: https://github.com/gardener/gardener
-  version: v1.137.1
-- name: github.com/gardener/other-component
-  sourceRepository: https://github.com/gardener/other-component
-  version: v2.0.0
-`)
-		})
-
-		It("should not produce duplicate entries when the user edits the injected default-version comment", func() {
-			fs := afero.Afero{Fs: afero.NewMemMapFs()}
-
-			overrideCV := []byte(`components:
-- name: github.com/gardener/gardener
-  sourceRepository: https://github.com/gardener/gardener
-  version: v1.99.0
-- name: github.com/gardener/other-component
-  sourceRepository: https://github.com/gardener/other-component
-  version: v2.0.0
-`)
-
-			// Run 1: write from default CV so no comment is injected.
-			Expect(WriteComponentVectorFile(fs, outputDir, cv(componentvector.DefaultComponentsYAML))).To(Succeed())
-
-			// User changes the gardener version.
-			writtenFile := outputDir + "/components.yaml"
-			writtenData, err := fs.ReadFile(writtenFile)
-			Expect(err).NotTo(HaveOccurred())
-			Expect(fs.WriteFile(writtenFile,
-				[]byte(strings.ReplaceAll(string(writtenData), "version: v1.137.1", "version: v1.99.0")),
-				0600)).To(Succeed())
-
-			// Run 2: the injected default-version comment appears.
-			Expect(WriteComponentVectorFile(fs, outputDir, cv(overrideCV))).To(Succeed())
-
-			writtenData, err = fs.ReadFile(writtenFile)
-			Expect(err).NotTo(HaveOccurred())
-			Expect(string(writtenData)).To(ContainSubstring("# version: v1.137.1 # <-- gardener-landscape-kit version default"))
-
-			// User edits the injected comment (e.g. adds a personal annotation).
-			writtenData, err = fs.ReadFile(writtenFile)
-			Expect(err).NotTo(HaveOccurred())
-			Expect(fs.WriteFile(writtenFile,
-				[]byte(strings.ReplaceAll(string(writtenData),
-					"# version: v1.137.1 # <-- gardener-landscape-kit version default",
-					"# version: v1.137.1 # <-- default (my annotation)")),
-				0600)).To(Succeed())
-
-			// Run 3: must not duplicate gardener entry and amend the comment with a new default version comment.
-			Expect(WriteComponentVectorFile(fs, outputDir, cv(overrideCV))).To(Succeed())
-
-			Expect(componentNames(fs)).To(ConsistOf(
-				"github.com/gardener/gardener",
-				"github.com/gardener/other-component",
-			))
-
-			// The correct default-version comment must have been restored.
-			writtenData, err = fs.ReadFile(writtenFile)
-			Expect(err).NotTo(HaveOccurred())
-			Expect(string(writtenData)).To(ContainSubstring("# <-- gardener-landscape-kit version default"))
-			Expect(string(writtenData)).To(ContainSubstring("my annotation"))
-		})
-
-		It("should not re-add entries that the user removed from the file", func() {
-			fs := afero.Afero{Fs: afero.NewMemMapFs()}
-
-			// Run 1: write both entries.
-			Expect(WriteComponentVectorFile(fs, outputDir, cv(componentvector.DefaultComponentsYAML))).To(Succeed())
-
-			// User removes the other-component entry entirely.
-			writtenFile := outputDir + "/components.yaml"
-			writtenData, err := fs.ReadFile(writtenFile)
-			Expect(err).NotTo(HaveOccurred())
-			idx := strings.Index(string(writtenData), "- name: github.com/gardener/other-component")
-			Expect(idx).To(BeNumerically(">", 0))
-			Expect(fs.WriteFile(writtenFile, writtenData[:idx], 0600)).To(Succeed())
-
-			// Run 2: same vector — the removed entry must not come back.
-			Expect(WriteComponentVectorFile(fs, outputDir, cv(componentvector.DefaultComponentsYAML))).To(Succeed())
-
-			Expect(componentNames(fs)).To(ConsistOf("github.com/gardener/gardener"))
-		})
-	})
 })
diff --git a/pkg/utils/files/writer.go b/pkg/utils/files/writer.go
index 26f7602..e9f7930 100644
--- a/pkg/utils/files/writer.go
+++ b/pkg/utils/files/writer.go
@@ -10,9 +10,11 @@ import (
 	"os"
 	"path"
 	"path/filepath"
+	"strings"
 
 	"github.com/spf13/afero"
 
+	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 	"github.com/gardener/gardener-landscape-kit/pkg/utils/meta"
 )
 
@@ -44,10 +46,34 @@ func isSecret(contents []byte) bool {
 	return bytes.HasPrefix(contents, []byte(kindSecret)) || bytes.Contains(contents, []byte("\n"+kindSecret))
 }
 
+// stripGLKManagedAnnotations removes GLK-managed annotation comments from YAML bytes.
+// A line is annotated when it contains both GLKDefaultPrefix and GLKManagedMarker.
+func stripGLKManagedAnnotations(data []byte) []byte {
+	lines := strings.Split(string(data), "\n")
+	out := make([]string, 0, len(lines))
+	for _, line := range lines {
+		if !strings.Contains(line, meta.GLKManagedMarker) {
+			out = append(out, line)
+			continue
+		}
+		// Strip from the start of the GLK annotation prefix.
+		if idx := strings.Index(line, meta.GLKDefaultPrefix); idx >= 0 {
+			stripped := strings.TrimRight(line[:idx], " \t")
+			// If the entire line was a head comment annotation, drop the line entirely.
+			if strings.TrimSpace(stripped) == "" {
+				continue
+			}
+			out = append(out, stripped)
+		}
+		// If for some reason the marker is present but the prefix is not, drop the line.
+	}
+	return []byte(strings.Join(out, "\n"))
+}
+
 // WriteObjectsToFilesystem writes the given objects to the filesystem at the specified rootDir and relativeFilePath.
 // If the manifest file already exists, it patches changes from the new default.
 // Additionally, it maintains a default version of the manifest in a separate directory for future diff checks.
-func WriteObjectsToFilesystem(objects map[string][]byte, rootDir, relativeFilePath string, fs afero.Afero) error {
+func WriteObjectsToFilesystem(objects map[string][]byte, rootDir, relativeFilePath string, fs afero.Afero, mode configv1alpha1.MergeMode) error {
 	if err := fs.MkdirAll(path.Join(rootDir, relativeFilePath), 0700); err != nil {
 		return err
 	}
@@ -81,7 +107,10 @@ func WriteObjectsToFilesystem(objects map[string][]byte, rootDir, relativeFilePa
 			object = append([]byte(secretEncryptionDisclaimer), object...)
 		}
 
-		output, err := meta.ThreeWayMergeManifest(oldDefaultYaml, object, currentYaml)
+		// Strip GLK-managed annotations from the current file before merging, so they are always re-evaluated (idempotency: the annotation reflects the *current* GLK default).
+		currentYaml = stripGLKManagedAnnotations(currentYaml)
+
+		output, err := meta.ThreeWayMergeManifest(oldDefaultYaml, object, currentYaml, mode)
 		if err != nil {
 			return err
 		}
diff --git a/pkg/utils/files/writer_test.go b/pkg/utils/files/writer_test.go
index 8d2a91b..547682d 100644
--- a/pkg/utils/files/writer_test.go
+++ b/pkg/utils/files/writer_test.go
@@ -15,7 +15,9 @@ import (
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"sigs.k8s.io/yaml"
 
+	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 	"github.com/gardener/gardener-landscape-kit/pkg/utils/files"
+	"github.com/gardener/gardener-landscape-kit/pkg/utils/meta"
 )
 
 var _ = Describe("Writer", func() {
@@ -53,7 +55,7 @@ var _ = Describe("Writer", func() {
 			baseDir := "/path/to"
 			path := "my/files"
 
-			Expect(files.WriteObjectsToFilesystem(objects, baseDir, path, fs)).To(Succeed())
+			Expect(files.WriteObjectsToFilesystem(objects, baseDir, path, fs, configv1alpha1.MergeModeSilent)).To(Succeed())
 
 			contents, err := fs.ReadFile("/path/to/my/files/file.yaml")
 			Expect(err).NotTo(HaveOccurred())
@@ -65,7 +67,7 @@ var _ = Describe("Writer", func() {
 		})
 
 		It("should overwrite the manifest file if no meta file is present yet", func() {
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"config.yaml": objYaml}, "/landscape", "manifest", fs)).To(Succeed())
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"config.yaml": objYaml}, "/landscape", "manifest", fs, configv1alpha1.MergeModeSilent)).To(Succeed())
 
 			content, err := fs.ReadFile("/landscape/.glk/defaults/manifest/config.yaml")
 			Expect(err).ToNot(HaveOccurred())
@@ -77,7 +79,7 @@ var _ = Describe("Writer", func() {
 		})
 
 		It("should patch only changed default values on subsequent generates and retain custom modifications", func() {
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"config.yaml": objYaml}, "/landscape", "manifest", fs)).To(Succeed())
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"config.yaml": objYaml}, "/landscape", "manifest", fs, configv1alpha1.MergeModeSilent)).To(Succeed())
 
 			content, err := fs.ReadFile("/landscape/manifest/config.yaml")
 			Expect(err).ToNot(HaveOccurred())
@@ -96,7 +98,7 @@ var _ = Describe("Writer", func() {
 			objYaml, err = yaml.Marshal(obj)
 			Expect(err).NotTo(HaveOccurred())
 
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"config.yaml": objYaml}, "/landscape", "manifest", fs)).To(Succeed())
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"config.yaml": objYaml}, "/landscape", "manifest", fs, configv1alpha1.MergeModeSilent)).To(Succeed())
 
 			content, err = fs.ReadFile("/landscape/.glk/defaults/manifest/config.yaml")
 			Expect(err).ToNot(HaveOccurred())
@@ -112,7 +114,7 @@ var _ = Describe("Writer", func() {
 			objYaml, err := yaml.Marshal(obj)
 			Expect(err).NotTo(HaveOccurred())
 
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"secret.yaml": objYaml}, "/landscape", "manifest", fs)).To(Succeed())
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"secret.yaml": objYaml}, "/landscape", "manifest", fs, configv1alpha1.MergeModeSilent)).To(Succeed())
 
 			content, err := fs.ReadFile("/landscape/manifest/secret.yaml")
 			Expect(err).ToNot(HaveOccurred())
@@ -129,7 +131,7 @@ spec:
     kind: Secret
     name: my-secret`)
 
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"secret.yaml": objYaml}, "/landscape", "manifest", fs)).To(Succeed())
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"secret.yaml": objYaml}, "/landscape", "manifest", fs, configv1alpha1.MergeModeSilent)).To(Succeed())
 
 			content, err := fs.ReadFile("/landscape/manifest/secret.yaml")
 			Expect(err).ToNot(HaveOccurred())
@@ -140,6 +142,103 @@ spec:
 		})
 	})
 
+	Describe("#WriteObjectsToFilesystem - MergeModeInformative", func() {
+		It("should annotate operator-overridden scalar values with the GLK default and preserve user comments idempotently", func() {
+			initial := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.0
+`)
+			// First generate: establish defaults
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": initial}, "/landscape", "manifest", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+
+			// Operator pins to a custom version with a comment explaining why
+			Expect(fs.WriteFile("/landscape/manifest/test.yaml", []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.5 # pinned for production
+`), 0600)).To(Succeed())
+
+			// GLK ships a new default with a newer version
+			updated := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.1.0
+`)
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": updated}, "/landscape", "manifest", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+
+			content, err := fs.ReadFile("/landscape/manifest/test.yaml")
+			Expect(err).NotTo(HaveOccurred())
+			// Operator's override is preserved
+			Expect(string(content)).To(ContainSubstring("version: v1.0.5"))
+			// User comment is preserved
+			Expect(string(content)).To(ContainSubstring("pinned for production"))
+			// GLK default annotation is added
+			Expect(string(content)).To(ContainSubstring("# glk default: v1.1.0"))
+			Expect(string(content)).To(ContainSubstring(meta.GLKManagedMarker))
+
+			// Re-run with the same inputs — annotation and user comment must not be doubled
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": updated}, "/landscape", "manifest", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+
+			content2, err := fs.ReadFile("/landscape/manifest/test.yaml")
+			Expect(err).NotTo(HaveOccurred())
+			Expect(string(content2)).To(Equal(string(content)))
+		})
+
+		It("should remove the annotation entirely when the GLK default reverts to the operator's value", func() {
+			initial := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.0
+`)
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": initial}, "/landscape", "revert", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+
+			// Operator pins to v1.0.5
+			Expect(fs.WriteFile("/landscape/revert/test.yaml", []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.5
+`), 0600)).To(Succeed())
+
+			// GLK ships v1.1.0 — annotation appears
+			updated := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.1.0
+`)
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": updated}, "/landscape", "revert", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+			content, err := fs.ReadFile("/landscape/revert/test.yaml")
+			Expect(err).NotTo(HaveOccurred())
+			Expect(string(content)).To(ContainSubstring(meta.GLKManagedMarker))
+
+			// GLK reverts to v1.0.5 — operator's value now matches the default, no annotation
+			reverted := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.5
+`)
+			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": reverted}, "/landscape", "revert", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+			content, err = fs.ReadFile("/landscape/revert/test.yaml")
+			Expect(err).NotTo(HaveOccurred())
+			Expect(string(content)).NotTo(ContainSubstring(meta.GLKManagedMarker))
+			Expect(string(content)).NotTo(ContainSubstring("# glk default:"))
+		})
+	})
+
 	Describe("#RelativePathFromDirDepth", func() {
 		It("should not go up if the passed relativeDir has no real depth", func() {
 			Expect(files.RelativePathFromDirDepth("")).To(Equal("."))
diff --git a/pkg/utils/meta/diff.go b/pkg/utils/meta/diff.go
index d5e8e10..7699ee7 100644
--- a/pkg/utils/meta/diff.go
+++ b/pkg/utils/meta/diff.go
@@ -13,6 +13,8 @@ import (
 
