diff --git a/common/common.go b/common/common.go
index 3872b0d7ef206..0b02807c29ba8 100644
--- a/common/common.go
+++ b/common/common.go
@@ -81,6 +81,10 @@ const (
 	// LabelValueSecretTypeCluster indicates a secret type of cluster
 	LabelValueSecretTypeCluster = "cluster"
 
+	// AnnotationCompareOptions is a comma-separated list of options for comparison
+	AnnotationCompareOptions = "argocd.argoproj.io/compare-options"
+	// AnnotationSyncOptions is a comma-separated list of options for syncing
+	AnnotationSyncOptions = "argocd.argoproj.io/sync-options"
 	// AnnotationSyncWave indicates which wave of the sync the resource or hook should be in
 	AnnotationSyncWave = "argocd.argoproj.io/sync-wave"
 	// AnnotationKeyHook contains the hook type of a resource
diff --git a/controller/state.go b/controller/state.go
index 65ab568c5a364..e3d8ce9ac3575 100644
--- a/controller/state.go
+++ b/controller/state.go
@@ -297,10 +297,11 @@ func (m *appStateManager) CompareAppState(app *v1alpha1.Application, revision st
 	syncCode := v1alpha1.SyncStatusCodeSynced
 	managedResources := make([]managedResource, len(targetObjs))
 	resourceSummaries := make([]v1alpha1.ResourceStatus, len(targetObjs))
-	for i := 0; i < len(targetObjs); i++ {
-		obj := managedLiveObj[i]
+	for i, targetObj := range targetObjs {
+		liveObj := managedLiveObj[i]
+		obj := liveObj
 		if obj == nil {
-			obj = targetObjs[i]
+			obj = targetObj
 		}
 		if obj == nil {
 			continue
@@ -319,13 +320,17 @@ func (m *appStateManager) CompareAppState(app *v1alpha1.Application, revision st
 		diffResult := diffResults.Diffs[i]
 		if resState.Hook || resource.Ignore(obj) {
 			// For resource hooks, don't store sync status, and do not affect overall sync status
-		} else if diffResult.Modified || targetObjs[i] == nil || managedLiveObj[i] == nil {
+		} else if diffResult.Modified || targetObj == nil || liveObj == nil {
 			// Set resource state to OutOfSync since one of the following is true:
 			// * target and live resource are different
 			// * target resource not defined and live resource is extra
 			// * target resource present but live resource is missing
 			resState.Status = v1alpha1.SyncStatusCodeOutOfSync
-			syncCode = v1alpha1.SyncStatusCodeOutOfSync
+			// we ignore the status if the obj needs pruning AND we have the annotation
+			needsPruning := targetObj == nil && liveObj != nil
+			if !(needsPruning && resource.HasAnnotationOption(obj, common.AnnotationCompareOptions, "IgnoreExtraneous")) {
+				syncCode = v1alpha1.SyncStatusCodeOutOfSync
+			}
 		} else {
 			resState.Status = v1alpha1.SyncStatusCodeSynced
 		}
@@ -335,8 +340,8 @@ func (m *appStateManager) CompareAppState(app *v1alpha1.Application, revision st
 			Group:     resState.Group,
 			Kind:      resState.Kind,
 			Version:   resState.Version,
-			Live:      managedLiveObj[i],
-			Target:    targetObjs[i],
+			Live:      liveObj,
+			Target:    targetObj,
 			Diff:      diffResult,
 			Hook:      resState.Hook,
 		}
diff --git a/controller/state_test.go b/controller/state_test.go
index 2c7af500d3239..6ba9178f05aaa 100644
--- a/controller/state_test.go
+++ b/controller/state_test.go
@@ -117,6 +117,33 @@ func TestCompareAppStateHook(t *testing.T) {
 	assert.Equal(t, 0, len(compRes.conditions))
 }
 
