chore: Add test for skipping re-adding a modified external

internal/cmd/catconfigcmd.go

@@ -4,12 +4,13 @@ import "github.com/spf13/cobra"
 
 func (c *Config) newCatConfigCmd() *cobra.Command {
 	catConfigCmd := &cobra.Command{
-		Use:     "cat-config",
-		Short:   "Print the configuration file",
-		Long:    mustLongHelp("cat-config"),
-		Example: example("cat-config"),
-		Args:    cobra.NoArgs,
-		RunE:    c.runCatConfigCmd,
+		Use:               "cat-config",
+		Short:             "Print the configuration file",
+		Long:              mustLongHelp("cat-config"),
+		Example:           example("cat-config"),
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		RunE:              c.runCatConfigCmd,
 		Annotations: newAnnotations(
 			doesNotRequireValidConfig,
 			persistentStateModeReadOnly,

internal/cmd/config.go

@@ -1760,9 +1760,11 @@ func (c *Config) newRootCmd() (*cobra.Command, error) {
 		rootCmd.RegisterFlagCompletionFunc("color", autoBoolFlagCompletionFunc),
 		rootCmd.RegisterFlagCompletionFunc("config-format", c.configFormat.FlagCompletionFunc()),
 		rootCmd.RegisterFlagCompletionFunc("mode", chezmoi.ModeFlagCompletionFunc),
+		rootCmd.RegisterFlagCompletionFunc("progress", autoBoolFlagCompletionFunc),
 		rootCmd.RegisterFlagCompletionFunc("refresh-externals", chezmoi.RefreshExternalsFlagCompletionFunc),
 		rootCmd.RegisterFlagCompletionFunc("use-builtin-age", autoBoolFlagCompletionFunc),
 		rootCmd.RegisterFlagCompletionFunc("use-builtin-git", autoBoolFlagCompletionFunc),
+		rootCmd.MarkPersistentFlagDirname("working-tree"),
 	); err != nil {
 		return nil, err
 	}

internal/cmd/datacmd.go

@@ -14,12 +14,13 @@ type dataCmdConfig struct {
 
 func (c *Config) newDataCmd() *cobra.Command {
 	dataCmd := &cobra.Command{
-		Use:     "data",
-		Short:   "Print the template data",
-		Long:    mustLongHelp("data"),
-		Example: example("data"),
-		Args:    cobra.NoArgs,
-		RunE:    c.runDataCmd,
+		Use:               "data",
+		Short:             "Print the template data",
+		Long:              mustLongHelp("data"),
+		Example:           example("data"),
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		RunE:              c.runDataCmd,
 		Annotations: newAnnotations(
 			persistentStateModeReadOnly,
 		),

internal/cmd/doctorcmd.go

@@ -150,12 +150,13 @@ type doctorCmdConfig struct {
 
 func (c *Config) newDoctorCmd() *cobra.Command {
 	doctorCmd := &cobra.Command{
-		Args:    cobra.NoArgs,
-		Use:     "doctor",
-		Short:   "Check your system for potential problems",
-		Example: example("doctor"),
-		Long:    mustLongHelp("doctor"),
-		RunE:    c.runDoctorCmd,
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		Use:               "doctor",
+		Short:             "Check your system for potential problems",
+		Example:           example("doctor"),
+		Long:              mustLongHelp("doctor"),
+		RunE:              c.runDoctorCmd,
 		Annotations: newAnnotations(
 			doesNotRequireValidConfig,
 			persistentStateModeNone,

internal/cmd/dumpconfigcmd.go

@@ -12,12 +12,13 @@ type dumpConfigCmdConfig struct {
 
 func (c *Config) newDumpConfigCmd() *cobra.Command {
 	dumpConfigCmd := &cobra.Command{
-		Use:     "dump-config",
-		Short:   "Dump the configuration values",
-		Long:    mustLongHelp("dump-config"),
-		Example: example("dump-config"),
-		Args:    cobra.NoArgs,
-		RunE:    c.runDumpConfigCmd,
+		Use:               "dump-config",
+		Short:             "Dump the configuration values",
+		Long:              mustLongHelp("dump-config"),
+		Example:           example("dump-config"),
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		RunE:              c.runDumpConfigCmd,
 		Annotations: newAnnotations(
 			persistentStateModeReadOnly,
 		),