 	"github.com/elliotchance/orderedmap/v3"
 	"go.yaml.in/yaml/v4"
+
+	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 )
 
 // section represents a single section in a manifest file (either a manifest or a comment)
@@ -41,7 +43,7 @@ type manifestDiff struct {
 // It performs a three-way merge between the old default template, the new default template, and the current user-modified version.
 // It preserves user modifications while applying updates from the new default template.
 // Contents from the current manifest are prioritized and sorted first.
-func ThreeWayMergeManifest(oldDefaultYaml, newDefaultYaml, currentYaml []byte) ([]byte, error) {
+func ThreeWayMergeManifest(oldDefaultYaml, newDefaultYaml, currentYaml []byte, mode configv1alpha1.MergeMode) ([]byte, error) {
 	var (
 		output []byte
 
@@ -61,7 +63,7 @@ func ThreeWayMergeManifest(oldDefaultYaml, newDefaultYaml, currentYaml []byte) (
 		current := sect.content
 		newDefault, _ := diff.newDefault.Get(sect.key)
 		oldDefault, _ := diff.oldDefault.Get(sect.key)
-		merged, err := threeWayMergeSection(oldDefault, newDefault, current)
+		merged, err := threeWayMergeSection(oldDefault, newDefault, current, mode)
 		if err != nil {
 			return nil, err
 		}
@@ -75,7 +77,7 @@ func ThreeWayMergeManifest(oldDefaultYaml, newDefaultYaml, currentYaml []byte) (
 			continue
 		}
 		// Applying threeWayMergeSection with only the new section content to ensure proper formatting (idempotency).
-		merged, err := threeWayMergeSection(nil, sect.content, nil)
+		merged, err := threeWayMergeSection(nil, sect.content, nil, mode)
 		if err != nil {
 			return nil, err
 		}
diff --git a/pkg/utils/meta/diff_test.go b/pkg/utils/meta/diff_test.go
index c0aa175..29b766b 100644
--- a/pkg/utils/meta/diff_test.go
+++ b/pkg/utils/meta/diff_test.go
@@ -15,6 +15,7 @@ import (
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"sigs.k8s.io/yaml"
 
+	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 	"github.com/gardener/gardener-landscape-kit/pkg/utils/meta"
 )
 
@@ -41,7 +42,7 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			objYaml, err := yaml.Marshal(obj)
 			Expect(err).NotTo(HaveOccurred())
 
-			newContents, err := meta.ThreeWayMergeManifest(nil, objYaml, nil)
+			newContents, err := meta.ThreeWayMergeManifest(nil, objYaml, nil, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 
 			// Modify the manifest on disk
@@ -57,7 +58,7 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			newObjYaml, err := yaml.Marshal(obj)
 			Expect(err).NotTo(HaveOccurred())
 
-			content, err = meta.ThreeWayMergeManifest(objYaml, newObjYaml, content)
+			content, err = meta.ThreeWayMergeManifest(objYaml, newObjYaml, content, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 
 			expectedConfigMapOutputWithNewKey, err := testdata.ReadFile("testdata/expected_configmap_output_newkey.yaml")
@@ -76,7 +77,7 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			manifestGenerated, err := testdata.ReadFile("testdata/manifest-4-expected-generated.yaml")
 			Expect(err).NotTo(HaveOccurred())
 
-			mergedManifest, err := meta.ThreeWayMergeManifest(manifestDefault, manifestDefaultNew, manifestEdited)
+			mergedManifest, err := meta.ThreeWayMergeManifest(manifestDefault, manifestDefaultNew, manifestEdited, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(mergedManifest)).To(Equal(string(manifestGenerated)))
 		})
@@ -87,7 +88,7 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			expectedConfigMapOutputWithNewKey, err := testdata.ReadFile("testdata/expected_configmap_output_newkey.yaml")
 			Expect(err).NotTo(HaveOccurred())
 
-			content, err := meta.ThreeWayMergeManifest(nil, expectedConfigMapOutputWithNewKey, []byte(strings.ReplaceAll(string(expectedDefaultConfigMapOutput), "key: value", "key: newDefaultValue")))
+			content, err := meta.ThreeWayMergeManifest(nil, expectedConfigMapOutputWithNewKey, []byte(strings.ReplaceAll(string(expectedDefaultConfigMapOutput), "key: value", "key: newDefaultValue")), configv1alpha1.MergeModeSilent)
 			Expect(err).ToNot(HaveOccurred())
 			Expect(string(content)).To(Equal(strings.ReplaceAll(string(expectedConfigMapOutputWithNewKey), "key: value", "key: newDefaultValue") + "\n"))
 		})
@@ -102,21 +103,21 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			multipleManifestsExpectedGenerated, err := testdata.ReadFile("testdata/multiple-manifests-4-expected-generated.yaml")
 			Expect(err).NotTo(HaveOccurred())
 
-			content, err := meta.ThreeWayMergeManifest(nil, multipleManifestsInitial, nil)
+			content, err := meta.ThreeWayMergeManifest(nil, multipleManifestsInitial, nil, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(content)).To(Equal(string(multipleManifestsInitial)))
 
-			content, err = meta.ThreeWayMergeManifest(multipleManifestsInitial, multipleManifestsInitial, multipleManifestsInitial)
+			content, err = meta.ThreeWayMergeManifest(multipleManifestsInitial, multipleManifestsInitial, multipleManifestsInitial, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(content)).To(Equal(string(multipleManifestsInitial)))
 
 			// Editing the written manifest and updating the manifest with the same default content should not overwrite anything
-			content, err = meta.ThreeWayMergeManifest(multipleManifestsInitial, multipleManifestsInitial, multipleManifestsEdited)
+			content, err = meta.ThreeWayMergeManifest(multipleManifestsInitial, multipleManifestsInitial, multipleManifestsEdited, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(content)).To(Equal(string(multipleManifestsEdited)))
 
 			// New default manifest changes should be applied, while custom edits should be retained.
-			content, err = meta.ThreeWayMergeManifest(multipleManifestsInitial, multipleManifestsNewDefault, multipleManifestsEdited)
+			content, err = meta.ThreeWayMergeManifest(multipleManifestsInitial, multipleManifestsNewDefault, multipleManifestsEdited, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(content)).To(Equal(string(multipleManifestsExpectedGenerated)))
 		})
@@ -131,7 +132,7 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			expected, err := testdata.ReadFile("testdata/order-4-expected.yaml")
 			Expect(err).NotTo(HaveOccurred())
 
-			content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current)
+			content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(content)).To(Equal(string(expected)))
 		})
@@ -145,22 +146,22 @@ var _ = Describe("Meta Dir Config Diff", func() {
 				invalidYaml = []byte(`keyWith: colonSuffix:`)
 			)
 
-			_, err = meta.ThreeWayMergeManifest(emptyYaml, invalidYaml, emptyYaml)
+			_, err = meta.ThreeWayMergeManifest(emptyYaml, invalidYaml, emptyYaml, configv1alpha1.MergeModeSilent)
 			Expect(err).To(HaveOccurred())
 			Expect(err.Error()).To(ContainSubstring("parsing newDefault file for manifest diff failed"))
 
-			_, err = meta.ThreeWayMergeManifest(invalidYaml, validYaml, validYaml)
+			_, err = meta.ThreeWayMergeManifest(invalidYaml, validYaml, validYaml, configv1alpha1.MergeModeSilent)
 			Expect(err).To(HaveOccurred())
 			Expect(err.Error()).To(ContainSubstring("parsing oldDefault file for manifest diff failed"))
 
-			_, err = meta.ThreeWayMergeManifest(validYaml, validYaml, invalidYaml)
+			_, err = meta.ThreeWayMergeManifest(validYaml, validYaml, invalidYaml, configv1alpha1.MergeModeSilent)
 			Expect(err).To(HaveOccurred())
 			Expect(err.Error()).To(ContainSubstring("parsing current file for manifest diff failed"))
 
-			_, err = meta.ThreeWayMergeManifest(validYaml, validYaml, validYaml)
+			_, err = meta.ThreeWayMergeManifest(validYaml, validYaml, validYaml, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 
-			_, err = meta.ThreeWayMergeManifest(emptyYaml, emptyYaml, emptyYaml)
+			_, err = meta.ThreeWayMergeManifest(emptyYaml, emptyYaml, emptyYaml, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 		})
 
@@ -175,7 +176,7 @@ var _ = Describe("Meta Dir Config Diff", func() {
 				expected, err := testdata.ReadFile("testdata/replaced-file-4-expected-generated.yaml")
 				Expect(err).NotTo(HaveOccurred())
 
-				content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current)
+				content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current, configv1alpha1.MergeModeSilent)
 				Expect(err).NotTo(HaveOccurred())
 				Expect(string(content)).To(Equal(string(expected)))
 			})
@@ -190,7 +191,7 @@ var _ = Describe("Meta Dir Config Diff", func() {
 				expected, err := testdata.ReadFile("testdata/replaced-file-2-new-default.yaml")
 				Expect(err).NotTo(HaveOccurred())
 
-				content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current)
+				content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current, configv1alpha1.MergeModeSilent)
 				Expect(err).NotTo(HaveOccurred())
 				Expect(string(content)).To(Equal(string(expected)))
 			})
@@ -201,7 +202,7 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			// Two documents with the same structure should be treated as the same manifest across generations.
 			nonK8sYaml := []byte("foo: bar\nbaz: qux\n")
 
-			content, err := meta.ThreeWayMergeManifest(nonK8sYaml, nonK8sYaml, nonK8sYaml)
+			content, err := meta.ThreeWayMergeManifest(nonK8sYaml, nonK8sYaml, nonK8sYaml, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(content)).To(Equal(string(nonK8sYaml)))
 
@@ -210,7 +211,7 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			newDefault := []byte("foo: bar\nbaz: updated\n")
 			expected := []byte("foo: user-value\nbaz: updated\n")
 
-			content, err = meta.ThreeWayMergeManifest(nonK8sYaml, newDefault, edited)
+			content, err = meta.ThreeWayMergeManifest(nonK8sYaml, newDefault, edited, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(content)).To(MatchYAML(string(expected)))
 		})
@@ -225,7 +226,7 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			expected, err := testdata.ReadFile("testdata/replaced-file-6-different-name-merged.yaml")
 			Expect(err).NotTo(HaveOccurred())
 
-			content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current)
+			content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(content)).To(Equal(string(expected)))
 		})
@@ -240,9 +241,50 @@ var _ = Describe("Meta Dir Config Diff", func() {
 			expected, err := testdata.ReadFile("testdata/merge-slice-4-expected-generated.yaml")
 			Expect(err).NotTo(HaveOccurred())
 
