Filter file views rather than search (#5273)

### PR Description Way back when I implemented filter functionality I could not muster the motivation to apply it to the file views (files and commit files), but it really should be used on them. The text filter matches against the full file path (not just the filename), which is more useful for navigating large directory trees. When a text filter is active, all operations respect it consistently: - **Diffs**: selecting a filtered directory shows only the diff of visible files, not all files in the directory - **Staging/unstaging**: pressing space on a filtered directory only stages/unstages visible files - **Toggle all (a)**: only toggles staging for visible files - **Custom patch**: toggling a filtered directory only adds visible files to the patch Full disclosure, opus 4.6 wrote this entire PR but reviewing its changes they seem reasonable, and I have done some local testing and everything works as expected.
2026-09-12 16:46:25 -04:00 · 2026-03-07 20:06:36 +01:00 · 2026-03-07 20:06:36 +01:00 · 35911da3a6
parent 825784fbf4 615c566ac4
commit 35911da3a6
32 changed files with 669 additions and 101 deletions
--- a/docs-master/keybindings/Keybindings_en.md
+++ b/docs-master/keybindings/Keybindings_en.md
@ -71,7 +71,7 @@ _Legend: `<c-b>` means ctrl+b, `<a-b>` means alt+b, `B` means shift+b_
 | `` - `` | Collapse all files | Collapse all directories in the files tree |
 | `` = `` | Expand all files | Expand all directories in the file tree |
 | `` 0 `` | Focus main view |  |
-| `` / `` | Search the current view by text |  |
+| `` / `` | Filter the current view by text |  |

 ## Commit summary

@ -160,7 +160,7 @@ _Legend: `<c-b>` means ctrl+b, `<a-b>` means alt+b, `B` means shift+b_
 | `` - `` | Collapse all files | Collapse all directories in the files tree |
 | `` = `` | Expand all files | Expand all directories in the file tree |
 | `` 0 `` | Focus main view |  |
-| `` / `` | Search the current view by text |  |
+| `` / `` | Filter the current view by text |  |

 ## Input prompt

--- a/docs-master/keybindings/Keybindings_ja.md
+++ b/docs-master/keybindings/Keybindings_ja.md
@ -119,7 +119,7 @@ _凡例：`＜c-b＞` はctrl+b、`＜a-b＞` はalt+b、`B` はshift+bを意味
 | `` - `` | すべてのファイルを折りたたむ | ファイルツリー内のすべてのディレクトリを折りたたみます |
 | `` = `` | すべてのファイルを展開 | ファイルツリー内のすべてのディレクトリを展開します |
 | `` 0 `` | メインビューにフォーカス |  |
-| `` / `` | 現在のビューをテキストで検索 |  |
+| `` / `` | 現在のビューをテキストでフィルタリング |  |

 ## コミット概要

@ -242,7 +242,7 @@ _凡例：`＜c-b＞` はctrl+b、`＜a-b＞` はalt+b、`B` はshift+bを意味
 | `` - `` | すべてのファイルを折りたたむ | ファイルツリー内のすべてのディレクトリを折りたたみます |
 | `` = `` | すべてのファイルを展開 | ファイルツリー内のすべてのディレクトリを展開します |
 | `` 0 `` | メインビューにフォーカス |  |
-| `` / `` | 現在のビューをテキストで検索 |  |
+| `` / `` | 現在のビューをテキストでフィルタリング |  |

 ## メインパネル（ステージング）

--- a/docs-master/keybindings/Keybindings_ko.md
+++ b/docs-master/keybindings/Keybindings_ko.md
@ -349,7 +349,7 @@ _Legend: `<c-b>` means ctrl+b, `<a-b>` means alt+b, `B` means shift+b_
 | `` - `` | Collapse all files | Collapse all directories in the files tree |
 | `` = `` | Expand all files | Expand all directories in the file tree |
 | `` 0 `` | Focus main view |  |
-| `` / `` | 검색 시작 |  |
+| `` / `` | Filter the current view by text |  |

 ## 커밋메시지

@ -405,7 +405,7 @@ _Legend: `<c-b>` means ctrl+b, `<a-b>` means alt+b, `B` means shift+b_
 | `` - `` | Collapse all files | Collapse all directories in the files tree |
 | `` = `` | Expand all files | Expand all directories in the file tree |
 | `` 0 `` | Focus main view |  |
-| `` / `` | 검색 시작 |  |
+| `` / `` | Filter the current view by text |  |

 ## 확인 패널

--- a/docs-master/keybindings/Keybindings_nl.md
+++ b/docs-master/keybindings/Keybindings_nl.md
@ -84,7 +84,7 @@ _Legend: `<c-b>` means ctrl+b, `<a-b>` means alt+b, `B` means shift+b_
 | `` - `` | Collapse all files | Collapse all directories in the files tree |
 | `` = `` | Expand all files | Expand all directories in the file tree |
 | `` 0 `` | Focus main view |  |
-| `` / `` | Start met zoeken |  |
+| `` / `` | Filter the current view by text |  |

 ## Bevestigingspaneel

@ -149,7 +149,7 @@ _Legend: `<c-b>` means ctrl+b, `<a-b>` means alt+b, `B` means shift+b_
 | `` - `` | Collapse all files | Collapse all directories in the files tree |
 | `` = `` | Expand all files | Expand all directories in the file tree |
 | `` 0 `` | Focus main view |  |
-| `` / `` | Start met zoeken |  |
+| `` / `` | Filter the current view by text |  |

 ## Commits

--- a/docs-master/keybindings/Keybindings_pl.md
+++ b/docs-master/keybindings/Keybindings_pl.md
@ -260,7 +260,7 @@ _Legenda: `<c-b>` oznacza ctrl+b, `<a-b>` oznacza alt+b, `B` oznacza shift+b_
 | `` - `` | Collapse all files | Collapse all directories in the files tree |
 | `` = `` | Expand all files | Expand all directories in the file tree |
 | `` 0 `` | Focus main view |  |
-| `` / `` | Szukaj w bieżącym widoku po tekście |  |
+| `` / `` | Filtruj bieżący widok po tekście |  |

 ## Pliki commita

@ -280,7 +280,7 @@ _Legenda: `<c-b>` oznacza ctrl+b, `<a-b>` oznacza alt+b, `B` oznacza shift+b_
 | `` - `` | Collapse all files | Collapse all directories in the files tree |
 | `` = `` | Expand all files | Expand all directories in the file tree |
 | `` 0 `` | Focus main view |  |
-| `` / `` | Szukaj w bieżącym widoku po tekście |  |
+| `` / `` | Filtruj bieżący widok po tekście |  |

 ## Podsumowanie commita

--- a/docs-master/keybindings/Keybindings_pt.md
+++ b/docs-master/keybindings/Keybindings_pt.md
@ -84,7 +84,7 @@ _Legend: `<c-b>` means ctrl+b, `<a-b>` means alt+b, `B` means shift+b_
 | `` - `` | Recolher todos os arquivos | Recolher todos os diretórios na árvore de arquivos |
 | `` = `` | Expandir todos os arquivos | Expandir todos os diretórios na árvore do arquivo |
 | `` 0 `` | Focus main view |  |
-| `` / `` | Search the current view by text |  |
+| `` / `` | Filter the current view by text |  |

 ## Branches locais

@ -153,7 +153,7 @@ _Legend: `<c-b>` means ctrl+b, `<a-b>` means alt+b, `B` means shift+b_
 | `` - `` | Recolher todos os arquivos | Recolher todos os diretórios na árvore de arquivos |
 | `` = `` | Expandir todos os arquivos | Expandir todos os diretórios na árvore do arquivo |
 | `` 0 `` | Focus main view |  |
-| `` / `` | Search the current view by text |  |
+| `` / `` | Filter the current view by text |  |