internal/cmd/editconfigcmd.go

@@ -6,12 +6,13 @@ import (
 
 func (c *Config) newEditConfigCmd() *cobra.Command {
 	editConfigCmd := &cobra.Command{
-		Use:     "edit-config",
-		Short:   "Edit the configuration file",
-		Long:    mustLongHelp("edit-config"),
-		Example: example("edit-config"),
-		Args:    cobra.NoArgs,
-		RunE:    c.runEditConfigCmd,
+		Use:               "edit-config",
+		Short:             "Edit the configuration file",
+		Long:              mustLongHelp("edit-config"),
+		Example:           example("edit-config"),
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		RunE:              c.runEditConfigCmd,
 		Annotations: newAnnotations(
 			doesNotRequireValidConfig,
 			modifiesConfigFile,

internal/cmd/editconfigtemplatecmd.go

@@ -11,12 +11,13 @@ import (
 
 func (c *Config) newEditConfigTemplateCmd() *cobra.Command {
 	editConfigCmd := &cobra.Command{
-		Use:     "edit-config-template",
-		Short:   "Edit the configuration file template",
-		Long:    mustLongHelp("edit-config-template"),
-		Example: example("edit-config-template"),
-		Args:    cobra.NoArgs,
-		RunE:    c.makeRunEWithSourceState(c.runEditConfigTemplateCmd),
+		Use:               "edit-config-template",
+		Short:             "Edit the configuration file template",
+		Long:              mustLongHelp("edit-config-template"),
+		Example:           example("edit-config-template"),
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		RunE:              c.makeRunEWithSourceState(c.runEditConfigTemplateCmd),
 		Annotations: newAnnotations(
 			doesNotRequireValidConfig,
 			modifiesSourceDirectory,

internal/cmd/helpcmd.go

@@ -9,11 +9,12 @@ import (
 
 func (c *Config) newHelpCmd() *cobra.Command {
 	helpCmd := &cobra.Command{
-		Use:     "help [command]",
-		Short:   "Print help about a command",
-		Long:    mustLongHelp("help"),
-		Example: example("help"),
-		RunE:    c.runHelpCmd,
+		Use:               "help [command]",
+		Short:             "Print help about a command",
+		Long:              mustLongHelp("help"),
+		Example:           example("help"),
+		RunE:              c.runHelpCmd,
+		ValidArgsFunction: cobra.NoFileCompletions,
 		Annotations: newAnnotations(
 			doesNotRequireValidConfig,
 			persistentStateModeNone,

internal/cmd/ignoredcmd.go

@@ -13,12 +13,13 @@ type ignoredCmdConfig struct {
 
 func (c *Config) newIgnoredCmd() *cobra.Command {
 	ignoredCmd := &cobra.Command{
-		Use:     "ignored",
-		Short:   "Print ignored targets",
-		Long:    mustLongHelp("ignored"),
-		Example: example("ignored"),
-		Args:    cobra.NoArgs,
-		RunE:    c.makeRunEWithSourceState(c.runIgnoredCmd),
+		Use:               "ignored",
+		Short:             "Print ignored targets",
+		Long:              mustLongHelp("ignored"),
+		Example:           example("ignored"),
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		RunE:              c.makeRunEWithSourceState(c.runIgnoredCmd),
 		Annotations: newAnnotations(
 			persistentStateModeReadMockWrite,
 		),