+// checks that ignore resources are detected, but excluded from status
+func TestCompareAppStateCompareOptionIgnoreExtraneous(t *testing.T) {
+	pod := test.NewPod()
+	pod.SetAnnotations(map[string]string{common.AnnotationCompareOptions: "IgnoreExtraneous"})
+	app := newFakeApp()
+	data := fakeData{
+		apps: []runtime.Object{app},
+		manifestResponse: &repository.ManifestResponse{
+			Manifests: []string{},
+			Namespace: test.FakeDestNamespace,
+			Server:    test.FakeClusterURL,
+			Revision:  "abc123",
+		},
+		managedLiveObjs: make(map[kube.ResourceKey]*unstructured.Unstructured),
+	}
+	ctrl := newFakeController(&data)
+
+	compRes, err := ctrl.appStateManager.CompareAppState(app, "", app.Spec.Source, false)
+
+	assert.NoError(t, err)
+	assert.NotNil(t, compRes)
+	assert.Equal(t, argoappv1.SyncStatusCodeSynced, compRes.syncStatus.Status)
+	assert.Len(t, compRes.resources, 0)
+	assert.Len(t, compRes.managedResources, 0)
+	assert.Len(t, compRes.conditions, 0)
+}
+
 // TestCompareAppStateExtraHook tests when there is an extra _hook_ object in live but not defined in git
 func TestCompareAppStateExtraHook(t *testing.T) {
 	pod := test.NewPod()
diff --git a/controller/sync.go b/controller/sync.go
index f6e7ca065b655..896a05fc29a24 100644
--- a/controller/sync.go
+++ b/controller/sync.go
@@ -16,6 +16,7 @@ import (
 	"k8s.io/client-go/dynamic"
 	"k8s.io/client-go/rest"
 
+	"github.com/argoproj/argo-cd/common"
 	"github.com/argoproj/argo-cd/controller/metrics"
 	"github.com/argoproj/argo-cd/pkg/apis/application/v1alpha1"
 	listersv1alpha1 "github.com/argoproj/argo-cd/pkg/client/listers/application/v1alpha1"
@@ -23,6 +24,7 @@ import (
 	"github.com/argoproj/argo-cd/util/health"
 	"github.com/argoproj/argo-cd/util/hook"
 	"github.com/argoproj/argo-cd/util/kube"
+	"github.com/argoproj/argo-cd/util/resource"
 )
 
 type syncContext struct {
@@ -473,7 +475,11 @@ func (sc *syncContext) applyObject(targetObj *unstructured.Unstructured, dryRun
 
 // pruneObject deletes the object if both prune is true and dryRun is false. Otherwise appropriate message
 func (sc *syncContext) pruneObject(liveObj *unstructured.Unstructured, prune, dryRun bool) (v1alpha1.ResultCode, string) {
-	if prune {
+	if !prune {
+		return v1alpha1.ResultCodePruneSkipped, "ignored (requires pruning)"
+	} else if resource.HasAnnotationOption(liveObj, common.AnnotationSyncOptions, "Prune=false") {
+		return v1alpha1.ResultCodePruneSkipped, "ignored (no prune)"
+	} else {
 		if dryRun {
 			return v1alpha1.ResultCodePruned, "pruned (dry run)"
 		} else {
@@ -487,8 +493,6 @@ func (sc *syncContext) pruneObject(liveObj *unstructured.Unstructured, prune, dr
 			}
 			return v1alpha1.ResultCodePruned, "pruned"
 		}
-	} else {
-		return v1alpha1.ResultCodePruneSkipped, "ignored (requires pruning)"
 	}
 }
 
diff --git a/controller/sync_test.go b/controller/sync_test.go
index 202130777055f..d6af8ce3f0970 100644
--- a/controller/sync_test.go
+++ b/controller/sync_test.go
@@ -305,6 +305,26 @@ func TestDontSyncOrPruneHooks(t *testing.T) {
 	assert.Equal(t, v1alpha1.OperationSucceeded, syncCtx.opState.Phase)
 }
 