 ## Commits

--- a/docs-master/keybindings/Keybindings_ru.md
+++ b/docs-master/keybindings/Keybindings_ru.md
@ -308,7 +308,7 @@ _Связки клавиш_
 | `` - `` | Collapse all files | Collapse all directories in the files tree |
 | `` = `` | Expand all files | Expand all directories in the file tree |
 | `` 0 `` | Focus main view |  |
-| `` / `` | Найти |  |
+| `` / `` | Filter the current view by text |  |

 ## Статус

@ -399,7 +399,7 @@ _Связки клавиш_
 | `` - `` | Collapse all files | Collapse all directories in the files tree |
 | `` = `` | Expand all files | Expand all directories in the file tree |
 | `` 0 `` | Focus main view |  |
-| `` / `` | Найти |  |
+| `` / `` | Filter the current view by text |  |

 ## Хранилище

--- a/docs-master/keybindings/Keybindings_zh-CN.md
+++ b/docs-master/keybindings/Keybindings_zh-CN.md
@ -183,7 +183,7 @@ _图例：`<c-b>` 意味着ctrl+b, `<a-b>意味着Alt+b, `B` 意味着shift+b_
 | `` - `` | 折叠全部文件 | 折叠文件树中的全部目录 |
 | `` = `` | 展开全部文件 | 展开文件树中的全部目录 |
 | `` 0 `` | 聚焦主视图 |  |
-| `` / `` | 开始搜索 |  |
+| `` / `` | 通过文本过滤当前视图 |  |

 ## 文件

@ -216,7 +216,7 @@ _图例：`<c-b>` 意味着ctrl+b, `<a-b>意味着Alt+b, `B` 意味着shift+b_
 | `` - `` | 折叠全部文件 | 折叠文件树中的全部目录 |
 | `` = `` | 展开全部文件 | 展开文件树中的全部目录 |
 | `` 0 `` | 聚焦主视图 |  |
-| `` / `` | 开始搜索 |  |
+| `` / `` | 通过文本过滤当前视图 |  |

 ## 本地分支

--- a/pkg/commands/git_commands/working_tree.go
+++ b/pkg/commands/git_commands/working_tree.go
@ -253,11 +253,14 @@ func (self *WorkingTreeCommands) Exclude(filename string) error {
 // WorktreeFileDiff returns the diff of a file
 func (self *WorkingTreeCommands) WorktreeFileDiff(file *models.File, plain bool, cached bool) string {
 	// for now we assume an error means the file was deleted
-	s, _ := self.WorktreeFileDiffCmdObj(file, plain, cached).RunWithOutput()
+	s, _ := self.WorktreeFileDiffCmdObj(file, plain, cached, nil).RunWithOutput()
 	return s
 }

-func (self *WorkingTreeCommands) WorktreeFileDiffCmdObj(node models.IFile, plain bool, cached bool) *oscommands.CmdObj {
+// WorktreeFileDiffCmdObj returns a command object for diffing a file or directory
+// in the working tree. When pathOverrides is non-empty, those paths are used instead of
+// the node's path (used to diff only filtered/visible files within a directory).
+func (self *WorkingTreeCommands) WorktreeFileDiffCmdObj(node models.IFile, plain bool, cached bool, pathOverrides []string) *oscommands.CmdObj {
 	colorArg := self.pagerConfig.GetColorArg()
 	if plain {
 		colorArg = "never"
@ -270,6 +273,11 @@ func (self *WorkingTreeCommands) WorktreeFileDiffCmdObj(node models.IFile, plain
 	useExtDiff := extDiffCmd != "" && !plain
 	useExtDiffGitConfig := self.pagerConfig.GetUseExternalDiffGitConfig() && !plain

+	paths := pathOverrides
+	if len(paths) == 0 {
+		paths = []string{node.GetPath()}
+	}
+
 	cmdArgs := NewGitCmd("diff").
 		ConfigIf(useExtDiff, "diff.external="+extDiffCmd).
 		ArgIfElse(useExtDiff || useExtDiffGitConfig, "--ext-diff", "--no-ext-diff").
@ -282,7 +290,7 @@ func (self *WorkingTreeCommands) WorktreeFileDiffCmdObj(node models.IFile, plain
 		ArgIf(noIndex, "--no-index").
 		Arg("--").
 		ArgIf(noIndex, "/dev/null").
-		Arg(node.GetPath()).
+		Arg(paths...).
 		ArgIf(prevPath != "", prevPath).
 		Dir(self.repoPaths.worktreePath).
 		ToArgv()
@ -293,10 +301,10 @@ func (self *WorkingTreeCommands) WorktreeFileDiffCmdObj(node models.IFile, plain
 // ShowFileDiff get the diff of specified from and to. Typically this will be used for a single commit so it'll be 123abc^..123abc
 // but when we're in diff mode it could be any 'from' to any 'to'. The reverse flag is also here thanks to diff mode.
 func (self *WorkingTreeCommands) ShowFileDiff(from string, to string, reverse bool, fileName string, plain bool) (string, error) {
-	return self.ShowFileDiffCmdObj(from, to, reverse, fileName, plain).RunWithOutput()
+	return self.ShowFileDiffCmdObj(from, to, reverse, []string{fileName}, plain).RunWithOutput()
 }

-func (self *WorkingTreeCommands) ShowFileDiffCmdObj(from string, to string, reverse bool, fileName string, plain bool) *oscommands.CmdObj {
+func (self *WorkingTreeCommands) ShowFileDiffCmdObj(from string, to string, reverse bool, fileNames []string, plain bool) *oscommands.CmdObj {
 	contextSize := self.UserConfig().Git.DiffContextSize

 	colorArg := self.pagerConfig.GetColorArg()
@ -321,7 +329,7 @@ func (self *WorkingTreeCommands) ShowFileDiffCmdObj(from string, to string, reve
 		ArgIf(reverse, "-R").
 		ArgIf(!plain && self.UserConfig().Git.IgnoreWhitespaceInDiffView, "--ignore-all-space").
 		Arg("--").
-		Arg(fileName).
+		Arg(fileNames...).
 		Dir(self.repoPaths.worktreePath).
 		ToArgv()

--- a/pkg/gui/context/commit_files_context.go
+++ b/pkg/gui/context/commit_files_context.go
@ -3,7 +3,6 @@ package context
 import (
 	"fmt"

-	"github.com/jesseduffield/gocui"
 	"github.com/jesseduffield/lazygit/pkg/commands/models"
 	"github.com/jesseduffield/lazygit/pkg/gui/filetree"
 	"github.com/jesseduffield/lazygit/pkg/gui/presentation"
@ -17,13 +16,12 @@ type CommitFilesContext struct {
 	*filetree.CommitFileTreeViewModel
 	*ListContextTrait
 	*DynamicTitleBuilder
-	*SearchTrait
 }

 var (
 	_ types.IListContext       = (*CommitFilesContext)(nil)
 	_ types.DiffableContext    = (*CommitFilesContext)(nil)
-	_ types.ISearchableContext = (*CommitFilesContext)(nil)
+	_ types.IFilterableContext = (*CommitFilesContext)(nil)
 )

 func NewCommitFilesContext(c *ContextCommon) *CommitFilesContext {
@ -48,7 +46,6 @@ func NewCommitFilesContext(c *ContextCommon) *CommitFilesContext {
 	ctx := &CommitFilesContext{
 		CommitFileTreeViewModel: viewModel,
 		DynamicTitleBuilder:     NewDynamicTitleBuilder(c.Tr.CommitFilesDynamicTitle),
-		SearchTrait:             NewSearchTrait(c),
 		ListContextTrait: &ListContextTrait{
 			Context: NewSimpleContext(
 				NewBaseContext(NewBaseContextOpts{
@ -68,9 +65,6 @@ func NewCommitFilesContext(c *ContextCommon) *CommitFilesContext {
 		},
 	}

