deprecate some cfg commands

cmd/config/internal/commands/annotate.go

@@ -27,6 +27,9 @@ func NewAnnotateRunner(parent string) *AnnotateRunner {
 		Long:    commands.AnnotateLong,
 		Example: commands.AnnotateExamples,
 		RunE:    r.runE,
+		Deprecated:
+			"use the `commonAnnotations` field in your kustomization file\n" +
+			"or a KRM function such as https://catalog.kpt.dev/set-annotations/v0.1/ instead.",
 	}
 	runner.FixDocs(parent, c)
 	r.Command = c

cmd/config/internal/commands/annotate_test.go

@@ -501,7 +501,10 @@ func TestAnnotateSubPackages(t *testing.T) {
 			name:    "annotate-recurse-subpackages",
 			dataset: "dataset-without-setters",
 			args:    []string{"--kv", "foo=bar", "-R"},
-			expected: `${baseDir}/
+			expected: `Command "annotate" is deprecated, use the ` + "`commonAnnotations`" +
+				` field in your kustomization file
+or a KRM function such as https:/catalog.kpt.dev/set-annotations/v0.1/ instead.
+${baseDir}/
 added annotations in the package
 
 ${baseDir}/mysql/
@@ -516,7 +519,10 @@ added annotations in the package
 			dataset:     "dataset-without-setters",
 			packagePath: "mysql",
 			args:        []string{"--kv", "foo=bar"},
-			expected: `${baseDir}/mysql/
+			expected: `Command "annotate" is deprecated, use the ` + "`commonAnnotations`" +
+				` field in your kustomization file
+or a KRM function such as https:/catalog.kpt.dev/set-annotations/v0.1/ instead.
+${baseDir}/mysql/
 added annotations in the package
 `,
 		},
@@ -525,7 +531,10 @@ added annotations in the package
 			dataset:     "dataset-without-setters",
 			packagePath: "mysql/storage",
 			args:        []string{"--kv", "foo=bar"},
-			expected: `${baseDir}/mysql/storage/
+			expected: `Command "annotate" is deprecated, use the ` + "`commonAnnotations`" +
+				` field in your kustomization file
+or a KRM function such as https:/catalog.kpt.dev/set-annotations/v0.1/ instead.
+${baseDir}/mysql/storage/
 added annotations in the package
 `,
 		},

cmd/config/internal/commands/cmdcreatesetter.go

@@ -32,6 +32,8 @@ func NewCreateSetterRunner(parent string) *CreateSetterRunner {
 		Example: commands.CreateSetterExamples,
 		PreRunE: r.preRunE,
 		RunE:    r.runE,
+		Deprecated: "setter commands will no longer be available in kustomize v5.\n" +
+			"See discussion in https://github.com/kubernetes-sigs/kustomize/issues/3953.",
 	}
 	set.Flags().StringVar(&r.FieldValue, "value", "",
 		"optional flag, alternative to specifying the value as an argument. e.g. used to specify values that start with '-'")

cmd/config/internal/commands/cmdcreatesetter_test.go

@@ -799,7 +799,9 @@ func TestCreateSetterSubPackages(t *testing.T) {
 			name:    "create-setter-recurse-subpackages",
 			dataset: "dataset-without-setters",
 			args:    []string{"namespace", "myspace", "-R"},
-			expected: `${baseDir}/mysql/
+			expected: `Command "create-setter" is deprecated, setter commands will no longer be available in kustomize v5.
+See discussion in https:/github.com/kubernetes-sigs/kustomize/issues/3953.
+${baseDir}/mysql/
 created setter "namespace"
 
 ${baseDir}/mysql/storage/
@@ -811,7 +813,9 @@ created setter "namespace"
 			dataset:     "dataset-without-setters",
 			packagePath: "mysql",
 			args:        []string{"namespace", "myspace"},
-			expected: `${baseDir}/mysql/
+			expected: `Command "create-setter" is deprecated, setter commands will no longer be available in kustomize v5.
+See discussion in https:/github.com/kubernetes-sigs/kustomize/issues/3953.
+${baseDir}/mysql/
 created setter "namespace"
 `,
 		},
@@ -820,7 +824,9 @@ created setter "namespace"
 			dataset:     "dataset-without-setters",
 			packagePath: "mysql/storage",
 			args:        []string{"namespace", "myspace"},
-			expected: `${baseDir}/mysql/storage/
+			expected: `Command "create-setter" is deprecated, setter commands will no longer be available in kustomize v5.
+See discussion in https:/github.com/kubernetes-sigs/kustomize/issues/3953.
+${baseDir}/mysql/storage/
 created setter "namespace"
 `,
 		},
@@ -829,7 +835,9 @@ created setter "namespace"
 			dataset:     "dataset-with-setters",
 			packagePath: "mysql",
 			args:        []string{"namespace", "myspace", "-R"},
-			expected: `${baseDir}/mysql/
+			expected: `Command "create-setter" is deprecated, setter commands will no longer be available in kustomize v5.
+See discussion in https:/github.com/kubernetes-sigs/kustomize/issues/3953.
+${baseDir}/mysql/
 setter with name "namespace" already exists, if you want to modify it, please delete the existing setter and recreate it
 