+// make sure that we do not prune resources with Prune=false
+func TestDontPrunePruneFalse(t *testing.T) {
+	syncCtx := newTestSyncCtx()
+	pod := test.NewPod()
+	pod.SetAnnotations(map[string]string{common.AnnotationSyncOptions: "Prune=false"})
+	pod.SetNamespace(test.FakeArgoCDNamespace)
+	syncCtx.compareResult = &comparisonResult{managedResources: []managedResource{{Live: pod}}}
+
+	syncCtx.sync()
+
+	assert.Equal(t, v1alpha1.OperationRunning, syncCtx.opState.Phase)
+	assert.Len(t, syncCtx.syncRes.Resources, 1)
+	assert.Equal(t, v1alpha1.ResultCodePruneSkipped, syncCtx.syncRes.Resources[0].Status)
+	assert.Equal(t, "ignored (no prune)", syncCtx.syncRes.Resources[0].Message)
+
+	syncCtx.sync()
+
+	assert.Equal(t, v1alpha1.OperationSucceeded, syncCtx.opState.Phase)
+}
+
 func TestSelectiveSyncOnly(t *testing.T) {
 	syncCtx := newTestSyncCtx()
 	pod1 := test.NewPod()
diff --git a/docs/assets/compare-option-ignore-needs-pruning.png b/docs/assets/compare-option-ignore-needs-pruning.png
new file mode 100644
index 0000000000000..78cfe688f9a07
Binary files /dev/null and b/docs/assets/compare-option-ignore-needs-pruning.png differ
diff --git a/docs/assets/sync-option-no-prune-sync-status.png b/docs/assets/sync-option-no-prune-sync-status.png
new file mode 100644
index 0000000000000..ae117e31d3759
Binary files /dev/null and b/docs/assets/sync-option-no-prune-sync-status.png differ
diff --git a/docs/assets/sync-option-no-prune.png b/docs/assets/sync-option-no-prune.png
new file mode 100644
index 0000000000000..1da6a0e1b8c46
Binary files /dev/null and b/docs/assets/sync-option-no-prune.png differ
diff --git a/docs/user-guide/compare-options.md b/docs/user-guide/compare-options.md
new file mode 100644
index 0000000000000..88d9350f7f97a
--- /dev/null
+++ b/docs/user-guide/compare-options.md
@@ -0,0 +1,34 @@
+# Compare Options
+
+## Ignoring Resources That Are Extraneous
+
+You may wish to exclude resources from the app's overall sync status under certain circumstances. E.g. if they are generated by a tool. This can be done by adding this annotation:
+
+```yaml
+metadata:
+  annotations:
+    argocd.argoproj.io/compare-options: IgnoreExtraneous
+```
+
+![compare option needs pruning](../assets/compare-option-ignore-needs-pruning.png)
+
+!!! note
+    This only affects the sync status. If the resource's health is degraded, then the app will also be degraded.
+
+Kustomize has a feature that allows you to generate config maps ([read more ⧉](https://github.com/kubernetes-sigs/kustomize/blob/master/examples/configGeneration.md)). You can set `generatorOptions` to add this annotation so that your app remains in sync:
+
+```yaml
+configMapGenerator:
+  - name: my-map
+    literals:
+      - foo=bar
+generatorOptions:
+  annotations:
+    argocd.argoproj.io/compare-options: IgnoreExtraneous
+kind: Kustomization
+``` 
+ 
+!!! note
+    `generatorOptions` adds annotations to both config maps and secrets ([read more ⧉](https://github.com/kubernetes-sigs/kustomize/blob/master/examples/generatorOptions.md)).
+    
+You may wish to combine this with the [`Prune=false` sync option](sync-options.md).
diff --git a/docs/user-guide/kustomize.md b/docs/user-guide/kustomize.md
index be6f485ec0877..fc9303070f242 100644
--- a/docs/user-guide/kustomize.md
+++ b/docs/user-guide/kustomize.md
@@ -10,4 +10,7 @@ You have three configuration options for Kustomize:
 * `imageTags` is a list of Kustomize 1.0 image tag overrides
 * `images` is a list of Kustomize 2.0 image overrides
     