-	ctx.GetView().SetRenderSearchStatus(ctx.SearchTrait.RenderSearchStatus)
-	ctx.GetView().SetOnSelectItem(ctx.OnSearchSelect)
-
 	return ctx
 }

@ -93,10 +87,6 @@ func (self *CommitFilesContext) GetFromAndToForDiff() (string, string) {
 	return ref.ParentRefName(), ref.RefName()
 }

-func (self *CommitFilesContext) ModelSearchResults(searchStr string, caseSensitive bool) []gocui.SearchPosition {
-	return nil
-}
-
 func (self *CommitFilesContext) ReInit(ref models.Ref, refRange *types.RefRange) {
 	self.SetRef(ref)
 	self.SetRefRange(refRange)
--- a/pkg/gui/context/working_tree_context.go
+++ b/pkg/gui/context/working_tree_context.go
@ -1,7 +1,6 @@
 package context

 import (
-	"github.com/jesseduffield/gocui"
 	"github.com/jesseduffield/lazygit/pkg/commands/models"
 	"github.com/jesseduffield/lazygit/pkg/gui/filetree"
 	"github.com/jesseduffield/lazygit/pkg/gui/presentation"
@ -13,12 +12,11 @@ import (
 type WorkingTreeContext struct {
 	*filetree.FileTreeViewModel
 	*ListContextTrait
-	*SearchTrait
 }

 var (
 	_ types.IListContext       = (*WorkingTreeContext)(nil)
-	_ types.ISearchableContext = (*WorkingTreeContext)(nil)
+	_ types.IFilterableContext = (*WorkingTreeContext)(nil)
 )

 func NewWorkingTreeContext(c *ContextCommon) *WorkingTreeContext {
@ -38,7 +36,6 @@ func NewWorkingTreeContext(c *ContextCommon) *WorkingTreeContext {
 	}

 	ctx := &WorkingTreeContext{
-		SearchTrait:       NewSearchTrait(c),
 		FileTreeViewModel: viewModel,
 		ListContextTrait: &ListContextTrait{
 			Context: NewSimpleContext(NewBaseContext(NewBaseContextOpts{
@ -56,12 +53,5 @@ func NewWorkingTreeContext(c *ContextCommon) *WorkingTreeContext {
 		},
 	}

-	ctx.GetView().SetRenderSearchStatus(ctx.SearchTrait.RenderSearchStatus)
-	ctx.GetView().SetOnSelectItem(ctx.OnSearchSelect)
-
 	return ctx
 }
-
-func (self *WorkingTreeContext) ModelSearchResults(searchStr string, caseSensitive bool) []gocui.SearchPosition {
-	return nil
-}
--- a/pkg/gui/controllers/commits_files_controller.go
+++ b/pkg/gui/controllers/commits_files_controller.go
@ -152,7 +152,8 @@ func (self *CommitFilesController) GetOnRenderToMain() func() {
 		from, to := self.context().GetFromAndToForDiff()
 		from, reverse := self.c.Modes().Diffing.GetFromAndReverseArgsForDiff(from)

-		cmdObj := self.c.Git().WorkingTree.ShowFileDiffCmdObj(from, to, reverse, node.GetPath(), false)
+		paths := self.pathsForDiff(node)
+		cmdObj := self.c.Git().WorkingTree.ShowFileDiffCmdObj(from, to, reverse, paths, false)
 		task := types.NewRunPtyTask(cmdObj.GetCmd())

 		self.c.RenderToMainViews(types.RefreshMainOpts{
@ -171,7 +172,7 @@ func (self *CommitFilesController) copyDiffToClipboard(path string, toastMessage
 	from, to := self.context().GetFromAndToForDiff()
 	from, reverse := self.c.Modes().Diffing.GetFromAndReverseArgsForDiff(from)

-	cmdObj := self.c.Git().WorkingTree.ShowFileDiffCmdObj(from, to, reverse, path, true)
+	cmdObj := self.c.Git().WorkingTree.ShowFileDiffCmdObj(from, to, reverse, []string{path}, true)
 	diff, err := cmdObj.RunWithOutput()
 	if err != nil {
 		return err
@ -571,6 +572,21 @@ func (self *CommitFilesController) GetOnClickFocusedMainView() func(mainViewName
 	}
 }

+// pathsForDiff returns the file paths to use for a diff command. When a text
+// filter is active and the node is a directory, only the visible (filtered)
+// file paths are returned so the diff reflects what the user sees.
+func (self *CommitFilesController) pathsForDiff(node *filetree.CommitFileNode) []string {
+	if !node.IsFile() && self.context().IsFiltering() {
+		var paths []string
+		_ = node.ForEachFile(func(file *models.CommitFile) error {
+			paths = append(paths, file.Path)
+			return nil
+		})
+		return paths
+	}
+	return []string{node.GetPath()}
+}
+
 // NOTE: these functions are identical to those in files_controller.go (except for types) and
 // could also be cleaned up with some generics
 func normalisedSelectedCommitFileNodes(selectedNodes []*filetree.CommitFileNode) []*filetree.CommitFileNode {
--- a/pkg/gui/controllers/files_controller.go
+++ b/pkg/gui/controllers/files_controller.go
@ -294,7 +294,8 @@ func (self *FilesController) GetOnRenderToMain() func() {
 			split := self.c.UserConfig().Gui.SplitDiff == "always" || (node.GetHasUnstagedChanges() && node.GetHasStagedChanges())
 			mainShowsStaged := !split && node.GetHasStagedChanges()

-			cmdObj := self.c.Git().WorkingTree.WorktreeFileDiffCmdObj(node, false, mainShowsStaged)
+			pathOverrides := self.pathOverridesForDiff(node)
+			cmdObj := self.c.Git().WorkingTree.WorktreeFileDiffCmdObj(node, false, mainShowsStaged, pathOverrides)
 			title := self.c.Tr.UnstagedChanges
 			if mainShowsStaged {
 				title = self.c.Tr.StagedChanges
@ -309,7 +310,7 @@ func (self *FilesController) GetOnRenderToMain() func() {
 			}

 			if split {
-				cmdObj := self.c.Git().WorkingTree.WorktreeFileDiffCmdObj(node, false, true)
+				cmdObj := self.c.Git().WorkingTree.WorktreeFileDiffCmdObj(node, false, true, pathOverrides)

 				title := self.c.Tr.StagedChanges
 				if mainShowsStaged {
@ -434,7 +435,19 @@ func (self *FilesController) pressWithLock(selectedNodes []*filetree.FileNode) e
 		}
 	}

+	// When filtering, expand directory nodes to individual visible file paths
+	// so that only filtered files are staged/unstaged.
 	toPaths := func(nodes []*filetree.FileNode) []string {
+		if self.context().IsFiltering() {
+			var paths []string
+			for _, node := range nodes {
+				_ = node.ForEachFile(func(file *models.File) error {
+					paths = append(paths, file.Path)
+					return nil
+				})
+			}
+			return paths
+		}
 		return lo.Map(nodes, func(node *filetree.FileNode, _ int) string {
 			return node.GetPath()
 		})
@ -449,7 +462,7 @@ func (self *FilesController) pressWithLock(selectedNodes []*filetree.FileNode) e
 	if len(unstagedSelectedNodes) > 0 {
 		var extraArgs []string

-		if self.context().GetFilter() == filetree.DisplayTracked {
+		if self.context().GetStatusFilter() == filetree.DisplayTracked {
 			extraArgs = []string{"-u"}
 		}

@ -469,22 +482,29 @@ func (self *FilesController) pressWithLock(selectedNodes []*filetree.FileNode) e
 			return err
 		}