 ${baseDir}/mysql/nosetters/

cmd/config/internal/commands/cmdcreatesubstitution.go

@@ -23,6 +23,8 @@ func NewCreateSubstitutionRunner(parent string) *CreateSubstitutionRunner {
 		Args:   cobra.ExactArgs(2),
 		PreRun: r.preRun,
 		RunE:   r.runE,
+		Deprecated: "imperative substitutions will no longer be available in kustomize v5.\n" +
+			"See discussion in https://github.com/kubernetes-sigs/kustomize/issues/3953.",
 	}
 	cs.Flags().StringVar(&r.CreateSubstitution.FieldName, "field", "",
 		"name of the field to set -- e.g. --field image")

cmd/config/internal/commands/cmdinit.go

@@ -26,6 +26,8 @@ func GetInitRunner(name string) *InitRunner {
 		Long:    commands.InitLong,
 		Example: commands.InitExamples,
 		RunE:    r.runE,
+		Deprecated: "setter commands and substitutions will no longer be available in kustomize v5.\n" +
+			"See discussion in https://github.com/kubernetes-sigs/kustomize/issues/3953.",
 	}
 	runner.FixDocs(name, c)
 	r.Command = c

cmd/config/internal/commands/cmdlistsetters.go

@@ -31,6 +31,8 @@ func NewListSettersRunner(parent string) *ListSettersRunner {
 		Example: commands.ListSettersExamples,
 		PreRunE: r.preRunE,
 		RunE:    r.runE,
+		Deprecated: "setter commands will no longer be available in kustomize v5.\n" +
+			"See discussion in https://github.com/kubernetes-sigs/kustomize/issues/3953.",
 	}
 	c.Flags().BoolVar(&r.Markdown, "markdown", false,
 		"output as github markdown")

cmd/config/internal/commands/cmdset.go

@@ -27,6 +27,8 @@ func NewSetRunner(parent string) *SetRunner {
 		Example: commands.SetExamples,
 		PreRunE: r.preRunE,
 		RunE:    r.runE,
+		Deprecated: "setter commands will no longer be available in kustomize v5.\n" +
+			"See discussion in https://github.com/kubernetes-sigs/kustomize/issues/3953.",
 	}
 	runner.FixDocs(parent, c)
 	r.Command = c

cmd/config/internal/commands/fmt.go

@@ -25,6 +25,8 @@ func GetFmtRunner(name string) *FmtRunner {
 		Example: commands.FmtExamples,
 		RunE:    r.runE,
 		PreRunE: r.preRunE,
+		Deprecated: "imperative formatting will no longer be available in kustomize v5.\n" +
+			"Declare a formatting transformer in your kustomization instead.",
 	}
 	runner.FixDocs(name, c)
 	c.Flags().StringVar(&r.FilenamePattern, "pattern", filters.DefaultFilenamePattern,

cmd/config/internal/commands/merge.go

@@ -19,6 +19,7 @@ func GetMergeRunner(name string) *MergeRunner {
 		Long:    commands.MergeLong,
 		Example: commands.MergeExamples,
 		RunE:    r.runE,
+		Deprecated: "this will no longer be available in kustomize v5.",
 	}
 	runner.FixDocs(name, c)
 	r.Command = c

cmd/config/internal/commands/merge3.go

@@ -18,6 +18,7 @@ func GetMerge3Runner(name string) *Merge3Runner {
 		Long:    commands.Merge3Long,
 		Example: commands.Merge3Examples,
 		RunE:    r.runE,
+		Deprecated: "this will no longer be available in kustomize v5.",
 	}
 	runner.FixDocs(name, c)
 	c.Flags().StringVar(&r.ancestor, "ancestor", "",