-			content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current)
+			content, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current, configv1alpha1.MergeModeSilent)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(content)).To(Equal(string(expected)))
 		})
 	})
+
+	Describe("#ThreeWayMergeManifest - MergeModeInformative", func() {
+		It("should annotate a scalar value that the operator overrode and GLK updated, but not when there is no conflict", func() {
+			oldDefault := []byte(`
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.0
+`)
+			newDefault := []byte(`
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.1.0
+`)
+			// Operator pinned to v1.0.5 — conflicts with GLK's new default v1.1.0
+			current := []byte(`
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.5
+`)
+			result, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current, configv1alpha1.MergeModeInformative)
+			Expect(err).NotTo(HaveOccurred())
+			Expect(string(result)).To(ContainSubstring("version: v1.0.5"))
+			Expect(string(result)).To(ContainSubstring("# glk default: v1.1.0"))
+			Expect(string(result)).To(ContainSubstring(meta.GLKManagedMarker))
+
+			// No conflict: operator did not change the value → new default taken silently, no annotation
+			result, err = meta.ThreeWayMergeManifest(oldDefault, newDefault, oldDefault, configv1alpha1.MergeModeInformative)
+			Expect(err).NotTo(HaveOccurred())
+			Expect(string(result)).To(ContainSubstring("version: v1.1.0"))
+			Expect(string(result)).NotTo(ContainSubstring(meta.GLKManagedMarker))
+		})
+	})
 })
diff --git a/pkg/utils/meta/merge.go b/pkg/utils/meta/merge.go
index 4ecab8d..18d4757 100644
--- a/pkg/utils/meta/merge.go
+++ b/pkg/utils/meta/merge.go
@@ -6,10 +6,22 @@ package meta
 
 import (
 	"go.yaml.in/yaml/v4"
+
+	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
+)
+
+const (
+	// GLKManagedMarker is the suffix that marks a comment as GLK-managed.
+	// It is used to strip GLK-owned annotations before re-running the merge (idempotency).
+	GLKManagedMarker = "# <-- glk-managed"
+
+	// GLKDefaultPrefix is the comment prefix for GLK-managed default annotations.
+	// It is exported so callers can use it as the strip anchor when removing annotations.
+	GLKDefaultPrefix = "# glk default: "
 )
 
 // threeWayMergeSection performs a three-way merge on a single YAML section
-func threeWayMergeSection(oldDefaultYaml, newDefaultYaml, currentYaml []byte) ([]byte, error) {
+func threeWayMergeSection(oldDefaultYaml, newDefaultYaml, currentYaml []byte, mode configv1alpha1.MergeMode) ([]byte, error) {
 	// Parse all three versions
 	var oldDefault, newDefault, current yaml.Node
 	if err := yaml.Unmarshal(newDefaultYaml, &newDefault); err != nil {
@@ -26,14 +38,14 @@ func threeWayMergeSection(oldDefaultYaml, newDefaultYaml, currentYaml []byte) ([
 		}
 	}
 
-	return EncodeResult(threeWayMerge(&oldDefault, &newDefault, &current))
+	return EncodeResult(threeWayMerge(&oldDefault, &newDefault, &current, mode))
 }
 
 // threeWayMerge performs a three-way merge of YAML nodes
 // oldDefault: the previous default template
 // newDefault: the new default template
 // current: the user's current version (possibly modified)
-func threeWayMerge(oldDefault, newDefault, current *yaml.Node) *yaml.Node {
+func threeWayMerge(oldDefault, newDefault, current *yaml.Node, mode configv1alpha1.MergeMode) *yaml.Node {
 	// Unwrap document nodes
 	if oldDefault.Kind == yaml.DocumentNode {
 		oldDefault = oldDefault.Content[0]
@@ -44,7 +56,7 @@ func threeWayMerge(oldDefault, newDefault, current *yaml.Node) *yaml.Node {
 	if current.Kind == yaml.DocumentNode {
 		return &yaml.Node{
 			Kind:    yaml.DocumentNode,
-			Content: []*yaml.Node{threeWayMerge(oldDefault, newDefault, current.Content[0])},
+			Content: []*yaml.Node{threeWayMerge(oldDefault, newDefault, current.Content[0], mode)},
 		}
 	}
 
@@ -97,12 +109,12 @@ func threeWayMerge(oldDefault, newDefault, current *yaml.Node) *yaml.Node {
 				if !oldExists {
 					oldValue = &yaml.Node{Kind: yaml.MappingNode}
 				}
-				resultValue = threeWayMerge(oldValue, newValueNode, currentValue)
+				resultValue = threeWayMerge(oldValue, newValueNode, currentValue, mode)
 			case currentValue.Kind == yaml.SequenceNode && newValueNode.Kind == yaml.SequenceNode:
 				if !oldExists {
 					oldValue = &yaml.Node{Kind: yaml.SequenceNode}
 				}
-				resultValue = threeWayMergeSequence(oldValue, newValueNode, currentValue)
+				resultValue = threeWayMergeSequence(oldValue, newValueNode, currentValue, mode)
 			case oldExists && !nodesEqual(oldValue, newValueNode, false) && nodesEqual(oldValue, currentValue, false):
 				// Default changed and current was not modified: take the new default.
 				resultValue = &yaml.Node{
@@ -115,10 +127,17 @@ func threeWayMerge(oldDefault, newDefault, current *yaml.Node) *yaml.Node {
 				// Both default and current changed: keep current (user's value wins).
 				resultValue = currentValue
 				mergeNodeComments(oldValue, newValueNode, resultValue)
+				if mode == configv1alpha1.MergeModeInformative && !nodesEqual(newValueNode, currentValue, false) {
+					annotateConflict(resultKeyNode, resultValue, newValueNode)
+				}
 			default:
 				resultValue = currentValue
 				if oldExists {
 					mergeNodeComments(oldValue, newValueNode, resultValue)
+					if mode == configv1alpha1.MergeModeInformative && !nodesEqual(newValueNode, currentValue, false) {
+						// The operator's value differs from the current GLK default: annotate it.
+						annotateConflict(resultKeyNode, resultValue, newValueNode)
+					}
 				}
 			}
 		}
@@ -143,6 +162,39 @@ func threeWayMerge(oldDefault, newDefault, current *yaml.Node) *yaml.Node {
 	return result
 }
 
+// annotateConflict adds a GLK-managed annotation comment to resultValue (or resultKeyNode for complex nodes) indicating the current GLK default.
+// This is used in MergeModeInformative when an operator override conflicts with an updated GLK default, so the user is informed of the divergence.
+//
+// For scalar nodes, the annotation is a line comment on the value node (same line as the value).
+// For complex nodes (mappings/sequences), the annotation is a head comment on the key node (line above the key).
+func annotateConflict(resultKeyNode, resultValue, newDefaultNode *yaml.Node) {
+	switch newDefaultNode.Kind {
+	case yaml.ScalarNode:
+		annotation := glkManagedLineComment(newDefaultNode.Value)
+		if resultValue.LineComment != "" {
+			resultValue.LineComment = resultValue.LineComment + "  " + annotation
+		} else {
+			resultValue.LineComment = annotation
+		}
+	default:
+		resultKeyNode.HeadComment = glkManagedHeadComment(resultKeyNode.HeadComment)
+	}
+}
+
+// glkManagedLineComment returns a GLK-managed line comment for a scalar value conflict.
+func glkManagedLineComment(newValue string) string {
+	return GLKDefaultPrefix + newValue + "  " + GLKManagedMarker
+}
+
+// glkManagedHeadComment returns a GLK-managed head comment for a complex node conflict.
+func glkManagedHeadComment(existingHead string) string {
+	annotation := GLKDefaultPrefix + "(complex node changed)  " + GLKManagedMarker
+	if existingHead == "" {
+		return annotation
+	}
+	return existingHead + "\n" + annotation
+}
+
 // mergeComment performs a three-way merge on a single comment string.
 // If the default comment changed (old != new), the new default is applied — unless the user
 // has also modified the comment (current != old), in which case the user's comment is kept
@@ -177,7 +229,7 @@ func mergeNodeComments(oldNode, newNode, resultNode *yaml.Node) {
 }
 
 // Order is preserved based on newDefault, with user additions appended at the end
-func threeWayMergeSequence(oldDefault, newDefault, current *yaml.Node) *yaml.Node {
+func threeWayMergeSequence(oldDefault, newDefault, current *yaml.Node, mode configv1alpha1.MergeMode) *yaml.Node {
 	if nodesEqual(oldDefault, current, true) {
 		return newDefault
 	}
@@ -234,7 +286,7 @@ func threeWayMergeSequence(oldDefault, newDefault, current *yaml.Node) *yaml.Nod
 			if !existsInOld {
 				oldItem = &yaml.Node{Kind: yaml.MappingNode}
 			}
-			result.Content = append(result.Content, threeWayMerge(oldItem, newItem, currentItem))
+			result.Content = append(result.Content, threeWayMerge(oldItem, newItem, currentItem, mode))
 		}
 
 		// Append items from newDefault that are truly new (not in old) and not already in current.
diff --git a/pkg/utils/meta/preprocessing_test.go b/pkg/utils/meta/preprocessing_test.go
index f879d0e..8e1971a 100644
--- a/pkg/utils/meta/preprocessing_test.go
+++ b/pkg/utils/meta/preprocessing_test.go
@@ -10,6 +10,7 @@ import (
 	"github.com/spf13/afero"
 	"go.yaml.in/yaml/v4"
 
+	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 	"github.com/gardener/gardener-landscape-kit/pkg/utils/files"
 	"github.com/gardener/gardener-landscape-kit/pkg/utils/meta"
 )
@@ -68,7 +69,7 @@ var _ = Describe("YAML Preprocessing", func() {
 				Expect(err).ToNot(HaveOccurred())
 
 				Expect(fs.WriteFile("/landscape/manifest/test.yaml", testFile, 0600)).To(Succeed())
-				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": {}}, "/landscape", "manifest", fs)).To(Succeed())
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": {}}, "/landscape", "manifest", fs, configv1alpha1.MergeModeSilent)).To(Succeed())
 
 				content, err := fs.ReadFile("/landscape/manifest/test.yaml")
 				Expect(err).ToNot(HaveOccurred())
@@ -82,7 +83,7 @@ var _ = Describe("YAML Preprocessing", func() {
 				Expect(err).ToNot(HaveOccurred())
 
 				Expect(fs.WriteFile("/landscape/manifest/test.yaml", testFile, 0600)).To(Succeed())
-				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": {}}, "/landscape", "manifest", fs)).To(Succeed())
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": {}}, "/landscape", "manifest", fs, configv1alpha1.MergeModeSilent)).To(Succeed())
 
 				content, err := fs.ReadFile("/landscape/manifest/test.yaml")
 				Expect(err).ToNot(HaveOccurred())

From a513021283c07761eea041b78261bf1a7b51cb31 Mon Sep 17 00:00:00 2001
From: Luca Bernstein <luca.bernstein@sap.com>
Date: Wed, 1 Apr 2026 13:39:24 +0200
Subject: [PATCH 5/8] Update all `WriteObjectsToFilesystem` and
 `ThreeWayMergeManifest` call-sites

Existing callers pass `MergeModeSilent` (zero value, no behaviour change).
plain.go passes `MergeModeInformative` so the components.yaml file gets
GLK default annotations for operator-overridden component versions.
---
 hack/tools/prettify/main.go                       |  3 ++-
 pkg/components/flux/component.go                  |  2 +-
 .../networking-calico/component.go                |  4 ++--
 .../networking-cilium/component.go                |  4 ++--
 .../os-gardenlinux/component.go                   |  4 ++--
 .../os-suse-chost/component.go                    |  4 ++--
 .../provider-alicloud/component.go                |  4 ++--
 .../gardener-extensions/provider-aws/component.go |  4 ++--
 .../provider-azure/component.go                   |  4 ++--
 .../gardener-extensions/provider-gcp/component.go |  4 ++--
 .../provider-openstack/component.go               |  4 ++--
 .../runtime-gvisor/component.go                   |  4 ++--
 .../shoot-cert-service/component.go               |  4 ++--
 .../shoot-dns-service/component.go                |  4 ++--
 .../shoot-networking-problemdetector/component.go |  4 ++--
 .../shoot-oidc-service/component.go               |  4 ++--
 pkg/components/gardener/garden/component.go       |  4 ++--
 pkg/components/gardener/operator/component.go     |  4 ++--
 .../gardener/virtual-garden-access/component.go   |  4 ++--
 .../virtual-garden/garden-config/component.go     |  4 ++--
 pkg/utils/kustomization/kustomization.go          | 15 ++++++++-------
 pkg/utils/kustomization/kustomization_test.go     |  3 ++-
 22 files changed, 49 insertions(+), 46 deletions(-)

diff --git a/hack/tools/prettify/main.go b/hack/tools/prettify/main.go
index dbd33c7..1b27837 100644
--- a/hack/tools/prettify/main.go
+++ b/hack/tools/prettify/main.go
@@ -11,6 +11,7 @@ import (
 
 	flag "github.com/spf13/pflag"
 