-		// need to partition the paths into tracked and untracked (where we assume directories are tracked). Then we'll run the commands separately.
-		trackedNodes, untrackedNodes := utils.Partition(selectedNodes, func(node *filetree.FileNode) bool {
-			// We treat all directories as tracked. I'm not actually sure why we do this but
-			// it's been the existing behaviour for a while and nobody has complained
-			return !node.IsFile() || node.GetIsTracked()
-		})
-
-		if len(untrackedNodes) > 0 {
-			if err := self.c.Git().WorkingTree.UnstageUntrackedFiles(toPaths(untrackedNodes)); err != nil {
+		if self.context().IsFiltering() {
+			// When filtering, only unstage visible files
+			if err := self.unstageFilteredFiles(selectedNodes); err != nil {
 				return err
 			}
-		}
+		} else {
+			// need to partition the paths into tracked and untracked (where we assume directories are tracked). Then we'll run the commands separately.
+			trackedNodes, untrackedNodes := utils.Partition(selectedNodes, func(node *filetree.FileNode) bool {
+				// We treat all directories as tracked. I'm not actually sure why we do this but
+				// it's been the existing behaviour for a while and nobody has complained
+				return !node.IsFile() || node.GetIsTracked()
+			})

-		if len(trackedNodes) > 0 {
-			if err := self.c.Git().WorkingTree.UnstageTrackedFiles(toPaths(trackedNodes)); err != nil {
-				return err
+			if len(untrackedNodes) > 0 {
+				if err := self.c.Git().WorkingTree.UnstageUntrackedFiles(toPaths(untrackedNodes)); err != nil {
+					return err
+				}
+			}
+
+			if len(trackedNodes) > 0 {
+				if err := self.c.Git().WorkingTree.UnstageTrackedFiles(toPaths(trackedNodes)); err != nil {
+					return err
+				}
 			}
 		}
 	}
@ -503,6 +523,48 @@ func (self *FilesController) press(nodes []*filetree.FileNode) error {
 	return nil
 }

+// pathOverridesForDiff returns file paths to override the node's path in diff
+// commands when a text filter is active and the node is a directory. This
+// ensures the diff only shows filtered/visible files.
+func (self *FilesController) pathOverridesForDiff(node *filetree.FileNode) []string {
+	if !node.IsFile() && self.context().IsFiltering() {
+		var paths []string
+		_ = node.ForEachFile(func(file *models.File) error {
+			paths = append(paths, file.Path)
+			return nil
+		})
+		return paths
+	}
+	return nil
+}
+
+// unstageFilteredFiles unstages only the visible (filtered) files from the
+// given nodes, correctly partitioning by tracked/untracked.
+func (self *FilesController) unstageFilteredFiles(nodes []*filetree.FileNode) error {
+	var trackedPaths, untrackedPaths []string
+	for _, node := range nodes {
+		_ = node.ForEachFile(func(file *models.File) error {
+			if file.Tracked || file.HasStagedChanges {
+				trackedPaths = append(trackedPaths, file.Path)
+			} else {
+				untrackedPaths = append(untrackedPaths, file.Path)
+			}
+			return nil
+		})
+	}
+	if len(untrackedPaths) > 0 {
+		if err := self.c.Git().WorkingTree.UnstageUntrackedFiles(untrackedPaths); err != nil {
+			return err
+		}
+	}
+	if len(trackedPaths) > 0 {
+		if err := self.c.Git().WorkingTree.UnstageTrackedFiles(trackedPaths); err != nil {
+			return err
+		}
+	}
+	return nil
+}
+
 func (self *FilesController) Context() types.Context {
 	return self.context()
 }
@ -648,9 +710,21 @@ func (self *FilesController) toggleStagedAllWithLock() error {
 			return err
 		}

-		onlyTrackedFiles := self.context().GetFilter() == filetree.DisplayTracked
-		if err := self.c.Git().WorkingTree.StageAll(onlyTrackedFiles); err != nil {
-			return err
+		if self.context().IsFiltering() {
+			// When filtering, only stage visible files
+			var paths []string
+			_ = root.ForEachFile(func(file *models.File) error {
+				paths = append(paths, file.Path)
+				return nil
+			})
+			if err := self.c.Git().WorkingTree.StageFiles(paths, nil); err != nil {
+				return err
+			}
+		} else {
+			onlyTrackedFiles := self.context().GetStatusFilter() == filetree.DisplayTracked
+			if err := self.c.Git().WorkingTree.StageAll(onlyTrackedFiles); err != nil {
+				return err
+			}
 		}
 	} else {
 		self.c.LogAction(self.c.Tr.Actions.UnstageAllFiles)
@ -659,8 +733,15 @@ func (self *FilesController) toggleStagedAllWithLock() error {
 			return err
 		}

-		if err := self.c.Git().WorkingTree.UnstageAll(); err != nil {
-			return err
+		if self.context().IsFiltering() {
+			// When filtering, only unstage visible files
+			if err := self.unstageFilteredFiles([]*filetree.FileNode{root}); err != nil {
+				return err
+			}
+		} else {
+			if err := self.c.Git().WorkingTree.UnstageAll(); err != nil {
+				return err
+			}
 		}
 	}

@ -836,7 +917,7 @@ func (self *FilesController) isResolvingConflicts() bool {
 }

 func (self *FilesController) handleStatusFilterPressed() error {
-	currentFilter := self.context().GetFilter()
+	currentFilter := self.context().GetStatusFilter()
 	return self.c.Menu(types.CreateMenuOptions{
 		Title: self.c.Tr.FilteringMenuTitle,
 		Items: []*types.MenuItem{
@ -904,7 +985,7 @@ func (self *FilesController) filteringLabel(filter filetree.FileTreeDisplayFilte
 }

 func (self *FilesController) setStatusFiltering(filter filetree.FileTreeDisplayFilter) error {
-	previousFilter := self.context().GetFilter()
+	previousFilter := self.context().GetStatusFilter()

 	self.context().FileTreeViewModel.SetStatusFilter(filter)
 	self.c.Contexts().Files.GetView().Subtitle = self.filteringLabel(filter)
--- a/pkg/gui/controllers/helpers/refresh_helper.go
+++ b/pkg/gui/controllers/helpers/refresh_helper.go
@ -584,11 +584,11 @@ func (self *RefreshHelper) refreshStateFiles() error {

 	// only taking over the filter if it hasn't already been set by the user.
 	if conflictFileCount > 0 && prevConflictFileCount == 0 {
-		if fileTreeViewModel.GetFilter() == filetree.DisplayAll {
+		if fileTreeViewModel.GetStatusFilter() == filetree.DisplayAll {
 			fileTreeViewModel.SetStatusFilter(filetree.DisplayConflicted)
 			self.c.Contexts().Files.GetView().Subtitle = self.c.Tr.FilterLabelConflictingFiles
 		}
-	} else if conflictFileCount == 0 && fileTreeViewModel.GetFilter() == filetree.DisplayConflicted {
+	} else if conflictFileCount == 0 && fileTreeViewModel.GetStatusFilter() == filetree.DisplayConflicted {
 		fileTreeViewModel.SetStatusFilter(filetree.DisplayAll)
 		self.c.Contexts().Files.GetView().Subtitle = ""
 	}
--- a/pkg/gui/controllers/helpers/search_helper.go
+++ b/pkg/gui/controllers/helpers/search_helper.go
@ -33,6 +33,8 @@ func NewSearchHelper(
 func (self *SearchHelper) OpenFilterPrompt(context types.IFilterableContext) error {
 	state := self.searchState()

