Don't stage nested repositories

If you staged the directory of a removed submodule, a nested repository
or a worktree inside the repo, git added it as an embedded repository: a
gitlink without an entry in .gitmodules. For a removed submodule, this
brings it back in a broken state. git warns about it, but lazygit didn't
show the warning. Staging all files did the same to every such
directory.

Disable staging a selection that contains one of these, and disable
staging all files if that would stage one. The disabled reason tells you
how to get rid of it.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>

pkg/commands/models/file.go

@@ -53,6 +53,13 @@ const (
 	RemovedSubmodule
 )
 
+// IsNestedRepository reports whether the file is a git repository of its own
+// inside the working tree, such as a linked worktree or the directory of a
+// removed submodule
+func (f *File) IsNestedRepository() bool {
+	return f.DirectoryKind == NestedRepository || f.DirectoryKind == RemovedSubmodule
+}
+
 // sometimes we need to deal with either a node (which contains a file) or an actual file
 type IFile interface {
 	GetHasUnstagedChanges() bool

pkg/gui/controllers/files_controller.go

@@ -137,7 +137,7 @@ func (self *FilesController) GetKeybindings(opts types.KeybindingsOpts) []*types
 		{
 			Keys:              opts.GetKeys(opts.Config.Files.ToggleStagedAll),
 			Handler:           self.toggleStagedAll,
-			GetDisabledReason: self.require(self.anyFilesDisplayed),
+			GetDisabledReason: self.require(self.anyFilesDisplayed, self.canStageAll),
 			Description:       self.c.Tr.ToggleStagedAll,
 			Tooltip:           self.c.Tr.ToggleStagedAllTooltip,
 		},
@@ -842,7 +842,8 @@ func (self *FilesController) conflictNeedsResolutionDialog(file *models.File) bo
 
 // canStageSelection disables staging when a multiple selection includes a file
 // with a conflict that must be resolved through a dialog; those have to be
-// resolved one at a time.
+// resolved one at a time. It also disables it when the selection includes a
+// nested repository.
 func (self *FilesController) canStageSelection(nodes []*filetree.FileNode) *types.DisabledReason {
 	if len(nodes) > 1 {
 		for _, node := range nodes {
@@ -858,6 +859,33 @@ func (self *FilesController) canStageSelection(nodes []*filetree.FileNode) *type
 		}
 	}
 
+	for _, node := range nodes {
+		if nestedRepository := node.FindFirstFileBy((*models.File).IsNestedRepository); nestedRepository != nil {
+			return self.c.Helpers().WorkingTree.CantStageNestedRepository(nestedRepository)
+		}
+	}
+
+	return nil
+}
+
+// canStageAll disables staging all files when that would stage a nested
+// repository.
+func (self *FilesController) canStageAll() *types.DisabledReason {
+	var nestedRepository *models.File
+	switch self.stageAllScope() {
+	case stageAllVisibleFiles:
+		nestedRepository = self.context().FileTreeViewModel.GetRoot().FindFirstFileBy((*models.File).IsNestedRepository)
+	case stageAllTrackedFiles:
+		// A nested repository is never tracked
+		return nil
+	default:
+		nestedRepository, _ = lo.Find(self.c.Model().Files, (*models.File).IsNestedRepository)
+	}
+
+	if nestedRepository != nil {
+		return self.c.Helpers().WorkingTree.CantStageNestedRepository(nestedRepository)
+	}
+
 	return nil
 }
 

pkg/gui/controllers/helpers/working_tree_helper.go

@@ -13,6 +13,7 @@ import (
 	"github.com/jesseduffield/lazygit/pkg/gui/context"
 	"github.com/jesseduffield/lazygit/pkg/gui/style"
 	"github.com/jesseduffield/lazygit/pkg/gui/types"
+	"github.com/jesseduffield/lazygit/pkg/utils"
 	"github.com/samber/lo"
 )
 
@@ -131,6 +132,21 @@ func (self *WorkingTreeHelper) NestedRepositoryPlaceholders(file *models.File) m
 	}
 }
 