-To use Kustomize with an overlay, point your path to the overlay.
\ No newline at end of file
+To use Kustomize with an overlay, point your path to the overlay.
+
+!!! tip
+    If you're generating resources, you should read up how to ignore those generated resources using the [`IgnoreExtraneous` compare option](compare-options.md).
diff --git a/docs/user-guide/sync-options.md b/docs/user-guide/sync-options.md
new file mode 100644
index 0000000000000..4e8e5f6c7b41c
--- /dev/null
+++ b/docs/user-guide/sync-options.md
@@ -0,0 +1,24 @@
+# Sync Options
+
+## No Prune Resources
+
+You may wish to prevent an object from being pruned:
+
+```yaml
+metadata:
+  annotations:
+    argocd.argoproj.io/sync-options: Prune=false
+```
+
+In the UI, the pod will simply appear as out-of-sync:
+
+![sync option no prune](../assets/sync-option-no-prune.png)
+
+
+The sync-status panel shows that pruning was skipped, and why:
+
+![sync option no prune](../assets/sync-option-no-prune-sync-status.png)
+
+!!! note
+    The app will be out of sync if Argo CD expects a resource to be pruned. You may wish to use this along with [compare options](compare-options.md).
+
diff --git a/mkdocs.yml b/mkdocs.yml
index 6f502141eff32..b8954e7bb8d37 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -48,6 +48,8 @@ nav:
     - user-guide/private-repositories.md
     - user-guide/auto_sync.md
     - user-guide/diffing.md
+    - user-guide/compare-options.md
+    - user-guide/sync-options.md
     - user-guide/parameters.md
     - user-guide/tracking_strategies.md
     - user-guide/resource_hooks.md
diff --git a/test/e2e/app_management_test.go b/test/e2e/app_management_test.go
index 23b67dcdd579c..c5a7c57b4a9dd 100644
--- a/test/e2e/app_management_test.go
+++ b/test/e2e/app_management_test.go
@@ -306,15 +306,19 @@ func TestResourceDiffing(t *testing.T) {
 }
 
 func TestDeprecatedExtensions(t *testing.T) {
-	testEdgeCasesApplicationResources(t, "deprecated-extensions")
+	testEdgeCasesApplicationResources(t, "deprecated-extensions", OperationRunning, HealthStatusProgressing)
 }
 
 func TestCRDs(t *testing.T) {
-	testEdgeCasesApplicationResources(t, "crd-creation")
+	testEdgeCasesApplicationResources(t, "crd-creation", OperationSucceeded, HealthStatusHealthy)
 }
 
 func TestDuplicatedResources(t *testing.T) {
-	testEdgeCasesApplicationResources(t, "duplicated-resources")
+	testEdgeCasesApplicationResources(t, "duplicated-resources", OperationSucceeded, HealthStatusHealthy)
+}
+
+func TestConfigMap(t *testing.T) {
+	testEdgeCasesApplicationResources(t, "config-map", OperationSucceeded, HealthStatusHealthy)
 }
 
 func TestFailedConversion(t *testing.T) {
@@ -323,17 +327,19 @@ func TestFailedConversion(t *testing.T) {
 		errors.FailOnErr(fixture.Run("", "kubectl", "delete", "apiservice", "v1beta1.metrics.k8s.io"))
 	}()
 
-	testEdgeCasesApplicationResources(t, "failed-conversion")
+	testEdgeCasesApplicationResources(t, "failed-conversion", OperationSucceeded, HealthStatusHealthy)
 }
 