+	state.PrevSearchIndex = -1
+
 	state.Context = context

 	self.searchPrefixView().SetContent(context.FilterPrefix(self.c.Tr))
@ -238,7 +240,7 @@ func (self *SearchHelper) ReApplyFilter(context types.Context) {
 	filterableContext, ok := context.(types.IFilterableContext)
 	if ok {
 		state := self.searchState()
-		if context == state.Context {
+		if context == state.Context && self.c.Context().Current().GetKey() == self.c.Contexts().Search.GetKey() {
 			filterableContext.SetSelection(0)
 			filterableContext.GetView().SetOriginY(0)
 		}
--- a/pkg/gui/controllers/submodules_controller.go
+++ b/pkg/gui/controllers/submodules_controller.go
@ -125,7 +125,7 @@ func (self *SubmodulesController) GetOnRenderToMain() func() {
 				if file == nil {
 					task = types.NewRenderStringTask(prefix)
 				} else {
-					cmdObj := self.c.Git().WorkingTree.WorktreeFileDiffCmdObj(file, false, !file.HasUnstagedChanges && file.HasStagedChanges)
+					cmdObj := self.c.Git().WorkingTree.WorktreeFileDiffCmdObj(file, false, !file.HasUnstagedChanges && file.HasStagedChanges, nil)
 					task = types.NewRunCommandTaskWithPrefix(cmdObj.GetCmd(), prefix)
 				}
 			}
--- a/pkg/gui/controllers/switch_to_diff_files_controller.go
+++ b/pkg/gui/controllers/switch_to_diff_files_controller.go
@ -80,12 +80,12 @@ func (self *SwitchToDiffFilesController) enter() error {
 		}
 	}

+	commitFilesContext.ClearFilter()
 	commitFilesContext.ReInit(ref, refsRange)
 	commitFilesContext.SetSelection(0)
 	commitFilesContext.SetCanRebase(canRebase)
 	commitFilesContext.SetParentContext(self.context)
 	commitFilesContext.SetWindowName(self.context.GetWindowName())
-	commitFilesContext.ClearSearchString()
 	commitFilesContext.GetView().TitlePrefix = self.context.GetView().TitlePrefix

 	self.c.Refresh(types.RefreshOptions{
--- a/pkg/gui/filetree/commit_file_tree.go
+++ b/pkg/gui/filetree/commit_file_tree.go
@ -15,6 +15,8 @@ type ICommitFileTree interface {
 	GetAllItems() []*CommitFileNode
 	GetAllFiles() []*models.CommitFile
 	GetRoot() *CommitFileNode
+	SetTextFilter(filter string, useFuzzySearch bool)
+	GetTextFilter() string
 }

 type CommitFileTree struct {
@ -23,6 +25,8 @@ type CommitFileTree struct {
 	showTree       bool
 	common         *common.Common
 	collapsedPaths *CollapsedPaths
+	textFilter     string
+	useFuzzySearch bool
 }

 func (self *CommitFileTree) CollapseAll() {
@ -93,15 +97,34 @@ func (self *CommitFileTree) GetAllFiles() []*models.CommitFile {
 	return self.getFiles()
 }

+func (self *CommitFileTree) getFilesForDisplay() []*models.CommitFile {
+	files := self.getFiles()
+	if self.textFilter != "" {
+		files = filterCommitFilesByText(files, self.textFilter, self.useFuzzySearch)
+	}
+	return files
+}
+
 func (self *CommitFileTree) SetTree() {
+	filesForDisplay := self.getFilesForDisplay()
 	showRootItem := self.common.UserConfig().Gui.ShowRootItemInFileTree
 	if self.showTree {
-		self.tree = BuildTreeFromCommitFiles(self.getFiles(), showRootItem)
+		self.tree = BuildTreeFromCommitFiles(filesForDisplay, showRootItem)
 	} else {
-		self.tree = BuildFlatTreeFromCommitFiles(self.getFiles(), showRootItem)
+		self.tree = BuildFlatTreeFromCommitFiles(filesForDisplay, showRootItem)
 	}
 }

+func (self *CommitFileTree) SetTextFilter(filter string, useFuzzySearch bool) {
+	self.textFilter = filter
+	self.useFuzzySearch = useFuzzySearch
+	self.SetTree()
+}
+
+func (self *CommitFileTree) GetTextFilter() string {
+	return self.textFilter
+}
+
 func (self *CommitFileTree) IsCollapsed(path string) bool {
 	return self.collapsedPaths.IsCollapsed(path)
 }
--- a/pkg/gui/filetree/commit_file_tree_view_model.go
+++ b/pkg/gui/filetree/commit_file_tree_view_model.go
@ -8,6 +8,8 @@ import (
 	"github.com/jesseduffield/lazygit/pkg/common"
 	"github.com/jesseduffield/lazygit/pkg/gui/context/traits"
 	"github.com/jesseduffield/lazygit/pkg/gui/types"
+	"github.com/jesseduffield/lazygit/pkg/i18n"
+	"github.com/jesseduffield/lazygit/pkg/utils"
 	"github.com/samber/lo"
 )

@ -39,6 +41,8 @@ type CommitFileTreeViewModel struct {
 	// we set this to true when you're viewing the files within the checked-out branch's commits.
 	// If you're viewing the files of some random other branch we can't do any rebase stuff.
 	canRebase bool
+
+	searchHistory *utils.HistoryBuffer[string]
 }

 var _ ICommitFileTreeViewModel = &CommitFileTreeViewModel{}
@ -52,6 +56,7 @@ func NewCommitFileTreeViewModel(getFiles func() []*models.CommitFile, common *co
 		ref:             nil,
 		refRange:        nil,
 		canRebase:       false,
+		searchHistory:   utils.NewHistoryBuffer[string](1000),
 	}
 }

@ -203,3 +208,51 @@ func (self *CommitFileTreeViewModel) SelectPath(filepath string, showRootItem bo
 		self.SetSelection(index)
 	}
 }
+
+// IFilterableContext methods
+
+func (self *CommitFileTreeViewModel) SetFilter(filter string, useFuzzySearch bool) {
+	self.ICommitFileTree.SetTextFilter(filter, useFuzzySearch)
+}
+
+func (self *CommitFileTreeViewModel) GetFilter() string {
+	return self.ICommitFileTree.GetTextFilter()
+}
+
+func (self *CommitFileTreeViewModel) ClearFilter() {
+	selectedNode := self.GetSelected()
+	var selectedPath string
+	if selectedNode != nil {
+		selectedPath = selectedNode.GetInternalPath()
+	}
+
+	self.ICommitFileTree.SetTextFilter("", false)
+
+	if selectedPath != "" {
+		self.ExpandToPath(selectedPath)
+		if idx, found := self.GetIndexForPath(selectedPath); found {
+			self.SetSelection(idx)
+			return
+		}
+	}
+	self.ClampSelection()
+}
+
+func (self *CommitFileTreeViewModel) ReApplyFilter(useFuzzySearch bool) {
+	self.ICommitFileTree.SetTextFilter(self.ICommitFileTree.GetTextFilter(), useFuzzySearch)
+}
+
+func (self *CommitFileTreeViewModel) IsFiltering() bool {
+	return self.ICommitFileTree.GetTextFilter() != ""
+}
+
+// used for type switch
+func (self *CommitFileTreeViewModel) IsFilterableContext() {}
+
+func (self *CommitFileTreeViewModel) FilterPrefix(tr *i18n.TranslationSet) string {
+	return tr.FilterPrefix
+}
+
+func (self *CommitFileTreeViewModel) GetSearchHistory() *utils.HistoryBuffer[string] {
+	return self.searchHistory
+}
--- a/pkg/gui/filetree/file_filter.go
+++ b/pkg/gui/filetree/file_filter.go
@ -0,0 +1,48 @@
+package filetree
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/commands/models"
+	"github.com/jesseduffield/lazygit/pkg/utils"
+	"github.com/sahilm/fuzzy"
+	"github.com/samber/lo"
+)
+
+type filePathSource struct {
+	files []*models.File
+}
+
+func (s *filePathSource) String(i int) string {
+	return s.files[i].Path
+}
+
+func (s *filePathSource) Len() int {
+	return len(s.files)
+}
+
+func filterFilesByText(files []*models.File, filter string, useFuzzySearch bool) []*models.File {
+	source := &filePathSource{files: files}
+	matches := utils.FindFrom(filter, source, useFuzzySearch)
+	return lo.Map(matches, func(match fuzzy.Match, _ int) *models.File {
+		return files[match.Index]
+	})
+}
+
+type commitFilePathSource struct {
+	files []*models.CommitFile
+}
+
+func (s *commitFilePathSource) String(i int) string {
+	return s.files[i].Path
+}
+
+func (s *commitFilePathSource) Len() int {
+	return len(s.files)
+}
+
+func filterCommitFilesByText(files []*models.CommitFile, filter string, useFuzzySearch bool) []*models.CommitFile {
+	source := &commitFilePathSource{files: files}
+	matches := utils.FindFrom(filter, source, useFuzzySearch)
+	return lo.Map(matches, func(match fuzzy.Match, _ int) *models.CommitFile {
+		return files[match.Index]
+	})
+}
--- a/pkg/gui/filetree/file_tree.go
+++ b/pkg/gui/filetree/file_tree.go
@ -46,8 +46,10 @@ type IFileTree interface {
 	GetFile(path string) *models.File
 	GetAllItems() []*FileNode
 	GetAllFiles() []*models.File
-	GetFilter() FileTreeDisplayFilter
+	GetStatusFilter() FileTreeDisplayFilter
 	GetRoot() *FileNode
+	SetTextFilter(filter string, useFuzzySearch bool)
+	GetTextFilter() string
 }