+	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 	"github.com/gardener/gardener-landscape-kit/pkg/utils/meta"
 )
 
@@ -31,7 +32,7 @@ func main() {
 	if err != nil {
 		log.Fatalf("Error reading file: %s", err)
 	}
-	prettified, err := meta.ThreeWayMergeManifest(nil, content, nil)
+	prettified, err := meta.ThreeWayMergeManifest(nil, content, nil, configv1alpha1.MergeModeSilent)
 	if err != nil {
 		log.Fatalf("Marshalling failed: %s", err)
 	}
diff --git a/pkg/components/flux/component.go b/pkg/components/flux/component.go
index 6a47c9a..54b2e4f 100644
--- a/pkg/components/flux/component.go
+++ b/pkg/components/flux/component.go
@@ -94,7 +94,7 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 	delete(objects, "flux-system/gitignore")
 	delete(objects, "flux-system/doc.go")
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), DirName, opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), DirName, opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeGitignoreFile(options components.LandscapeOptions) error {
diff --git a/pkg/components/gardener-extensions/networking-calico/component.go b/pkg/components/gardener-extensions/networking-calico/component.go
index c297146..eeb3d19 100644
--- a/pkg/components/gardener-extensions/networking-calico/component.go
+++ b/pkg/components/gardener-extensions/networking-calico/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/networking-cilium/component.go b/pkg/components/gardener-extensions/networking-cilium/component.go
index b934ce4..e39d969 100644
--- a/pkg/components/gardener-extensions/networking-cilium/component.go
+++ b/pkg/components/gardener-extensions/networking-cilium/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/os-gardenlinux/component.go b/pkg/components/gardener-extensions/os-gardenlinux/component.go
index 2cc5eb0..0ee9de5 100644
--- a/pkg/components/gardener-extensions/os-gardenlinux/component.go
+++ b/pkg/components/gardener-extensions/os-gardenlinux/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/os-suse-chost/component.go b/pkg/components/gardener-extensions/os-suse-chost/component.go
index 3e93384..2c7be6a 100644
--- a/pkg/components/gardener-extensions/os-suse-chost/component.go
+++ b/pkg/components/gardener-extensions/os-suse-chost/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/provider-alicloud/component.go b/pkg/components/gardener-extensions/provider-alicloud/component.go
index b703f15..3870483 100644
--- a/pkg/components/gardener-extensions/provider-alicloud/component.go
+++ b/pkg/components/gardener-extensions/provider-alicloud/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/provider-aws/component.go b/pkg/components/gardener-extensions/provider-aws/component.go
index 76e3408..2d65d34 100644
--- a/pkg/components/gardener-extensions/provider-aws/component.go
+++ b/pkg/components/gardener-extensions/provider-aws/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/provider-azure/component.go b/pkg/components/gardener-extensions/provider-azure/component.go
index 6bbb7f7..2b75ca2 100644
--- a/pkg/components/gardener-extensions/provider-azure/component.go
+++ b/pkg/components/gardener-extensions/provider-azure/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/provider-gcp/component.go b/pkg/components/gardener-extensions/provider-gcp/component.go
index dbbd327..c050ecf 100644
--- a/pkg/components/gardener-extensions/provider-gcp/component.go
+++ b/pkg/components/gardener-extensions/provider-gcp/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/provider-openstack/component.go b/pkg/components/gardener-extensions/provider-openstack/component.go
index 6ffc8e8..071b468 100644
--- a/pkg/components/gardener-extensions/provider-openstack/component.go
+++ b/pkg/components/gardener-extensions/provider-openstack/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/runtime-gvisor/component.go b/pkg/components/gardener-extensions/runtime-gvisor/component.go
index 3a6e0cb..c095911 100644
--- a/pkg/components/gardener-extensions/runtime-gvisor/component.go
+++ b/pkg/components/gardener-extensions/runtime-gvisor/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/shoot-cert-service/component.go b/pkg/components/gardener-extensions/shoot-cert-service/component.go
index b8c1c6b..0364518 100644
--- a/pkg/components/gardener-extensions/shoot-cert-service/component.go
+++ b/pkg/components/gardener-extensions/shoot-cert-service/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/shoot-dns-service/component.go b/pkg/components/gardener-extensions/shoot-dns-service/component.go
index b452074..c0a87bd 100644
--- a/pkg/components/gardener-extensions/shoot-dns-service/component.go
+++ b/pkg/components/gardener-extensions/shoot-dns-service/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/shoot-networking-problemdetector/component.go b/pkg/components/gardener-extensions/shoot-networking-problemdetector/component.go
index ab35beb..9053be4 100644
--- a/pkg/components/gardener-extensions/shoot-networking-problemdetector/component.go
+++ b/pkg/components/gardener-extensions/shoot-networking-problemdetector/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener-extensions/shoot-oidc-service/component.go b/pkg/components/gardener-extensions/shoot-oidc-service/component.go
index 9e8d9dc..9dbcd84 100644
--- a/pkg/components/gardener-extensions/shoot-oidc-service/component.go
+++ b/pkg/components/gardener-extensions/shoot-oidc-service/component.go
@@ -78,7 +78,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -100,5 +100,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener/garden/component.go b/pkg/components/gardener/garden/component.go
index eefa0f2..5cbc3c3 100644
--- a/pkg/components/gardener/garden/component.go
+++ b/pkg/components/gardener/garden/component.go
@@ -71,7 +71,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -88,5 +88,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/gardener/operator/component.go b/pkg/components/gardener/operator/component.go
index 5873ca7..0221ed8 100644
--- a/pkg/components/gardener/operator/component.go
+++ b/pkg/components/gardener/operator/component.go
@@ -80,7 +80,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func getTemplateValues(opts components.Options) (map[string]any, error) {
@@ -134,7 +134,7 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func getOCIImageReferenceFromComponentVector(name string, cv *utilscomponentvector.ComponentVector) (string, error) {
diff --git a/pkg/components/gardener/virtual-garden-access/component.go b/pkg/components/gardener/virtual-garden-access/component.go
index 513753c..81dc414 100644
--- a/pkg/components/gardener/virtual-garden-access/component.go
+++ b/pkg/components/gardener/virtual-garden-access/component.go
@@ -73,7 +73,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -90,5 +90,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/components/virtual-garden/garden-config/component.go b/pkg/components/virtual-garden/garden-config/component.go
index 56227b0..1104f31 100644
--- a/pkg/components/virtual-garden/garden-config/component.go
+++ b/pkg/components/virtual-garden/garden-config/component.go
@@ -73,7 +73,7 @@ func writeBaseTemplateFiles(opts components.Options) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
 
 func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
@@ -90,5 +90,5 @@ func writeLandscapeTemplateFiles(opts components.LandscapeOptions) error {
 		return err
 	}
 
-	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem())
+	return files.WriteObjectsToFilesystem(objects, opts.GetTargetPath(), path.Join(components.DirName, ComponentDirectory), opts.GetFilesystem(), opts.GetMergeMode())
 }
diff --git a/pkg/utils/kustomization/kustomization.go b/pkg/utils/kustomization/kustomization.go
index 01e1123..6ea15ad 100644
--- a/pkg/utils/kustomization/kustomization.go
+++ b/pkg/utils/kustomization/kustomization.go
@@ -16,6 +16,7 @@ import (
 	kustomize "sigs.k8s.io/kustomize/api/types"
 	"sigs.k8s.io/yaml"
 
+	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 	"github.com/gardener/gardener-landscape-kit/pkg/components"
 	"github.com/gardener/gardener-landscape-kit/pkg/utils/files"
 )
@@ -51,14 +52,14 @@ func NewKustomization(resources []string, patches []kustomize.Patch) *kustomize.
 // WriteKustomizationComponent writes the objects and a Kustomization file to the fs.
 // The Kustomization file references all other objects.
 // The objects map will be modified to include the Kustomization file.
-func WriteKustomizationComponent(objects map[string][]byte, baseDir, componentDir string, fs afero.Afero) error {
+func WriteKustomizationComponent(objects map[string][]byte, baseDir, componentDir string, fs afero.Afero, mode configv1alpha1.MergeMode) error {
 	kustomization := NewKustomization(slices.Collect(maps.Keys(objects)), nil)
 	content, err := yaml.Marshal(kustomization)
 	if err != nil {
 		return err
 	}
 	objects[KustomizationFileName] = content
-	return files.WriteObjectsToFilesystem(objects, baseDir, componentDir, fs)
+	return files.WriteObjectsToFilesystem(objects, baseDir, componentDir, fs, mode)
 }
 
 // WriteLandscapeComponentsKustomizations traverses through the generated components directory and adds
@@ -68,10 +69,10 @@ func WriteLandscapeComponentsKustomizations(options components.Options) error {
 	targetDir := options.GetTargetPath()
 	componentsDir := filepath.Join(targetDir, components.DirName)
 
-	return fs.Walk(componentsDir, writeKustomizationsToFileTree(fs, targetDir))
+	return fs.Walk(componentsDir, writeKustomizationsToFileTree(fs, targetDir, options.GetMergeMode()))
 }
 
-func writeKustomizationsToFileTree(fs afero.Afero, targetDir string) func(dir string, info os.FileInfo, err error) error {
+func writeKustomizationsToFileTree(fs afero.Afero, targetDir string, mode configv1alpha1.MergeMode) func(dir string, info os.FileInfo, err error) error {
 	var completedPaths []string
 
 	return func(dir string, info os.FileInfo, err error) error {
@@ -115,11 +116,11 @@ func writeKustomizationsToFileTree(fs afero.Afero, targetDir string) func(dir st
 		}
 
 		relativePath, _ := strings.CutPrefix(dir, targetDir)
-		return writeKustomizationFile(fs, targetDir, relativePath, directories)
+		return writeKustomizationFile(fs, targetDir, relativePath, directories, mode)
 	}
 }
 
-func writeKustomizationFile(fs afero.Afero, landscapeDir, relativePath string, directories []string) error {
+func writeKustomizationFile(fs afero.Afero, landscapeDir, relativePath string, directories []string, mode configv1alpha1.MergeMode) error {
 	var (
 		err     error
 		objects = make(map[string][]byte)
@@ -132,5 +133,5 @@ func writeKustomizationFile(fs afero.Afero, landscapeDir, relativePath string, d
 
 	objects[KustomizationFileName] = append([]byte(autoGenerationNotice), objects[KustomizationFileName]...)
 