+// CantStageNestedRepository returns why the given nested repository can't be
+// staged. git add records a nested repository as an embedded repository: a
+// gitlink without an entry in .gitmodules. Nobody wants that, so we don't let
+// you stage one, and say how to get rid of it instead.
+func (self *WorkingTreeHelper) CantStageNestedRepository(file *models.File) *types.DisabledReason {
+	text := self.c.Tr.StageNestedRepositoryDisabled
+	if file.IsWorktree {
+		text = self.c.Tr.StageWorktreeDisabled
+	}
+
+	return &types.DisabledReason{
+		Text: utils.ResolvePlaceholderString(text, self.NestedRepositoryPlaceholders(file)),
+	}
+}
+
 func (self *WorkingTreeHelper) OpenMergeTool() error {
 	self.c.LogAction(self.c.Tr.Actions.OpenMergeTool)
 	return self.c.RunSubprocessAndRefresh(

pkg/i18n/english.go

@@ -115,6 +115,8 @@ type TranslationSet struct {
 	NestedRepositoryStatus                string
 	PlainDirectoryDescription             string
 	PlainDirectoryFiles                   string
+	StageNestedRepositoryDisabled         string
+	StageWorktreeDisabled                 string
 	StageConflictsRangeDisabled           string
 	Checkout                              string
 	CheckoutTooltip                       string
@@ -1291,6 +1293,8 @@ func EnglishTranslationSet() *TranslationSet {
 		NestedRepositoryDiscardWarning:       "Pressing {{.discardKey}} discards the directory, including the repository with all of its history.",
 		WorktreeInsideRepoDescription:        "'{{.path}}' is a linked worktree of this repository. Git doesn't look into it, so it shows up as a single untracked entry.\n\nTo remove the worktree, press {{.removeKey}}. If you keep worktrees inside the repository, add their directory to .gitignore so that they don't show up here.",
 		NestedRepositoryStatus:               "Status of '{{.path}}'",
+		StageNestedRepositoryDisabled:        "Can't stage '{{.path}}' because it is a git repository of its own. Discard it with {{.discardKey}}, or ignore it with {{.ignoreKey}}.",
+		StageWorktreeDisabled:                "Can't stage '{{.path}}' because it is a worktree. Remove it with {{.removeKey}}, or ignore it with {{.ignoreKey}}.",
 		PlainDirectoryDescription:            "'{{.path}}' is an untracked directory. Git shows it as a single entry because status.showUntrackedFiles is set to \"normal\".",
 		PlainDirectoryFiles:                  "Files in '{{.path}}'",
 		StageConflictsRangeDisabled:          "Cannot stage a selection that includes files with merge conflicts; resolve them individually with {{.goIntoKey}} first.",

pkg/integration/tests/file/stage_nested_repository.go

@@ -0,0 +1,51 @@
+package file
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/config"
+	. "github.com/jesseduffield/lazygit/pkg/integration/components"
+)
+
+var StageNestedRepository = NewIntegrationTest(NewIntegrationTestArgs{
+	Description:  "Staging a nested repository, or all files while there is one, is not supported, because git would add it as an embedded repository",
+	ExtraCmdArgs: []string{},
+	Skip:         false,
+	SetupConfig: func(config *config.AppConfig) {
+		config.GetUserConfig().Gui.ShowFileTree = false
+	},
+	SetupRepo: func(shell *Shell) {
+		shell.EmptyCommit("first commit")
+		shell.CloneIntoSubmodule("sub", "modules/sub")
+		shell.Commit("add submodule")
+		shell.RunCommand([]string{"git", "rm", "--cached", "modules/sub"})
+		shell.RunCommand([]string{"git", "rm", ".gitmodules"})
+		shell.Commit("remove submodule")
+
+		shell.CreateFile("file", "content")
+	},
+	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Views().Files().
+			IsFocused().
+			Lines(
+				Equals("?? file").IsSelected(),
+				Equals("?? modules/sub (removed submodule)"),
+			).
+			Press(keys.Files.ToggleStagedAll).
+			Tap(func() {
+				t.ExpectToast(Equals("Disabled: Can't stage 'modules/sub' because it is a git repository of its own. Discard it with d, or ignore it with i."))
+			}).
+			NavigateToLine(Contains("modules/sub")).
+			PressPrimaryAction().
+			Tap(func() {
+				t.ExpectToast(Equals("Disabled: Can't stage 'modules/sub' because it is a git repository of its own. Discard it with d, or ignore it with i."))
+			}).
+			// Staging all files works if the nested repository is filtered out
+			FilterOrSearch("file").
+			Lines(
+				Equals("?? file").IsSelected(),
+			).
+			Press(keys.Files.ToggleStagedAll).
+			Lines(
+				Equals("A  file").IsSelected(),
+			)
+	},
+})

pkg/integration/tests/test_list.go

@@ -266,6 +266,7 @@ var tests = []*components.IntegrationTest{
 	file.StageAllWithoutChangedFiles,
 	file.StageChildrenRangeSelect,
 	file.StageDeletedRangeSelect,
+	file.StageNestedRepository,
 	file.StageRangeSelect,
 	file.StagedChangesInLowerPane,
 	filter_and_search.FilterByFileStatus,