 type FileTree struct {
@ -57,6 +59,8 @@ type FileTree struct {
 	common         *common.Common
 	filter         FileTreeDisplayFilter
 	collapsedPaths *CollapsedPaths
+	textFilter     string
+	useFuzzySearch bool
 }

 var _ IFileTree = &FileTree{}
@ -80,24 +84,31 @@ func (self *FileTree) ExpandToPath(path string) {
 }

 func (self *FileTree) getFilesForDisplay() []*models.File {
+	var files []*models.File
 	switch self.filter {
 	case DisplayAll:
-		return self.getFiles()
+		files = self.getFiles()
 	case DisplayStaged:
-		return self.FilterFiles(func(file *models.File) bool { return file.HasStagedChanges })
+		files = self.FilterFiles(func(file *models.File) bool { return file.HasStagedChanges })
 	case DisplayUnstaged:
-		return self.FilterFiles(func(file *models.File) bool { return file.HasUnstagedChanges })
+		files = self.FilterFiles(func(file *models.File) bool { return file.HasUnstagedChanges })
 	case DisplayTracked:
 		// untracked but staged files are technically not tracked by git
 		// but including such files in the filtered mode helps see what files are getting committed
-		return self.FilterFiles(func(file *models.File) bool { return file.Tracked || file.HasStagedChanges })
+		files = self.FilterFiles(func(file *models.File) bool { return file.Tracked || file.HasStagedChanges })
 	case DisplayUntracked:
-		return self.FilterFiles(func(file *models.File) bool { return !(file.Tracked || file.HasStagedChanges) })
+		files = self.FilterFiles(func(file *models.File) bool { return !(file.Tracked || file.HasStagedChanges) })
 	case DisplayConflicted:
-		return self.FilterFiles(func(file *models.File) bool { return file.HasMergeConflicts })
+		files = self.FilterFiles(func(file *models.File) bool { return file.HasMergeConflicts })
 	default:
 		panic(fmt.Sprintf("Unexpected files display filter: %d", self.filter))
 	}
+
+	if self.textFilter != "" {
+		files = filterFilesByText(files, self.textFilter, self.useFuzzySearch)
+	}
+
+	return files
 }

 func (self *FileTree) ForceShowUntracked() bool {
@ -210,6 +221,16 @@ func (self *FileTree) CollapsedPaths() *CollapsedPaths {
 	return self.collapsedPaths
 }

-func (self *FileTree) GetFilter() FileTreeDisplayFilter {
+func (self *FileTree) GetStatusFilter() FileTreeDisplayFilter {
 	return self.filter
 }
+
+func (self *FileTree) SetTextFilter(filter string, useFuzzySearch bool) {
+	self.textFilter = filter
+	self.useFuzzySearch = useFuzzySearch
+	self.SetTree()
+}
+
+func (self *FileTree) GetTextFilter() string {
+	return self.textFilter
+}
--- a/pkg/gui/filetree/file_tree_view_model.go
+++ b/pkg/gui/filetree/file_tree_view_model.go
@ -8,6 +8,7 @@ import (
 	"github.com/jesseduffield/lazygit/pkg/common"
 	"github.com/jesseduffield/lazygit/pkg/gui/context/traits"
 	"github.com/jesseduffield/lazygit/pkg/gui/types"
+	"github.com/jesseduffield/lazygit/pkg/i18n"
 	"github.com/jesseduffield/lazygit/pkg/utils"
 	"github.com/samber/lo"
 )
@ -24,6 +25,7 @@ type FileTreeViewModel struct {
 	sync.RWMutex
 	types.IListCursor
 	IFileTree
+	searchHistory *utils.HistoryBuffer[string]
 }

 var _ IFileTreeViewModel = &FileTreeViewModel{}
@ -32,8 +34,9 @@ func NewFileTreeViewModel(getFiles func() []*models.File, common *common.Common,
 	fileTree := NewFileTree(getFiles, common, showTree)
 	listCursor := traits.NewListCursor(fileTree.Len)
 	return &FileTreeViewModel{
-		IFileTree:   fileTree,
-		IListCursor: listCursor,
+		IFileTree:     fileTree,
+		IListCursor:   listCursor,
+		searchHistory: utils.NewHistoryBuffer[string](1000),
 	}
 }