internal/cmd/licensecmd.go

@@ -6,12 +6,13 @@ import (
 
 func (c *Config) newLicenseCmd() *cobra.Command {
 	licenseCmd := &cobra.Command{
-		Use:     "license",
-		Short:   "Print license",
-		Long:    mustLongHelp("license"),
-		Example: example("license"),
-		Args:    cobra.NoArgs,
-		RunE:    c.runLicenseCmd,
+		Use:               "license",
+		Short:             "Print license",
+		Long:              mustLongHelp("license"),
+		Example:           example("license"),
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		RunE:              c.runLicenseCmd,
 		Annotations: newAnnotations(
 			doesNotRequireValidConfig,
 			persistentStateModeNone,

internal/cmd/purgecmd.go

@@ -19,12 +19,13 @@ type purgeCmdConfig struct {
 
 func (c *Config) newPurgeCmd() *cobra.Command {
 	purgeCmd := &cobra.Command{
-		Use:     "purge",
-		Short:   "Purge chezmoi's configuration and data",
-		Long:    mustLongHelp("purge"),
-		Example: example("purge"),
-		Args:    cobra.NoArgs,
-		RunE:    c.runPurgeCmd,
+		Use:               "purge",
+		Short:             "Purge chezmoi's configuration and data",
+		Long:              mustLongHelp("purge"),
+		Example:           example("purge"),
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		RunE:              c.runPurgeCmd,
 		Annotations: newAnnotations(
 			modifiesDestinationDirectory,
 			modifiesSourceDirectory,

internal/cmd/testdata/scripts/issue4358.txtar

@@ -0,0 +1,22 @@
+httpd www
+
+exec chezmoi apply
+cmp $HOME/.file golden/.file
+
+# check that modifying an external file and then running chezmoi re-add does not result in an inconsistent state
+edit $HOME/.file
+! cmp $HOME/.file golden/.file
+exec chezmoi --exclude=externals re-add
+exec chezmoi status
+cmp stdout golden/status
+
+-- golden/.file --
+# contents of .file
+-- golden/status --
+MM .file
+-- home/user/.local/share/chezmoi/.chezmoiexternal.toml.tmpl --
+[".file"]
+    type = "file"
+    url = "{{ env "HTTPD_URL" }}/.file"
+-- www/.file --
+# contents of .file

internal/cmd/updatecmd.go

@@ -22,12 +22,13 @@ type updateCmdConfig struct {
 
 func (c *Config) newUpdateCmd() *cobra.Command {
 	updateCmd := &cobra.Command{
-		Use:     "update",
-		Short:   "Pull and apply any changes",
-		Long:    mustLongHelp("update"),
-		Example: example("update"),
-		Args:    cobra.NoArgs,
-		RunE:    c.runUpdateCmd,
+		Use:               "update",
+		Short:             "Pull and apply any changes",
+		Long:              mustLongHelp("update"),
+		Example:           example("update"),
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		RunE:              c.runUpdateCmd,
 		Annotations: newAnnotations(
 			modifiesDestinationDirectory,
 			persistentStateModeReadWrite,

internal/cmd/upgradecmd.go

@@ -49,12 +49,13 @@ type upgradeCmdConfig struct {
 
 func (c *Config) newUpgradeCmd() *cobra.Command {
 	upgradeCmd := &cobra.Command{
-		Use:     "upgrade",
-		Short:   "Upgrade chezmoi to the latest released version",
-		Long:    mustLongHelp("upgrade"),
-		Example: example("upgrade"),
-		Args:    cobra.NoArgs,
-		RunE:    c.runUpgradeCmd,
+		Use:               "upgrade",
+		Short:             "Upgrade chezmoi to the latest released version",
+		Long:              mustLongHelp("upgrade"),
+		Example:           example("upgrade"),
+		Args:              cobra.NoArgs,
+		ValidArgsFunction: cobra.NoFileCompletions,
+		RunE:              c.runUpgradeCmd,
 		Annotations: newAnnotations(
 			persistentStateModeNone,
 			runsCommands,