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/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,