@ -220,3 +223,51 @@ func (self *FileTreeViewModel) ExpandAll() {
 		self.SetSelectedLineIdx(index)
 	}
 }
+
+// IFilterableContext methods
+
+func (self *FileTreeViewModel) SetFilter(filter string, useFuzzySearch bool) {
+	self.IFileTree.SetTextFilter(filter, useFuzzySearch)
+}
+
+func (self *FileTreeViewModel) GetFilter() string {
+	return self.IFileTree.GetTextFilter()
+}
+
+func (self *FileTreeViewModel) ClearFilter() {
+	selectedNode := self.GetSelected()
+	var selectedPath string
+	if selectedNode != nil {
+		selectedPath = selectedNode.GetInternalPath()
+	}
+
+	self.IFileTree.SetTextFilter("", false)
+
+	if selectedPath != "" {
+		self.ExpandToPath(selectedPath)
+		if idx, found := self.GetIndexForPath(selectedPath); found {
+			self.SetSelection(idx)
+			return
+		}
+	}
+	self.ClampSelection()
+}
+
+func (self *FileTreeViewModel) ReApplyFilter(useFuzzySearch bool) {
+	self.IFileTree.SetTextFilter(self.IFileTree.GetTextFilter(), useFuzzySearch)
+}
+
+func (self *FileTreeViewModel) IsFiltering() bool {
+	return self.IFileTree.GetTextFilter() != ""
+}
+
+// used for type switch
+func (self *FileTreeViewModel) IsFilterableContext() {}
+
+func (self *FileTreeViewModel) FilterPrefix(tr *i18n.TranslationSet) string {
+	return tr.FilterPrefix
+}
+
+func (self *FileTreeViewModel) GetSearchHistory() *utils.HistoryBuffer[string] {
+	return self.searchHistory
+}
--- a/pkg/integration/tests/filter_and_search/filter_commit_files.go
+++ b/pkg/integration/tests/filter_and_search/filter_commit_files.go
@ -8,7 +8,7 @@ import (
 var FilterCommitFiles = NewIntegrationTest(NewIntegrationTestArgs{
 	Description:  "Basic commit file filtering by text",
 	ExtraCmdArgs: []string{},
-	Skip:         true, // skipping until we have implemented file view filtering
+	Skip:         false,
 	SetupConfig:  func(config *config.AppConfig) {},
 	SetupRepo: func(shell *Shell) {
 		shell.CreateDir("folder1")
--- a/pkg/integration/tests/filter_and_search/filter_commit_files_toggle_directory.go
+++ b/pkg/integration/tests/filter_and_search/filter_commit_files_toggle_directory.go
@ -0,0 +1,61 @@
+package filter_and_search
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/config"
+	. "github.com/jesseduffield/lazygit/pkg/integration/components"
+)
+
+var FilterCommitFilesToggleDirectory = NewIntegrationTest(NewIntegrationTestArgs{
+	Description:  "Toggle a filtered directory for a custom patch only adds visible files",
+	ExtraCmdArgs: []string{},
+	Skip:         false,
+	SetupConfig:  func(config *config.AppConfig) {},
+	SetupRepo: func(shell *Shell) {
+		shell.CreateDir("dir1")
+		shell.CreateFileAndAdd("dir1/apple-grape", "apple-grape content\n")
+		shell.CreateFileAndAdd("dir1/apple-orange", "apple-orange content\n")
+		shell.CreateFileAndAdd("dir1/grape-orange", "grape-orange content\n")
+		shell.Commit("first commit")
+	},
+	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Views().Commits().
+			Focus().
+			Lines(
+				Contains("first commit").IsSelected(),
+			).
+			PressEnter()
+
+		t.Views().CommitFiles().
+			IsFocused().
+			Lines(
+				Equals("▼ dir1").IsSelected(),
+				Equals("  A apple-grape"),
+				Equals("  A apple-orange"),
+				Equals("  A grape-orange"),
+			).
+			// Filter to show only "apple" files (staying in tree view)
+			FilterOrSearch("apple").
+			Lines(
+				// first item is always selected after filtering
+				Equals("▼ dir1").IsSelected(),
+				Equals("  A apple-grape"),
+				Equals("  A apple-orange"),
+			).
+			// dir1 is already selected; toggle for patch
+			PressPrimaryAction().
+			Lines(
+				Equals("▼ dir1").IsSelected(),
+				Equals("  ● apple-grape"),
+				Equals("  ● apple-orange"),
+			)
+
+		t.Views().Information().Content(Contains("Building patch"))
+
+		// Verify only the filtered files are in the patch (not grape-orange)
+		t.Views().Secondary().Content(
+			Contains("apple-grape").
+				Contains("apple-orange").
+				DoesNotContain("grape-orange"),
+		)
+	},
+})
--- a/pkg/integration/tests/filter_and_search/filter_files.go
+++ b/pkg/integration/tests/filter_and_search/filter_files.go
@ -8,7 +8,7 @@ import (
 var FilterFiles = NewIntegrationTest(NewIntegrationTestArgs{
 	Description:  "Basic file filtering by text",
 	ExtraCmdArgs: []string{},
-	Skip:         true, // Skipping until we have implemented file view filtering
+	Skip:         false,
 	SetupConfig:  func(config *config.AppConfig) {},
 	SetupRepo: func(shell *Shell) {
 		shell.CreateDir("folder1")
--- a/pkg/integration/tests/filter_and_search/filter_files_stage_all.go
+++ b/pkg/integration/tests/filter_and_search/filter_files_stage_all.go
@ -0,0 +1,50 @@
+package filter_and_search
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/config"
+	. "github.com/jesseduffield/lazygit/pkg/integration/components"
+)
+
+var FilterFilesStageAll = NewIntegrationTest(NewIntegrationTestArgs{
+	Description:  "Toggle all staging with a filter only stages visible files",
+	ExtraCmdArgs: []string{},
+	Skip:         false,
+	SetupConfig:  func(config *config.AppConfig) {},
+	SetupRepo: func(shell *Shell) {
+		shell.CreateDir("dir1")
+		shell.CreateFile("dir1/apple-grape", "apple-grape content\n")
+		shell.CreateFile("dir1/apple-orange", "apple-orange content\n")
+		shell.CreateFile("dir1/grape-orange", "grape-orange content\n")
+	},
+	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Views().Files().
+			Focus().
+			Lines(
+				Equals("▼ dir1").IsSelected(),
+				Equals("  ?? apple-grape"),
+				Equals("  ?? apple-orange"),
+				Equals("  ?? grape-orange"),
+			).
+			// Filter to show only "apple" files
+			FilterOrSearch("apple").
+			Lines(
+				// first item is always selected after filtering
+				Equals("▼ dir1").IsSelected(),
+				Equals("  ?? apple-grape"),
+				Equals("  ?? apple-orange"),
+			).
+			// Stage all visible files
+			Press(keys.Files.ToggleStagedAll).
+			// Clear the filter and verify only apple files are staged
+			PressEscape()
+
+		t.Views().Files().
+			IsFocused().
+			Lines(
+				Equals("▼ dir1").IsSelected(),
+				Equals("  A  apple-grape"),
+				Equals("  A  apple-orange"),
+				Equals("  ?? grape-orange"),
+			)
+	},
+})
--- a/pkg/integration/tests/filter_and_search/filter_files_stage_directory.go
+++ b/pkg/integration/tests/filter_and_search/filter_files_stage_directory.go
@ -0,0 +1,50 @@
+package filter_and_search
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/config"
+	. "github.com/jesseduffield/lazygit/pkg/integration/components"
+)
+
+var FilterFilesStageDirectory = NewIntegrationTest(NewIntegrationTestArgs{
+	Description:  "Staging a filtered directory only stages visible files",
+	ExtraCmdArgs: []string{},
+	Skip:         false,
+	SetupConfig:  func(config *config.AppConfig) {},
+	SetupRepo: func(shell *Shell) {
+		shell.CreateDir("dir1")
+		shell.CreateFile("dir1/apple-grape", "apple-grape content\n")
+		shell.CreateFile("dir1/apple-orange", "apple-orange content\n")
+		shell.CreateFile("dir1/grape-orange", "grape-orange content\n")
+	},
+	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Views().Files().
+			Focus().
+			Lines(
+				Equals("▼ dir1").IsSelected(),
+				Equals("  ?? apple-grape"),
+				Equals("  ?? apple-orange"),
+				Equals("  ?? grape-orange"),
+			).
+			// Filter to show only "apple" files
+			FilterOrSearch("apple").
+			Lines(
+				// first item is always selected after filtering
+				Equals("▼ dir1").IsSelected(),
+				Equals("  ?? apple-grape"),
+				Equals("  ?? apple-orange"),
+			).
+			// dir1 is already selected; stage it
+			PressPrimaryAction().
+			// Clear the filter to see all files and verify only apple files are staged
+			PressEscape()
+
+		t.Views().Files().
+			IsFocused().
+			Lines(
+				Equals("▼ dir1"),
+				Equals("  A  apple-grape"),
+				Equals("  A  apple-orange"),
+				Equals("  ?? grape-orange"),
+			)
+	},
+})
--- a/pkg/integration/tests/filter_and_search/filter_preserves_selection_on_model_change.go
+++ b/pkg/integration/tests/filter_and_search/filter_preserves_selection_on_model_change.go
@ -0,0 +1,63 @@
+package filter_and_search
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/config"
+	. "github.com/jesseduffield/lazygit/pkg/integration/components"
+)
+
+var FilterPreservesSelectionOnModelChange = NewIntegrationTest(NewIntegrationTestArgs{
+	Description:  "Verify that when a filter is active and the model changes, the selection is preserved",
+	ExtraCmdArgs: []string{},
+	Skip:         false,
+	SetupConfig:  func(config *config.AppConfig) {},
+	SetupRepo: func(shell *Shell) {
+		shell.EmptyCommit("first commit")
+		shell.NewBranch("branch-alpha")
+		shell.NewBranch("branch-beta")
+		shell.NewBranch("branch-gamma")
+		shell.NewBranch("checked-out-branch")
+	},
+	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Views().Branches().
+			Focus().
+			Lines(
+				Contains("checked-out-branch").IsSelected(),
+				Contains("branch-alpha"),
+				Contains("branch-beta"),
+				Contains("branch-gamma"),
+				Contains("master"),
+			).
+			FilterOrSearch("branch-").
+			Lines(
+				Contains("branch-alpha").IsSelected(),
+				Contains("branch-beta"),
+				Contains("branch-gamma"),
+			).
+			// Move cursor to a non-zero position
+			SelectNextItem().
+			SelectNextItem().
+			Lines(
+				Contains("branch-alpha"),
+				Contains("branch-beta"),
+				Contains("branch-gamma").IsSelected(),
+			)
+
+		// Trigger a model update while staying on the Branches view.
+		// Using a shell command that creates a new branch sorting after
+		// branch-gamma, so the selection index still points to the same item.
+		t.GlobalPress(keys.Universal.ExecuteShellCommand)
+		t.ExpectPopup().Prompt().
+			Title(Equals("Shell command:")).
+			Type("git branch branch-zeta").
+			Confirm()
+
+		// Verify that the selection is still on branch-gamma (not reset to 0)
+		t.Views().Branches().
+			Lines(
+				Contains("branch-alpha"),
+				Contains("branch-beta"),
+				Contains("branch-gamma").IsSelected(),
+				Contains("branch-zeta"),
+			)
+	},
+})
--- a/pkg/integration/tests/filter_and_search/nested_filter.go
+++ b/pkg/integration/tests/filter_and_search/nested_filter.go
@ -70,10 +70,7 @@ var NestedFilter = NewIntegrationTest(NewIntegrationTestArgs{
 			).
 			FilterOrSearch("grape").
 			Lines(
-				Equals("▼ /"),
-				Equals("  A apple"),
-				Equals("  A grape").IsSelected(),
-				Equals("  A orange"),
+				Equals("A grape").IsSelected(),
 			).
 			PressEnter()