-	return files.WriteObjectsToFilesystem(objects, landscapeDir, relativePath, fs)
+	return files.WriteObjectsToFilesystem(objects, landscapeDir, relativePath, fs, mode)
 }
diff --git a/pkg/utils/kustomization/kustomization_test.go b/pkg/utils/kustomization/kustomization_test.go
index 909fe1f..ff1815a 100644
--- a/pkg/utils/kustomization/kustomization_test.go
+++ b/pkg/utils/kustomization/kustomization_test.go
@@ -16,6 +16,7 @@ import (
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"sigs.k8s.io/yaml"
 
+	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 	"github.com/gardener/gardener-landscape-kit/pkg/cmd"
 	generateoptions "github.com/gardener/gardener-landscape-kit/pkg/cmd/generate/options"
 	"github.com/gardener/gardener-landscape-kit/pkg/components"
@@ -59,7 +60,7 @@ var _ = Describe("Kustomization", func() {
 				}
 			)
 
-			Expect(WriteKustomizationComponent(objects, landscapeDir, componentDir, fs)).To(Succeed())
+			Expect(WriteKustomizationComponent(objects, landscapeDir, componentDir, fs, configv1alpha1.MergeModeSilent)).To(Succeed())
 
 			contents, err := fs.ReadFile(filepath.Join(landscapeDir, componentDir, "configmap.yaml"))
 			Expect(err).NotTo(HaveOccurred())

From 3ddf8fb15688e6d2f53bc71c7a7eaa97920ede0c Mon Sep 17 00:00:00 2001
From: Luca Bernstein <luca.bernstein@sap.com>
Date: Fri, 10 Apr 2026 17:12:15 +0200
Subject: [PATCH 6/8] Address review comments

---
 docs/api-reference/landscapekit-v1alpha1.md   |  17 ++
 example/20-componentconfig-glk.yaml           |   1 +
 pkg/apis/config/v1alpha1/types.go             |  18 +-
 .../config/v1alpha1/validation/validation.go  |   2 +-
 .../v1alpha1/validation/validation_test.go    |   2 +-
 pkg/components/types.go                       |   2 +-
 pkg/utils/files/writer.go                     |  28 ----
 pkg/utils/files/writer_test.go                | 158 +++++++++++++-----
 pkg/utils/meta/diff_test.go                   |   5 +-
 pkg/utils/meta/merge.go                       |  88 ++++++++--
 10 files changed, 219 insertions(+), 102 deletions(-)

diff --git a/docs/api-reference/landscapekit-v1alpha1.md b/docs/api-reference/landscapekit-v1alpha1.md
index 0e58c23..6e87bae 100644
--- a/docs/api-reference/landscapekit-v1alpha1.md
+++ b/docs/api-reference/landscapekit-v1alpha1.md
@@ -81,6 +81,23 @@ _Appears in:_
 
 
 
+#### MergeMode
+
+_Underlying type:_ _string_
+
+MergeMode controls how operator overwrites are handled during three-way merge.
+
+
+
+_Appears in:_
+- [LandscapeKitConfiguration](#landscapekitconfiguration)
+
+| Field | Description |
+| --- | --- |
+| `Informative` | MergeModeInformative annotates operator-overwritten values with a comment showing the current GLK default.<br /> |
+| `Silent` | MergeModeSilent retains operator overwrites without annotation.<br /> |
+
+
 #### OCMComponent
 
 
diff --git a/example/20-componentconfig-glk.yaml b/example/20-componentconfig-glk.yaml
index 2eab32f..8cc3905 100644
--- a/example/20-componentconfig-glk.yaml
+++ b/example/20-componentconfig-glk.yaml
@@ -19,3 +19,4 @@ kind: LandscapeKitConfiguration
 #   - component-name
 # versionConfig:
 #   defaultVersionsUpdateStrategy: ReleaseBranch
+# mergeMode: Informative
diff --git a/pkg/apis/config/v1alpha1/types.go b/pkg/apis/config/v1alpha1/types.go
index 1a79b16..076b929 100644
--- a/pkg/apis/config/v1alpha1/types.go
+++ b/pkg/apis/config/v1alpha1/types.go
@@ -26,8 +26,9 @@ type LandscapeKitConfiguration struct {
 	// VersionConfig is the configuration for versioning.
 	// +optional
 	VersionConfig *VersionConfiguration `json:"versionConfig,omitempty"`
-	// MergeMode controls how operator overrides conflicting with updated GLK defaults are handled during three-way merge.
-	// Possible values are "Informative" (default) and "Silent".
+	// MergeMode determines how merge conflicts are resolved:
+	// - "Informative" (default): New default values from GLK are added as comments after any customized values.
+	// - "Silent": Operator-customized values are retained, new default values are omitted.
 	// +optional
 	MergeMode *MergeMode `json:"mergeMode,omitempty"`
 }
@@ -124,13 +125,13 @@ type VersionConfiguration struct {
 	DefaultVersionsUpdateStrategy *DefaultVersionsUpdateStrategy `json:"defaultVersionsUpdateStrategy,omitempty"`
 }
 
-// MergeMode controls how operator overrides are handled during three-way merge.
+// MergeMode controls how operator overwrites are handled during three-way merge.
 type MergeMode string
 
 const (
-	// MergeModeInformative annotates operator-overridden values with a comment showing the current GLK default.
+	// MergeModeInformative annotates operator-overwritten values with a comment showing the current GLK default.
 	MergeModeInformative MergeMode = "Informative"
-	// MergeModeSilent retains operator overrides without annotation.
+	// MergeModeSilent retains operator overwrites without annotation.
 	MergeModeSilent MergeMode = "Silent"
 )
 
@@ -141,10 +142,9 @@ var AllowedMergeModes = []string{
 }
 
 // GetMergeMode returns the configured MergeMode, defaulting to MergeModeInformative.
-// It is safe to call on a nil receiver.
 func (c *LandscapeKitConfiguration) GetMergeMode() MergeMode {
-	if c != nil && c.MergeMode != nil {
-		return *c.MergeMode
+	if c == nil || c.MergeMode == nil {
+		return MergeModeInformative
 	}
-	return MergeModeInformative
+	return *c.MergeMode
 }
diff --git a/pkg/apis/config/v1alpha1/validation/validation.go b/pkg/apis/config/v1alpha1/validation/validation.go
index c0567e9..704cee8 100644
--- a/pkg/apis/config/v1alpha1/validation/validation.go
+++ b/pkg/apis/config/v1alpha1/validation/validation.go
@@ -37,7 +37,7 @@ func ValidateLandscapeKitConfiguration(conf *configv1alpha1.LandscapeKitConfigur
 	}
 
 	if conf.MergeMode != nil && !slices.Contains(configv1alpha1.AllowedMergeModes, string(*conf.MergeMode)) {
-		allErrs = append(allErrs, field.Invalid(field.NewPath("mergeMode"), *conf.MergeMode, "allowed values are: "+strings.Join(configv1alpha1.AllowedMergeModes, ", ")))
+		allErrs = append(allErrs, field.NotSupported(field.NewPath("mergeMode"), *conf.MergeMode, configv1alpha1.AllowedMergeModes))
 	}
 
 	return allErrs
diff --git a/pkg/apis/config/v1alpha1/validation/validation_test.go b/pkg/apis/config/v1alpha1/validation/validation_test.go
index 5ccd0e4..39be407 100644
--- a/pkg/apis/config/v1alpha1/validation/validation_test.go
+++ b/pkg/apis/config/v1alpha1/validation/validation_test.go
@@ -324,7 +324,7 @@ var _ = Describe("Validation", func() {
 				errList := validation.ValidateLandscapeKitConfiguration(conf)
 				Expect(errList).To(ConsistOf(
 					PointTo(MatchFields(IgnoreExtras, Fields{
-						"Type":     Equal(field.ErrorTypeInvalid),
+						"Type":     Equal(field.ErrorTypeNotSupported),
 						"Field":    Equal("mergeMode"),
 						"BadValue": Equal(invalid),
 					})),
diff --git a/pkg/components/types.go b/pkg/components/types.go
index 0b0c22a..17cdf45 100644
--- a/pkg/components/types.go
+++ b/pkg/components/types.go
@@ -36,7 +36,7 @@ type Options interface {
 	GetFilesystem() afero.Afero
 	// GetLogger returns the logger instance.
 	GetLogger() logr.Logger
-	// GetMergeMode returns the configured merge mode for three-way merges.
+	// GetMergeMode returns the configured mode to solve merge conflicts.
 	GetMergeMode() configv1alpha1.MergeMode
 }
 
diff --git a/pkg/utils/files/writer.go b/pkg/utils/files/writer.go
index e9f7930..755345f 100644
--- a/pkg/utils/files/writer.go
+++ b/pkg/utils/files/writer.go
@@ -10,7 +10,6 @@ import (
 	"os"
 	"path"
 	"path/filepath"
-	"strings"
 
 	"github.com/spf13/afero"
 
@@ -46,30 +45,6 @@ func isSecret(contents []byte) bool {
 	return bytes.HasPrefix(contents, []byte(kindSecret)) || bytes.Contains(contents, []byte("\n"+kindSecret))
 }
 
-// stripGLKManagedAnnotations removes GLK-managed annotation comments from YAML bytes.
-// A line is annotated when it contains both GLKDefaultPrefix and GLKManagedMarker.
-func stripGLKManagedAnnotations(data []byte) []byte {
-	lines := strings.Split(string(data), "\n")
-	out := make([]string, 0, len(lines))
-	for _, line := range lines {
-		if !strings.Contains(line, meta.GLKManagedMarker) {
-			out = append(out, line)
-			continue
-		}
-		// Strip from the start of the GLK annotation prefix.
-		if idx := strings.Index(line, meta.GLKDefaultPrefix); idx >= 0 {
-			stripped := strings.TrimRight(line[:idx], " \t")
-			// If the entire line was a head comment annotation, drop the line entirely.
-			if strings.TrimSpace(stripped) == "" {
-				continue
-			}
-			out = append(out, stripped)
-		}
-		// If for some reason the marker is present but the prefix is not, drop the line.
-	}
-	return []byte(strings.Join(out, "\n"))
-}
-
 // WriteObjectsToFilesystem writes the given objects to the filesystem at the specified rootDir and relativeFilePath.
 // If the manifest file already exists, it patches changes from the new default.
 // Additionally, it maintains a default version of the manifest in a separate directory for future diff checks.
@@ -107,9 +82,6 @@ func WriteObjectsToFilesystem(objects map[string][]byte, rootDir, relativeFilePa
 			object = append([]byte(secretEncryptionDisclaimer), object...)
 		}
 
-		// Strip GLK-managed annotations from the current file before merging, so they are always re-evaluated (idempotency: the annotation reflects the *current* GLK default).
-		currentYaml = stripGLKManagedAnnotations(currentYaml)
-
 		output, err := meta.ThreeWayMergeManifest(oldDefaultYaml, object, currentYaml, mode)
 		if err != nil {
 			return err
diff --git a/pkg/utils/files/writer_test.go b/pkg/utils/files/writer_test.go
index 547682d..6475d64 100644
--- a/pkg/utils/files/writer_test.go
+++ b/pkg/utils/files/writer_test.go
@@ -140,22 +140,20 @@ spec:
 				Not(ContainSubstring(`# SECURITY ADVISORY`)),
 			))
 		})
-	})
 
-	Describe("#WriteObjectsToFilesystem - MergeModeInformative", func() {
-		It("should annotate operator-overridden scalar values with the GLK default and preserve user comments idempotently", func() {
-			initial := []byte(`apiVersion: v1
+		DescribeTable("should annotate operator-overwritten values only in Informative mode",
+			func(mode configv1alpha1.MergeMode, expectAnnotation bool) {
+				initial := []byte(`apiVersion: v1
 kind: ConfigMap
 metadata:
   name: test
 data:
   version: v1.0.0
 `)
-			// First generate: establish defaults
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": initial}, "/landscape", "manifest", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": initial}, "/landscape", "manifest", fs, mode)).To(Succeed())
 
-			// Operator pins to a custom version with a comment explaining why
-			Expect(fs.WriteFile("/landscape/manifest/test.yaml", []byte(`apiVersion: v1
+				// Operator pins to a custom version with a comment explaining why
+				Expect(fs.WriteFile("/landscape/manifest/test.yaml", []byte(`apiVersion: v1
 kind: ConfigMap
 metadata:
   name: test
@@ -163,46 +161,113 @@ data:
   version: v1.0.5 # pinned for production
 `), 0600)).To(Succeed())
 
-			// GLK ships a new default with a newer version
-			updated := []byte(`apiVersion: v1
+				// GLK ships a new default with a newer version
+				updated := []byte(`apiVersion: v1
 kind: ConfigMap
 metadata:
   name: test
 data:
   version: v1.1.0
 `)
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": updated}, "/landscape", "manifest", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": updated}, "/landscape", "manifest", fs, mode)).To(Succeed())
+
+				content, err := fs.ReadFile("/landscape/manifest/test.yaml")
+				Expect(err).NotTo(HaveOccurred())
+				Expect(string(content)).To(ContainSubstring("version: v1.0.5"))
+				Expect(string(content)).To(ContainSubstring("pinned for production"))
+
+				if expectAnnotation {
+					Expect(string(content)).To(ContainSubstring(meta.GLKDefaultPrefix + "v1.1.0"))
+
+					// Re-run with the same default — annotation persists because the user did not remove it.
+					Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": updated}, "/landscape", "manifest", fs, mode)).To(Succeed())
+					content2, err := fs.ReadFile("/landscape/manifest/test.yaml")
+					Expect(err).NotTo(HaveOccurred())
+					Expect(string(content2)).To(Equal(string(content)))
+				} else {
+					Expect(string(content)).NotTo(ContainSubstring(meta.GLKDefaultPrefix))
+				}
+			},
+			Entry("Silent", configv1alpha1.MergeModeSilent, false),
+			Entry("Informative", configv1alpha1.MergeModeInformative, true),
+		)
 