-func testEdgeCasesApplicationResources(t *testing.T, appPath string) {
+func testEdgeCasesApplicationResources(t *testing.T, appPath string, phase OperationPhase, statusCode HealthStatusCode) {
 	Given(t).
 		Path(appPath).
 		When().
 		Create().
 		Sync().
 		Then().
+		Expect(OperationPhaseIs(phase)).
 		Expect(SyncStatusIs(SyncStatusCodeSynced)).
+		Expect(HealthIs(statusCode)).
 		And(func(app *Application) {
 			diffOutput, err := fixture.RunCli("app", "diff", app.Name, "--local", path.Join("testdata", appPath))
 			assert.Empty(t, diffOutput)
@@ -504,3 +510,51 @@ func TestPermissions(t *testing.T) {
 	assert.True(t, destinationErrorExist)
 	assert.True(t, sourceErrorExist)
 }
+
+// make sure that if we deleted a resource from the app, it is not pruned if annotated with Prune=false
+func TestSyncOptionPruneFalse(t *testing.T) {
+	Given(t).
+		Path("two-nice-pods").
+		When().
+		PatchFile("pod-1.yaml", `[{"op": "add", "path": "/metadata/annotations", "value": {"argocd.argoproj.io/sync-options": "Prune=false"}}]`).
+		Create().
+		Sync().
+		Then().
+		Expect(OperationPhaseIs(OperationSucceeded)).
+		Expect(SyncStatusIs(SyncStatusCodeSynced)).
+		When().
+		DeleteFile("pod-1.yaml").
+		Refresh(RefreshTypeHard).
+		Sync().
+		Then().
+		Expect(OperationPhaseIs(OperationSucceeded)).
+		Expect(SyncStatusIs(SyncStatusCodeOutOfSync)).
+		Expect(ResourceSyncStatusIs("Pod", "pod-1", SyncStatusCodeOutOfSync))
+}
+
+// make sure that, if we have a resource that needs pruning, but we're ignoring it, the app is in-sync
+func TestCompareOptionIgnoreExtraneous(t *testing.T) {
+	Given(t).
+		Path("two-nice-pods").
+		When().
+		PatchFile("pod-1.yaml", `[{"op": "add", "path": "/metadata/annotations", "value": {"argocd.argoproj.io/compare-options": "IgnoreExtraneous"}}]`).
+		Create().
+		Sync().
+		Then().
+		Expect(OperationPhaseIs(OperationSucceeded)).
+		Expect(SyncStatusIs(SyncStatusCodeSynced)).
+		When().
+		DeleteFile("pod-1.yaml").
+		Refresh(RefreshTypeHard).
+		Then().
+		Expect(SyncStatusIs(SyncStatusCodeSynced)).
+		And(func(app *Application) {
+			assert.Len(t, app.Status.Resources, 2)
+			assert.Equal(t, SyncStatusCodeOutOfSync, app.Status.Resources[1].Status)
+		}).
+		When().
+		Sync().
+		Then().
+		Expect(OperationPhaseIs(OperationSucceeded)).
+		Expect(SyncStatusIs(SyncStatusCodeSynced))
+}
diff --git a/test/e2e/fixture/fixture.go b/test/e2e/fixture/fixture.go
index 57a69cca9cf4b..abb7bc0c78859 100644
--- a/test/e2e/fixture/fixture.go
+++ b/test/e2e/fixture/fixture.go
@@ -170,7 +170,7 @@ func EnsureCleanState(t *testing.T) {
 
 	// new random ID
 	id = dnsFriendly(t.Name())
-	repoUrl = fmt.Sprintf("file:///%s", repoDirectory())
+	repoUrl = fmt.Sprintf("file://%s", repoDirectory())
 
