Add test demonstrating the problem

When filtering to show only tracked files, pressing `a` would also stage
untracked files, which is confusing and undesired.

pkg/integration/tests/filter_and_search/stage_all_stages_only_tracked_files_in_tracked_only_filter.go

@@ -0,0 +1,57 @@
+package filter_and_search
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/config"
+	. "github.com/jesseduffield/lazygit/pkg/integration/components"
+)
+
+var StageAllStagesOnlyTrackedFilesInTrackedOnlyFilter = NewIntegrationTest(NewIntegrationTestArgs{
+	Description:  "Staging all files in tracked only view should stage only tracked files",
+	ExtraCmdArgs: []string{},
+	Skip:         false,
+	SetupConfig: func(config *config.AppConfig) {
+	},
+	SetupRepo: func(shell *Shell) {
+		shell.CreateFileAndAdd("file-tracked", "foo")
+
+		shell.Commit("first commit")
+
+		shell.CreateFile("file-untracked", "bar")
+		shell.UpdateFile("file-tracked", "baz")
+	},
+	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Views().Files().
+			Focus().
+			Lines(
+				Equals("▼ /").IsSelected(),
+				Equals("   M file-tracked"),
+				Equals("  ?? file-untracked"),
+			).
+			Press(keys.Files.OpenStatusFilter).
+			Tap(func() {
+				t.ExpectPopup().Menu().
+					Title(Equals("Filtering")).
+					Select(Contains("Show only tracked files")).
+					Confirm()
+			}).
+			Lines(
+				Equals(" M file-tracked"),
+			).
+			Press(keys.Files.ToggleStagedAll).
+			Press(keys.Files.OpenStatusFilter).
+			Tap(func() {
+				t.ExpectPopup().Menu().
+					Title(Equals("Filtering")).
+					Select(Contains("No filter")).
+					Confirm()
+			}).
+			Lines(
+				Equals("▼ /").IsSelected(),
+				Equals("  M  file-tracked"), // 'M' is now in the left column, so file is staged
+				/* EXPECTED:
+				Equals("  ?? file-untracked"),
+				ACTUAL: */
+				Equals("  A  file-untracked"),
+			)
+	},
+})

pkg/integration/tests/test_list.go

@@ -229,6 +229,7 @@ var tests = []*components.IntegrationTest{
 	filter_and_search.NestedFilter,
 	filter_and_search.NestedFilterTransient,
 	filter_and_search.NewSearch,
+	filter_and_search.StageAllStagesOnlyTrackedFilesInTrackedOnlyFilter,
 	filter_and_search.StagingFolderStagesOnlyTrackedFilesInTrackedOnlyFilter,
 	filter_by_author.SelectAuthor,
 	filter_by_author.TypeAuthor,