-			content, err := fs.ReadFile("/landscape/manifest/test.yaml")
-			Expect(err).NotTo(HaveOccurred())
-			// Operator's override is preserved
-			Expect(string(content)).To(ContainSubstring("version: v1.0.5"))
-			// User comment is preserved
-			Expect(string(content)).To(ContainSubstring("pinned for production"))
-			// GLK default annotation is added
-			Expect(string(content)).To(ContainSubstring("# glk default: v1.1.0"))
-			Expect(string(content)).To(ContainSubstring(meta.GLKManagedMarker))
-
-			// Re-run with the same inputs — annotation and user comment must not be doubled
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": updated}, "/landscape", "manifest", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
-
-			content2, err := fs.ReadFile("/landscape/manifest/test.yaml")
-			Expect(err).NotTo(HaveOccurred())
-			Expect(string(content2)).To(Equal(string(content)))
-		})
+		Context("MergeMode Informative", func() {
+			It("should not re-add the annotation after the user removed it, until the default changes again", func() {
+				initial := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.0
+`)
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": initial}, "/landscape", "manifest", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+
+				// Operator pins to v1.0.5
+				Expect(fs.WriteFile("/landscape/manifest/test.yaml", []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.5
+`), 0600)).To(Succeed())
+
+				// GLK ships v1.1.0 — annotation appears
+				v110 := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.1.0
+`)
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": v110}, "/landscape", "manifest", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				content, err := fs.ReadFile("/landscape/manifest/test.yaml")
+				Expect(err).NotTo(HaveOccurred())
+				Expect(string(content)).To(ContainSubstring(meta.GLKDefaultPrefix))
+
+				// User acknowledges the annotation and removes it manually
+				Expect(fs.WriteFile("/landscape/manifest/test.yaml", []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.5
+`), 0600)).To(Succeed())
+
+				// Re-run with the same default — annotation stays removed
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": v110}, "/landscape", "manifest", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				content, err = fs.ReadFile("/landscape/manifest/test.yaml")
+				Expect(err).NotTo(HaveOccurred())
+				Expect(string(content)).To(ContainSubstring("version: v1.0.5"))
+				Expect(string(content)).NotTo(ContainSubstring(meta.GLKDefaultPrefix))
 
-		It("should remove the annotation entirely when the GLK default reverts to the operator's value", func() {
-			initial := []byte(`apiVersion: v1
+				// GLK ships v1.2.0 — annotation re-appears because the default changed
+				v120 := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.2.0
+`)
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": v120}, "/landscape", "manifest", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				content, err = fs.ReadFile("/landscape/manifest/test.yaml")
+				Expect(err).NotTo(HaveOccurred())
+				Expect(string(content)).To(ContainSubstring("version: v1.0.5"))
+				Expect(string(content)).To(ContainSubstring(meta.GLKDefaultPrefix + "v1.2.0"))
+			})
+
+			It("should remove the annotation entirely when the GLK default reverts to the operator's value", func() {
+				initial := []byte(`apiVersion: v1
 kind: ConfigMap
 metadata:
   name: test
 data:
   version: v1.0.0
 `)
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": initial}, "/landscape", "revert", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": initial}, "/landscape", "revert", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
 
-			// Operator pins to v1.0.5
-			Expect(fs.WriteFile("/landscape/revert/test.yaml", []byte(`apiVersion: v1
+				// Operator pins to v1.0.5
+				Expect(fs.WriteFile("/landscape/revert/test.yaml", []byte(`apiVersion: v1
 kind: ConfigMap
 metadata:
   name: test
@@ -210,32 +275,33 @@ data:
   version: v1.0.5
 `), 0600)).To(Succeed())
 
-			// GLK ships v1.1.0 — annotation appears
-			updated := []byte(`apiVersion: v1
+				// GLK ships v1.1.0 — annotation appears
+				updated := []byte(`apiVersion: v1
 kind: ConfigMap
 metadata:
   name: test
 data:
   version: v1.1.0
 `)
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": updated}, "/landscape", "revert", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
-			content, err := fs.ReadFile("/landscape/revert/test.yaml")
-			Expect(err).NotTo(HaveOccurred())
-			Expect(string(content)).To(ContainSubstring(meta.GLKManagedMarker))
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": updated}, "/landscape", "revert", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				content, err := fs.ReadFile("/landscape/revert/test.yaml")
+				Expect(err).NotTo(HaveOccurred())
+				Expect(string(content)).To(ContainSubstring(meta.GLKDefaultPrefix))
 
-			// GLK reverts to v1.0.5 — operator's value now matches the default, no annotation
-			reverted := []byte(`apiVersion: v1
+				// GLK reverts to v1.0.5 — operator's value now matches the default, no annotation
+				reverted := []byte(`apiVersion: v1
 kind: ConfigMap
 metadata:
   name: test
 data:
   version: v1.0.5
 `)
-			Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": reverted}, "/landscape", "revert", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
-			content, err = fs.ReadFile("/landscape/revert/test.yaml")
-			Expect(err).NotTo(HaveOccurred())
-			Expect(string(content)).NotTo(ContainSubstring(meta.GLKManagedMarker))
-			Expect(string(content)).NotTo(ContainSubstring("# glk default:"))
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": reverted}, "/landscape", "revert", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				content, err = fs.ReadFile("/landscape/revert/test.yaml")
+				Expect(err).NotTo(HaveOccurred())
+				Expect(string(content)).NotTo(ContainSubstring(meta.GLKDefaultPrefix))
+				Expect(string(content)).NotTo(ContainSubstring("# Attention - new default:"))
+			})
 		})
 	})
 
diff --git a/pkg/utils/meta/diff_test.go b/pkg/utils/meta/diff_test.go
index 29b766b..8fb8c73 100644
--- a/pkg/utils/meta/diff_test.go
+++ b/pkg/utils/meta/diff_test.go
@@ -277,14 +277,13 @@ data:
 			result, err := meta.ThreeWayMergeManifest(oldDefault, newDefault, current, configv1alpha1.MergeModeInformative)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(result)).To(ContainSubstring("version: v1.0.5"))
-			Expect(string(result)).To(ContainSubstring("# glk default: v1.1.0"))
-			Expect(string(result)).To(ContainSubstring(meta.GLKManagedMarker))
+			Expect(string(result)).To(ContainSubstring("# Attention - new default: v1.1.0"))
 
 			// No conflict: operator did not change the value → new default taken silently, no annotation
 			result, err = meta.ThreeWayMergeManifest(oldDefault, newDefault, oldDefault, configv1alpha1.MergeModeInformative)
 			Expect(err).NotTo(HaveOccurred())
 			Expect(string(result)).To(ContainSubstring("version: v1.1.0"))
-			Expect(string(result)).NotTo(ContainSubstring(meta.GLKManagedMarker))
+			Expect(string(result)).NotTo(ContainSubstring(meta.GLKDefaultPrefix))
 		})
 	})
 })
diff --git a/pkg/utils/meta/merge.go b/pkg/utils/meta/merge.go
index 18d4757..189cc66 100644
--- a/pkg/utils/meta/merge.go
+++ b/pkg/utils/meta/merge.go
@@ -5,21 +5,54 @@
 package meta
 
 import (
+	"strings"
+
 	"go.yaml.in/yaml/v4"
 
 	configv1alpha1 "github.com/gardener/gardener-landscape-kit/pkg/apis/config/v1alpha1"
 )
 
 const (
-	// GLKManagedMarker is the suffix that marks a comment as GLK-managed.
-	// It is used to strip GLK-owned annotations before re-running the merge (idempotency).
-	GLKManagedMarker = "# <-- glk-managed"
-
 	// GLKDefaultPrefix is the comment prefix for GLK-managed default annotations.
 	// It is exported so callers can use it as the strip anchor when removing annotations.
-	GLKDefaultPrefix = "# glk default: "
+	GLKDefaultPrefix = "# Attention - new default: "
 )
 
+// stripGLKAnnotation removes a GLK-managed annotation from a single comment string.
+// If the annotation is part of a multi-line comment, only the annotation line is removed.
+// If the annotation is appended to a value's line comment (e.g. "# user note  # Attention …"), the prefix and everything after it is stripped.
+func stripGLKAnnotation(comment string) string {
+	if !strings.Contains(comment, GLKDefaultPrefix) {
+		return comment
+	}
+	lines := strings.Split(comment, "\n")
+	out := make([]string, 0, len(lines))
+	for _, line := range lines {
+		idx := strings.Index(line, GLKDefaultPrefix)
+		if idx < 0 {
+			out = append(out, line)
+			continue
+		}
+		stripped := strings.TrimRight(line[:idx], " \t")
+		if stripped != "" {
+			out = append(out, stripped)
+		}
+	}
+	return strings.Join(out, "\n")
+}
+
+// stripGLKAnnotations removes GLK-managed annotations from all comment fields of a node.
+func stripGLKAnnotations(nodes ...*yaml.Node) {
+	for _, n := range nodes {
+		if n == nil {
+			continue
+		}
+		n.HeadComment = stripGLKAnnotation(n.HeadComment)
+		n.LineComment = stripGLKAnnotation(n.LineComment)
+		n.FootComment = stripGLKAnnotation(n.FootComment)
+	}
+}
+
 // threeWayMergeSection performs a three-way merge on a single YAML section
 func threeWayMergeSection(oldDefaultYaml, newDefaultYaml, currentYaml []byte, mode configv1alpha1.MergeMode) ([]byte, error) {
 	// Parse all three versions
@@ -127,16 +160,21 @@ func threeWayMerge(oldDefault, newDefault, current *yaml.Node, mode configv1alph
 				// Both default and current changed: keep current (user's value wins).
 				resultValue = currentValue
 				mergeNodeComments(oldValue, newValueNode, resultValue)
-				if mode == configv1alpha1.MergeModeInformative && !nodesEqual(newValueNode, currentValue, false) {
-					annotateConflict(resultKeyNode, resultValue, newValueNode)
+				if mode == configv1alpha1.MergeModeInformative {
+					if !nodesEqual(newValueNode, currentValue, false) {
+						annotateConflict(resultKeyNode, resultValue, newValueNode)
+					} else {
+						// Values converged — strip any lingering GLK annotation.
+						stripGLKAnnotations(resultKeyNode, resultValue)
+					}
 				}
 			default:
 				resultValue = currentValue
 				if oldExists {
 					mergeNodeComments(oldValue, newValueNode, resultValue)
-					if mode == configv1alpha1.MergeModeInformative && !nodesEqual(newValueNode, currentValue, false) {
-						// The operator's value differs from the current GLK default: annotate it.
-						annotateConflict(resultKeyNode, resultValue, newValueNode)
+					if mode == configv1alpha1.MergeModeInformative && nodesEqual(newValueNode, currentValue, false) {
+						// Values converged — strip any lingering GLK annotation.
+						stripGLKAnnotations(resultKeyNode, resultValue)
 					}
 				}
 			}
@@ -183,12 +221,12 @@ func annotateConflict(resultKeyNode, resultValue, newDefaultNode *yaml.Node) {
 
 // glkManagedLineComment returns a GLK-managed line comment for a scalar value conflict.
 func glkManagedLineComment(newValue string) string {
-	return GLKDefaultPrefix + newValue + "  " + GLKManagedMarker
+	return GLKDefaultPrefix + newValue
 }
 
 // glkManagedHeadComment returns a GLK-managed head comment for a complex node conflict.
 func glkManagedHeadComment(existingHead string) string {
-	annotation := GLKDefaultPrefix + "(complex node changed)  " + GLKManagedMarker
+	annotation := GLKDefaultPrefix + "(complex node changed)"
 	if existingHead == "" {
 		return annotation
 	}
@@ -306,7 +344,19 @@ func threeWayMergeSequence(oldDefault, newDefault, current *yaml.Node, mode conf
 		return result
 	}
 
-	// No identity key: fall back to full-string set-based merge.
+	// No identity key found.
+	// When all three sequences have the same length and all items are mappings,
+	// match items by position and three-way merge each pair. This handles cases
+	// where list items are modified but their count and order stay the same
+	// (e.g., a single scalar field in a mapping item is changed).
+	if len(oldDefault.Content) == len(newDefault.Content) && len(newDefault.Content) == len(current.Content) && allMappings(oldDefault, newDefault, current) {
+		for i := range current.Content {
+			result.Content = append(result.Content, threeWayMerge(oldDefault.Content[i], newDefault.Content[i], current.Content[i], mode))
+		}
+		return result
+	}
+
+	// Fall back to full-string set-based merge.
 	oldSet := make(map[string]bool)
 	for _, item := range oldDefault.Content {
 		oldSet[nodeToString(item)] = true
@@ -398,3 +448,15 @@ func mappingValue(node *yaml.Node, key string) string {
 	}
 	return ""
 }
+
+// allMappings reports whether every item in each of the given sequences is a mapping node.
+func allMappings(seqs ...*yaml.Node) bool {
+	for _, seq := range seqs {
+		for _, item := range seq.Content {
+			if item.Kind != yaml.MappingNode {
+				return false
+			}
+		}
+	}
+	return true
+}