 	// create tmp dir
 	FailOnErr(Run("", "mkdir", "-p", tmpDir))
diff --git a/test/e2e/kustomize_test.go b/test/e2e/kustomize_test.go
index 16a80dae5e1c3..75ccf131457fb 100644
--- a/test/e2e/kustomize_test.go
+++ b/test/e2e/kustomize_test.go
@@ -52,3 +52,56 @@ func TestKustomize2AppSource(t *testing.T) {
 		And(patchLabelMatchesFor("Service")).
 		And(patchLabelMatchesFor("Deployment"))
 }
+
+// when we have a config map generator, AND the ignore annotation, it is ignored in the app's sync status
+func TestSyncStatusOptionIgnore(t *testing.T) {
+	var mapName string
+	Given(t).
+		Path("kustomize-cm-gen").
+		When().
+		Create().
+		Sync().
+		Then().
+		Expect(OperationPhaseIs(OperationSucceeded)).
+		Expect(SyncStatusIs(SyncStatusCodeSynced)).
+		Expect(HealthIs(HealthStatusHealthy)).
+		And(func(app *Application) {
+			resourceStatus := app.Status.Resources[0]
+			assert.Contains(t, resourceStatus.Name, "my-map-")
+			assert.Equal(t, SyncStatusCodeSynced, resourceStatus.Status)
+
+			mapName = resourceStatus.Name
+		}).
+		When().
+		// we now force generation of a second CM
+		PatchFile("kustomization.yaml", `[{"op": "replace", "path": "/configMapGenerator/0/literals/0", "value": "foo=baz"}]`).
+		Refresh(RefreshTypeHard).
+		Then().
+		// this is standard logging from the command - tough one - true statement
+		When().
+		Sync().
+		Then().
+		Expect(Error("1 resources require pruning")).
+		Expect(OperationPhaseIs(OperationSucceeded)).
+		// this is a key check - we expect the app to be healthy because, even though we have a resources that needs
+		// pruning, because it is annotated with IgnoreExtraneous it should not contribute to the sync status
+		Expect(SyncStatusIs(SyncStatusCodeSynced)).
+		Expect(HealthIs(HealthStatusHealthy)).
+		And(func(app *Application) {
+			assert.Equal(t, 2, len(app.Status.Resources))
+			// new map in-sync
+			{
+				resourceStatus := app.Status.Resources[0]
+				assert.Contains(t, resourceStatus.Name, "my-map-")
+				// make sure we've a new map with changed name
+				assert.NotEqual(t, mapName, resourceStatus.Name)
+				assert.Equal(t, SyncStatusCodeSynced, resourceStatus.Status)
+			}
+			// old map is out of sync
+			{
+				resourceStatus := app.Status.Resources[1]
+				assert.Equal(t, mapName, resourceStatus.Name)
+				assert.Equal(t, SyncStatusCodeOutOfSync, resourceStatus.Status)
+			}
+		})
+}
diff --git a/test/e2e/testdata/config-map/config-map.yaml b/test/e2e/testdata/config-map/config-map.yaml
new file mode 100644
index 0000000000000..b781028c394f5
--- /dev/null
+++ b/test/e2e/testdata/config-map/config-map.yaml
@@ -0,0 +1,6 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: my-map
+data:
+  foo: bar
\ No newline at end of file
diff --git a/test/e2e/testdata/kustomize-cm-gen/kustomization.yaml b/test/e2e/testdata/kustomize-cm-gen/kustomization.yaml
new file mode 100644
index 0000000000000..5b47525454277
--- /dev/null
+++ b/test/e2e/testdata/kustomize-cm-gen/kustomization.yaml
@@ -0,0 +1,9 @@
+configMapGenerator:
+  - name: my-map
+    literals:
+      - foo=bar
+generatorOptions:
+  annotations:
+    argocd.argoproj.io/compare-options: IgnoreExtraneous
+    argocd.argoproj.io/sync-options: Prune=false
+kind: Kustomization
diff --git a/util/resource/annotations.go b/util/resource/annotations.go
new file mode 100644
index 0000000000000..0b6018f4dfa02
--- /dev/null
+++ b/util/resource/annotations.go
@@ -0,0 +1,16 @@
+package resource
+
+import (
+	"strings"
+
+	"k8s.io/apimachinery/pkg/apis/meta/v1/unstructured"
+)
+
+func HasAnnotationOption(obj *unstructured.Unstructured, key, val string) bool {
+	for _, item := range strings.Split(obj.GetAnnotations()[key], ",") {
+		if strings.TrimSpace(item) == val {
+			return true
+		}
+	}
+	return false
+}
diff --git a/util/resource/annotations_test.go b/util/resource/annotations_test.go
new file mode 100644
index 0000000000000..a437f3c9b4139
--- /dev/null
+++ b/util/resource/annotations_test.go
@@ -0,0 +1,41 @@
+package resource
+
+import (
+	"testing"
+
+	"k8s.io/apimachinery/pkg/apis/meta/v1/unstructured"
+
+	"github.com/argoproj/argo-cd/test"
+)
+
+func TestHasAnnotationOption(t *testing.T) {
+	type args struct {
+		obj *unstructured.Unstructured
+		key string
+		val string
+	}
+	tests := []struct {
+		name string
+		args args
+		want bool
+	}{
+		{"Nil", args{test.NewPod(), "foo", "bar"}, false},
+		{"Empty", args{example(""), "foo", "bar"}, false},
+		{"Single", args{example("bar"), "foo", "bar"}, true},
+		{"Double", args{example("bar,baz"), "foo", "baz"}, true},
+		{"Spaces", args{example("bar "), "foo", "bar"}, true},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if got := HasAnnotationOption(tt.args.obj, tt.args.key, tt.args.val); got != tt.want {
+				t.Errorf("HasAnnotationOption() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}
+
+func example(val string) *unstructured.Unstructured {
+	obj := test.NewPod()
+	obj.SetAnnotations(map[string]string{"foo": val})
+	return obj
+}