@ -91,15 +88,12 @@ var NestedFilter = NewIntegrationTest(NewIntegrationTestArgs{
 		t.Views().CommitFiles().
 			IsFocused().
 			Lines(
-				Equals("▼ /"),
-				Equals("  A apple"),
-				Equals("  A grape").IsSelected(),
-				Equals("  A orange"),
+				Equals("A grape").IsSelected(),
 			).
 			Tap(func() {
 				t.Views().Search().IsVisible().Content(Contains("matches for 'grape'"))
 			}).
-			// cancel search
+			// cancel filter
 			PressEscape().
 			Tap(func() {
 				t.Views().Search().IsInvisible()
--- a/pkg/integration/tests/filter_and_search/nested_filter_transient.go
+++ b/pkg/integration/tests/filter_and_search/nested_filter_transient.go
@ -75,9 +75,7 @@ var NestedFilterTransient = NewIntegrationTest(NewIntegrationTestArgs{
 			).
 			FilterOrSearch("two").
 			Lines(
-				Equals("▼ /"),
-				Equals("  A file-one"),
-				Equals("  A file-two").IsSelected(),
+				Equals("A file-two").IsSelected(),
 			)

 		t.Views().Branches().
@ -96,7 +94,7 @@ var NestedFilterTransient = NewIntegrationTest(NewIntegrationTestArgs{

 		t.Views().CommitFiles().
 			IsFocused().
-			// the search on the commit-files context has been cancelled
+			// the filter on the commit-files context has been cancelled
 			Lines(
 				Equals("▼ /").IsSelected(),
 				Equals("  A file-one"),
--- a/pkg/integration/tests/patch_building/toggle_directory.go
+++ b/pkg/integration/tests/patch_building/toggle_directory.go
@ -0,0 +1,64 @@
+package patch_building
+
+import (
+	"github.com/jesseduffield/lazygit/pkg/config"
+	. "github.com/jesseduffield/lazygit/pkg/integration/components"
+)
+
+var ToggleDirectory = NewIntegrationTest(NewIntegrationTestArgs{
+	Description:  "Toggle a directory for a custom patch",
+	ExtraCmdArgs: []string{},
+	Skip:         false,
+	SetupConfig:  func(config *config.AppConfig) {},
+	SetupRepo: func(shell *Shell) {
+		shell.CreateDir("dir1")
+		shell.CreateFileAndAdd("dir1/file1", "file1 content\n")
+		shell.CreateFileAndAdd("dir1/file2", "file2 content\n")
+		shell.CreateFileAndAdd("dir1/file3", "file3 content\n")
+		shell.CreateFileAndAdd("other-file", "other content\n")
+		shell.Commit("first commit")
+	},
+	Run: func(t *TestDriver, keys config.KeybindingConfig) {
+		t.Views().Commits().
+			Focus().
+			Lines(
+				Contains("first commit").IsSelected(),
+			).
+			PressEnter()
+
+		t.Views().CommitFiles().
+			IsFocused().
+			Lines(
+				Equals("▼ /").IsSelected(),
+				Equals("  ▼ dir1"),
+				Equals("    A file1"),
+				Equals("    A file2"),
+				Equals("    A file3"),
+				Equals("  A other-file"),
+			).
+			NavigateToLine(Contains("dir1")).
+			PressPrimaryAction().
+			Lines(
+				Equals("▼ /"),
+				Equals("  ▼ dir1").IsSelected(),
+				Equals("    ● file1"),
+				Equals("    ● file2"),
+				Equals("    ● file3"),
+				Equals("  A other-file"),
+			)
+
+		t.Views().Information().Content(Contains("Building patch"))
+
+		// Toggle the directory again to remove all files from the patch
+		t.Views().CommitFiles().
+			PressPrimaryAction().
+			Lines(
+				Equals("▼ /"),
+				Equals("  ▼ dir1").IsSelected(),
+				Equals("    A file1"),
+				Equals("    A file2"),
+				Equals("    A file3"),
+				Equals("  A other-file"),
+			)
+	},
+})
--- a/pkg/integration/tests/test_list.go
+++ b/pkg/integration/tests/test_list.go
@ -232,12 +232,16 @@ var tests = []*components.IntegrationTest{
 	file.StageRangeSelect,
 	filter_and_search.FilterByFileStatus,
 	filter_and_search.FilterCommitFiles,
+	filter_and_search.FilterCommitFilesToggleDirectory,
 	filter_and_search.FilterFiles,
+	filter_and_search.FilterFilesStageAll,
+	filter_and_search.FilterFilesStageDirectory,
 	filter_and_search.FilterFuzzy,
 	filter_and_search.FilterMenu,
 	filter_and_search.FilterMenuByKeybinding,
 	filter_and_search.FilterMenuCancelFilterWithEscape,
 	filter_and_search.FilterMenuWithNoKeybindings,
+	filter_and_search.FilterPreservesSelectionOnModelChange,
 	filter_and_search.FilterRemoteBranches,
 	filter_and_search.FilterRemotes,
 	filter_and_search.FilterSearchHistory,
@ -354,6 +358,7 @@ var tests = []*components.IntegrationTest{
 	patch_building.SelectAllFiles,
 	patch_building.SpecificSelection,
 	patch_building.StartNewPatch,
+	patch_building.ToggleDirectory,
 	patch_building.ToggleRange,
 	reflog.Checkout,
 	reflog.CherryPick,