From 3963393b2305a8a71603345bb5c1bad3e786ae8c Mon Sep 17 00:00:00 2001
From: Luca Bernstein <luca.bernstein@sap.com>
Date: Tue, 14 Apr 2026 11:29:21 +0200
Subject: [PATCH 7/8] Strip any pre-existing GLK annotation before appending
 the new one

---
 pkg/utils/files/writer_test.go | 64 ++++++++++++++++++++++++++++++++++
 pkg/utils/meta/merge.go        | 14 +++++---
 2 files changed, 73 insertions(+), 5 deletions(-)

diff --git a/pkg/utils/files/writer_test.go b/pkg/utils/files/writer_test.go
index 6475d64..65cf55c 100644
--- a/pkg/utils/files/writer_test.go
+++ b/pkg/utils/files/writer_test.go
@@ -256,6 +256,70 @@ data:
 				Expect(string(content)).To(ContainSubstring(meta.GLKDefaultPrefix + "v1.2.0"))
 			})
 
+			It("should replace the annotation when the GLK default changes again instead of accumulating", func() {
+				initial := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.0
+`)
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": initial}, "/landscape", "accum", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+
+				// Operator pins to v1.0.5
+				Expect(fs.WriteFile("/landscape/accum/test.yaml", []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.0.5 # pinned for production
+`), 0600)).To(Succeed())
+
+				// GLK ships v1.1.0 — annotation appears
+				v110 := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.1.0
+`)
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": v110}, "/landscape", "accum", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				content, err := fs.ReadFile("/landscape/accum/test.yaml")
+				Expect(err).NotTo(HaveOccurred())
+				Expect(string(content)).To(ContainSubstring(meta.GLKDefaultPrefix + "v1.1.0"))
+
+				// GLK ships v1.2.0 — annotation is replaced, not accumulated
+				v120 := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.2.0
+`)
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": v120}, "/landscape", "accum", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				content, err = fs.ReadFile("/landscape/accum/test.yaml")
+				Expect(err).NotTo(HaveOccurred())
+				Expect(string(content)).To(ContainSubstring("pinned for production"))
+				Expect(string(content)).To(ContainSubstring(meta.GLKDefaultPrefix + "v1.2.0"))
+				Expect(string(content)).NotTo(ContainSubstring(meta.GLKDefaultPrefix + "v1.1.0"))
+
+				// GLK ships v1.3.0 — again replaced, never more than one annotation
+				v130 := []byte(`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: test
+data:
+  version: v1.3.0
+`)
+				Expect(files.WriteObjectsToFilesystem(map[string][]byte{"test.yaml": v130}, "/landscape", "accum", fs, configv1alpha1.MergeModeInformative)).To(Succeed())
+				content, err = fs.ReadFile("/landscape/accum/test.yaml")
+				Expect(err).NotTo(HaveOccurred())
+				Expect(string(content)).To(ContainSubstring("pinned for production"))
+				Expect(string(content)).To(ContainSubstring(meta.GLKDefaultPrefix + "v1.3.0"))
+				Expect(string(content)).NotTo(ContainSubstring(meta.GLKDefaultPrefix + "v1.2.0"))
+				Expect(string(content)).NotTo(ContainSubstring(meta.GLKDefaultPrefix + "v1.1.0"))
+			})
+
 			It("should remove the annotation entirely when the GLK default reverts to the operator's value", func() {
 				initial := []byte(`apiVersion: v1
 kind: ConfigMap
diff --git a/pkg/utils/meta/merge.go b/pkg/utils/meta/merge.go
index 189cc66..d188642 100644
--- a/pkg/utils/meta/merge.go
+++ b/pkg/utils/meta/merge.go
@@ -28,12 +28,12 @@ func stripGLKAnnotation(comment string) string {
 	lines := strings.Split(comment, "\n")
 	out := make([]string, 0, len(lines))
 	for _, line := range lines {
-		idx := strings.Index(line, GLKDefaultPrefix)
-		if idx < 0 {
+		before, _, found := strings.Cut(line, GLKDefaultPrefix)
+		if !found {
 			out = append(out, line)
 			continue
 		}
-		stripped := strings.TrimRight(line[:idx], " \t")
+		stripped := strings.TrimRight(before, " \t")
 		if stripped != "" {
 			out = append(out, stripped)
 		}
@@ -209,12 +209,16 @@ func annotateConflict(resultKeyNode, resultValue, newDefaultNode *yaml.Node) {
 	switch newDefaultNode.Kind {
 	case yaml.ScalarNode:
 		annotation := glkManagedLineComment(newDefaultNode.Value)
-		if resultValue.LineComment != "" {
-			resultValue.LineComment = resultValue.LineComment + "  " + annotation
+		// Strip any pre-existing GLK annotation before appending the current one, so repeated runs replace rather than accumulate the comment.
+		stripped := stripGLKAnnotation(resultValue.LineComment)
+		if stripped != "" {
+			resultValue.LineComment = stripped + "  " + annotation
 		} else {
 			resultValue.LineComment = annotation
 		}
 	default:
+		// Strip existing GLK annotation from head comment before re-annotating.
+		resultKeyNode.HeadComment = stripGLKAnnotation(resultKeyNode.HeadComment)
 		resultKeyNode.HeadComment = glkManagedHeadComment(resultKeyNode.HeadComment)
 	}
 }

From 38709afad4293f37b191d90b193d4532c495527c Mon Sep 17 00:00:00 2001
From: Luca Bernstein <luca.bernstein@sap.com>
Date: Tue, 14 Apr 2026 17:01:52 +0200
Subject: [PATCH 8/8] Add defaults for LandscapeKitConfig

---
 pkg/apis/config/v1alpha1/defaults.go          | 14 +++++++++++++
 pkg/apis/config/v1alpha1/types.go             |  8 -------
 .../config/v1alpha1/zz_generated.defaults.go  |  5 +++++
 pkg/cmd/resolve/plain/plain.go                |  4 ++--
 pkg/components/flux/component_test.go         | 19 ++++++++++-------
 .../networking-calico/component_test.go       |  3 +++
 .../networking-cilium/component_test.go       |  3 +++
 .../os-gardenlinux/component_test.go          |  3 +++
 .../os-suse-chost/component_test.go           |  3 +++
 .../provider-alicloud/component_test.go       |  3 +++
 .../provider-aws/component_test.go            |  3 +++
 .../provider-azure/component_test.go          |  3 +++
 .../provider-gcp/component_test.go            |  3 +++
 .../provider-openstack/component_test.go      |  3 +++
 .../runtime-gvisor/component_test.go          |  3 +++
 .../shoot-cert-service/component_test.go      |  3 +++
 .../shoot-dns-service/component_test.go       |  3 +++
 .../component_test.go                         |  3 +++
 .../shoot-oidc-service/component_test.go      |  3 +++
 .../gardener/garden/component_test.go         |  3 +++
 .../gardener/operator/component_test.go       |  3 +++
 .../virtual-garden-access/component_test.go   |  3 +++
 pkg/components/types.go                       |  2 +-
 pkg/components/types_test.go                  | 21 +++++++------------
 .../garden-config/component_test.go           |  3 +++
 pkg/registry/registry_test.go                 |  6 +++++-
 pkg/utils/kustomization/kustomization_test.go |  4 ++++
 pkg/utils/test/kustomize.go                   |  1 +
 28 files changed, 105 insertions(+), 33 deletions(-)

diff --git a/pkg/apis/config/v1alpha1/defaults.go b/pkg/apis/config/v1alpha1/defaults.go
index 9c3a743..55c6c64 100644
--- a/pkg/apis/config/v1alpha1/defaults.go
+++ b/pkg/apis/config/v1alpha1/defaults.go
@@ -3,3 +3,17 @@
 // SPDX-License-Identifier: Apache-2.0
 
 package v1alpha1
+
+// SetDefaults_LandscapeKitConfiguration sets default values for LandscapeKitConfiguration fields.
+func SetDefaults_LandscapeKitConfiguration(obj *LandscapeKitConfiguration) {
+	if obj.VersionConfig == nil {
+		obj.VersionConfig = &VersionConfiguration{}
+	}
+	if obj.VersionConfig.DefaultVersionsUpdateStrategy == nil {
+		obj.VersionConfig.DefaultVersionsUpdateStrategy = new(DefaultVersionsUpdateStrategyDisabled)
+	}
+
+	if obj.MergeMode == nil {
+		obj.MergeMode = new(MergeModeInformative)
+	}
+}
diff --git a/pkg/apis/config/v1alpha1/types.go b/pkg/apis/config/v1alpha1/types.go
index 076b929..1ad665e 100644
--- a/pkg/apis/config/v1alpha1/types.go
+++ b/pkg/apis/config/v1alpha1/types.go
@@ -140,11 +140,3 @@ var AllowedMergeModes = []string{
 	string(MergeModeInformative),
 	string(MergeModeSilent),
 }
-
-// GetMergeMode returns the configured MergeMode, defaulting to MergeModeInformative.
-func (c *LandscapeKitConfiguration) GetMergeMode() MergeMode {
-	if c == nil || c.MergeMode == nil {
-		return MergeModeInformative
-	}
-	return *c.MergeMode
-}
diff --git a/pkg/apis/config/v1alpha1/zz_generated.defaults.go b/pkg/apis/config/v1alpha1/zz_generated.defaults.go
index dce68e6..e134802 100644
--- a/pkg/apis/config/v1alpha1/zz_generated.defaults.go
+++ b/pkg/apis/config/v1alpha1/zz_generated.defaults.go
@@ -17,5 +17,10 @@ import (
 // Public to allow building arbitrary schemes.
 // All generated defaulters are covering - they call all nested defaulters.
 func RegisterDefaults(scheme *runtime.Scheme) error {
+	scheme.AddTypeDefaultingFunc(&LandscapeKitConfiguration{}, func(obj interface{}) { SetObjectDefaults_LandscapeKitConfiguration(obj.(*LandscapeKitConfiguration)) })
 	return nil
 }
+
+func SetObjectDefaults_LandscapeKitConfiguration(in *LandscapeKitConfiguration) {
+	SetDefaults_LandscapeKitConfiguration(in)
+}
diff --git a/pkg/cmd/resolve/plain/plain.go b/pkg/cmd/resolve/plain/plain.go
index 6ac366d..96ce705 100644
--- a/pkg/cmd/resolve/plain/plain.go
+++ b/pkg/cmd/resolve/plain/plain.go
@@ -110,7 +110,7 @@ func (o *Options) loadConfigFile(filename string) error {
 
 func run(_ context.Context, opts *Options) error {
 	if opts.Config != nil && opts.Config.VersionConfig != nil {
-		if updateStrategy := opts.Config.VersionConfig.DefaultVersionsUpdateStrategy; updateStrategy != nil && *updateStrategy == configv1alpha1.DefaultVersionsUpdateStrategyReleaseBranch {
+		if *opts.Config.VersionConfig.DefaultVersionsUpdateStrategy == configv1alpha1.DefaultVersionsUpdateStrategyReleaseBranch {
 			opts.Log.Info("Updating default component vector file from the release branch", "branch", utilscomponentvector.GetReleaseBranchName())
 			var err error
 			// The componentvector.DefaultComponentsYAML is intentionally overridden, so that subsequently it can be used to extract the updated default component vector versions.
@@ -142,7 +142,7 @@ func run(_ context.Context, opts *Options) error {
 	}, "\n") + "\n")
 	newDefaultBytes = append(header, newDefaultBytes...)
 
-	if err := utilsfiles.WriteObjectsToFilesystem(map[string][]byte{utilscomponentvector.ComponentVectorFilename: newDefaultBytes}, opts.TargetDirPath, "", opts.fs, opts.Config.GetMergeMode()); err != nil {
+	if err := utilsfiles.WriteObjectsToFilesystem(map[string][]byte{utilscomponentvector.ComponentVectorFilename: newDefaultBytes}, opts.TargetDirPath, "", opts.fs, *opts.Config.MergeMode); err != nil {
 		return fmt.Errorf("failed to write updated component vector: %w", err)
 	}
 
diff --git a/pkg/components/flux/component_test.go b/pkg/components/flux/component_test.go
index e0df97f..562ced8 100644
--- a/pkg/components/flux/component_test.go
+++ b/pkg/components/flux/component_test.go
@@ -54,6 +54,16 @@ var _ = Describe("Flux Component Generation", func() {
 
 		fs = afero.Afero{Fs: afero.NewMemMapFs()}
 
+		config := &v1alpha1.LandscapeKitConfiguration{
+			Git: &v1alpha1.GitRepository{
+				URL: repoURL,
+				Paths: v1alpha1.PathConfiguration{
+					Landscape: relativeLandscapePath,
+				},
+			},
+		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(config)
+
 		var err error
 		opts, err = components.NewLandscapeOptions(
 			&generateoptions.Options{
@@ -61,14 +71,7 @@ var _ = Describe("Flux Component Generation", func() {
 					Log: logr.Discard(),
 				},
 				TargetDirPath: targetPath,
-				Config: &v1alpha1.LandscapeKitConfiguration{
-					Git: &v1alpha1.GitRepository{
-						URL: repoURL,
-						Paths: v1alpha1.PathConfiguration{
-							Landscape: relativeLandscapePath,
-						},
-					},
-				},
+				Config:        config,
 			},
 			fs,
 		)
diff --git a/pkg/components/gardener-extensions/networking-calico/component_test.go b/pkg/components/gardener-extensions/networking-calico/component_test.go
index 351e731..e1b6b34 100644
--- a/pkg/components/gardener-extensions/networking-calico/component_test.go
+++ b/pkg/components/gardener-extensions/networking-calico/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/networking-cilium/component_test.go b/pkg/components/gardener-extensions/networking-cilium/component_test.go
index 802045e..5093442 100644
--- a/pkg/components/gardener-extensions/networking-cilium/component_test.go
+++ b/pkg/components/gardener-extensions/networking-cilium/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/os-gardenlinux/component_test.go b/pkg/components/gardener-extensions/os-gardenlinux/component_test.go
index 096175c..c93dde5 100644
--- a/pkg/components/gardener-extensions/os-gardenlinux/component_test.go
+++ b/pkg/components/gardener-extensions/os-gardenlinux/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/os-suse-chost/component_test.go b/pkg/components/gardener-extensions/os-suse-chost/component_test.go
index fb3fa11..eb27155 100644
--- a/pkg/components/gardener-extensions/os-suse-chost/component_test.go
+++ b/pkg/components/gardener-extensions/os-suse-chost/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/provider-alicloud/component_test.go b/pkg/components/gardener-extensions/provider-alicloud/component_test.go
index 499a135..c94be71 100644
--- a/pkg/components/gardener-extensions/provider-alicloud/component_test.go
+++ b/pkg/components/gardener-extensions/provider-alicloud/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/provider-aws/component_test.go b/pkg/components/gardener-extensions/provider-aws/component_test.go
index 17a395e..678720d 100644
--- a/pkg/components/gardener-extensions/provider-aws/component_test.go
+++ b/pkg/components/gardener-extensions/provider-aws/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/provider-azure/component_test.go b/pkg/components/gardener-extensions/provider-azure/component_test.go
index 481f991..a65922f 100644
--- a/pkg/components/gardener-extensions/provider-azure/component_test.go
+++ b/pkg/components/gardener-extensions/provider-azure/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/provider-gcp/component_test.go b/pkg/components/gardener-extensions/provider-gcp/component_test.go
index 7b93256..0b1dd0f 100644
--- a/pkg/components/gardener-extensions/provider-gcp/component_test.go
+++ b/pkg/components/gardener-extensions/provider-gcp/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/provider-openstack/component_test.go b/pkg/components/gardener-extensions/provider-openstack/component_test.go
index bad84c5..f4119b9 100644
--- a/pkg/components/gardener-extensions/provider-openstack/component_test.go
+++ b/pkg/components/gardener-extensions/provider-openstack/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/runtime-gvisor/component_test.go b/pkg/components/gardener-extensions/runtime-gvisor/component_test.go
index 65aede9..9c73ecc 100644
--- a/pkg/components/gardener-extensions/runtime-gvisor/component_test.go
+++ b/pkg/components/gardener-extensions/runtime-gvisor/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/shoot-cert-service/component_test.go b/pkg/components/gardener-extensions/shoot-cert-service/component_test.go
index d7d21bb..35b75d9 100644
--- a/pkg/components/gardener-extensions/shoot-cert-service/component_test.go
+++ b/pkg/components/gardener-extensions/shoot-cert-service/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/shoot-dns-service/component_test.go b/pkg/components/gardener-extensions/shoot-dns-service/component_test.go
index 9fb02d3..747c03d 100644
--- a/pkg/components/gardener-extensions/shoot-dns-service/component_test.go
+++ b/pkg/components/gardener-extensions/shoot-dns-service/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/shoot-networking-problemdetector/component_test.go b/pkg/components/gardener-extensions/shoot-networking-problemdetector/component_test.go
index 1a7e7f3..7f4d2e5 100644
--- a/pkg/components/gardener-extensions/shoot-networking-problemdetector/component_test.go
+++ b/pkg/components/gardener-extensions/shoot-networking-problemdetector/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener-extensions/shoot-oidc-service/component_test.go b/pkg/components/gardener-extensions/shoot-oidc-service/component_test.go
index 667aedc..683bad3 100644
--- a/pkg/components/gardener-extensions/shoot-oidc-service/component_test.go
+++ b/pkg/components/gardener-extensions/shoot-oidc-service/component_test.go
@@ -35,7 +35,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -68,6 +70,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener/garden/component_test.go b/pkg/components/gardener/garden/component_test.go
index 781adff..455d17f 100644
--- a/pkg/components/gardener/garden/component_test.go
+++ b/pkg/components/gardener/garden/component_test.go
@@ -30,7 +30,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -62,6 +64,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener/operator/component_test.go b/pkg/components/gardener/operator/component_test.go
index 5870a6d..d080114 100644
--- a/pkg/components/gardener/operator/component_test.go
+++ b/pkg/components/gardener/operator/component_test.go
@@ -37,7 +37,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -86,6 +88,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/gardener/virtual-garden-access/component_test.go b/pkg/components/gardener/virtual-garden-access/component_test.go
index 58c8856..ed74d8f 100644
--- a/pkg/components/gardener/virtual-garden-access/component_test.go
+++ b/pkg/components/gardener/virtual-garden-access/component_test.go
@@ -30,7 +30,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -70,6 +72,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/components/types.go b/pkg/components/types.go
index 17cdf45..fa23a42 100644
--- a/pkg/components/types.go
+++ b/pkg/components/types.go
@@ -127,7 +127,7 @@ func NewOptions(opts *generateoptions.Options, fs afero.Afero) (Options, error)
 		targetPath:      path.Clean(opts.TargetDirPath),
 		filesystem:      fs,
 		logger:          opts.Log,
-		mergeMode:       opts.Config.GetMergeMode(),
+		mergeMode:       *opts.Config.MergeMode,
 	}, nil
 }
 
diff --git a/pkg/components/types_test.go b/pkg/components/types_test.go
index cf46888..c08cd7d 100644
--- a/pkg/components/types_test.go
+++ b/pkg/components/types_test.go
@@ -34,7 +34,9 @@ var _ = Describe("Types", func() {
 			opts = &options.Options{
 				Options:       &cmd.Options{},
 				TargetDirPath: "",
+				Config:        &v1alpha1.LandscapeKitConfiguration{},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(opts.Config)
 		})
 
 		Describe("#GetTargetPath", func() {
@@ -105,20 +107,9 @@ var _ = Describe("Types", func() {
 				Expect(exists).To(BeFalse())
 			})
 
-			It("should return an empty component vector when config is nil", func() {
-				opts.Config = nil
-
-				componentOpts, err := components.NewOptions(opts, fs)
-
-				Expect(err).NotTo(HaveOccurred())
-				Expect(componentOpts.GetComponentVector()).NotTo(BeNil())
-
-				_, exists := componentOpts.GetComponentVector().FindComponentVersion("test-component")
-				Expect(exists).To(BeFalse())
-			})
-
-			It("should return an empty component vector when VersionConfig is nil", func() {
+			It("should return an empty component vector when config is empty", func() {
 				opts.Config = &v1alpha1.LandscapeKitConfiguration{}
+				v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(opts.Config)
 
 				componentOpts, err := components.NewOptions(opts, fs)
 
@@ -199,7 +190,9 @@ var _ = Describe("Types", func() {
 						Log: logger,
 					},
 					TargetDirPath: "/path/to/target",
+					Config:        &v1alpha1.LandscapeKitConfiguration{},
 				}
+				v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(opts.Config)
 
 				result, err := components.NewOptions(opts, fs)
 
@@ -232,6 +225,7 @@ var _ = Describe("Types", func() {
 				},
 				TargetDirPath: "",
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(opts.Config)
 		})
 
 		Describe("#GetGitRepository", func() {
@@ -285,6 +279,7 @@ var _ = Describe("Types", func() {
 						},
 					},
 				}
+				v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(opts.Config)
 
 				result, err := components.NewLandscapeOptions(opts, fs)
 
diff --git a/pkg/components/virtual-garden/garden-config/component_test.go b/pkg/components/virtual-garden/garden-config/component_test.go
index b17dca5..5886dc9 100644
--- a/pkg/components/virtual-garden/garden-config/component_test.go
+++ b/pkg/components/virtual-garden/garden-config/component_test.go
@@ -30,7 +30,9 @@ var _ = Describe("Component Generation", func() {
 		generateOpts = &generateoptions.Options{
 			TargetDirPath: "/repo/baseDir",
 			Options:       cmdOpts,
+			Config:        &v1alpha1.LandscapeKitConfiguration{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 	})
 
 	Describe("#GenerateBase", func() {
@@ -67,6 +69,7 @@ var _ = Describe("Component Generation", func() {
 			generateOpts.Config = &v1alpha1.LandscapeKitConfiguration{
 				Git: &v1alpha1.GitRepository{Paths: v1alpha1.PathConfiguration{Landscape: "./landscapeDir", Base: "./baseDir"}},
 			}
+			v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 		})
 
 		It("should generate only the flux kustomization into the landscape dir", func() {
diff --git a/pkg/registry/registry_test.go b/pkg/registry/registry_test.go
index 396db1b..d53e0ed 100644
--- a/pkg/registry/registry_test.go
+++ b/pkg/registry/registry_test.go
@@ -35,10 +35,14 @@ var _ = Describe("Registry", func() {
 		config = &v1alpha1.LandscapeKitConfiguration{
 			Git: &v1alpha1.GitRepository{},
 		}
+		v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(config)
 
 		var err error
 		options, err = components.NewOptions(
-			&generateoptions.Options{Options: &cmd.Options{Log: logr.Discard()}},
+			&generateoptions.Options{
+				Options: &cmd.Options{Log: logr.Discard()},
+				Config:  config,
+			},
 			afero.Afero{Fs: afero.NewMemMapFs()},
 		)
 		Expect(err).NotTo(HaveOccurred())
diff --git a/pkg/utils/kustomization/kustomization_test.go b/pkg/utils/kustomization/kustomization_test.go
index ff1815a..b7cf67a 100644
--- a/pkg/utils/kustomization/kustomization_test.go
+++ b/pkg/utils/kustomization/kustomization_test.go
@@ -81,11 +81,15 @@ var _ = Describe("Kustomization", func() {
 		BeforeEach(func() {
 			fs = afero.Afero{Fs: afero.NewMemMapFs()}
 
+			config := &configv1alpha1.LandscapeKitConfiguration{}
+			configv1alpha1.SetObjectDefaults_LandscapeKitConfiguration(config)
+
 			var err error
 			opts, err = components.NewOptions(&generateoptions.Options{
 				Options: &cmd.Options{
 					Log: logr.Discard(),
 				},
+				Config:        config,
 				TargetDirPath: "/absolute/path/with/../to/repo/landscape",
 			}, fs)
 			Expect(err).NotTo(HaveOccurred())
diff --git a/pkg/utils/test/kustomize.go b/pkg/utils/test/kustomize.go
index 780b7a5..3f5eccf 100644
--- a/pkg/utils/test/kustomize.go
+++ b/pkg/utils/test/kustomize.go
@@ -118,6 +118,7 @@ func KustomizeComponent(
 			},
 		}
 	)
+	v1alpha1.SetObjectDefaults_LandscapeKitConfiguration(generateOpts.Config)
 
 	baseOpts, err := components.NewOptions(generateOpts, fs)
 	if err != nil {