Stage only tracked files when staging all in filter-by-tracked-files view

Also, fix two other commands that stage all files under the hood:
- when continuing a rebase after resolving conflicts, we auto-stage all files,
  but in this case we never want to include untracked files, regardless of the
  filter
- likewise, pressing ctrl-f to find a base commit for fixup stages all files for
  convenience, but again, this should only stage files that are already tracked

pkg/gui/controllers/helpers/merge_and_rebase_helper.go

@@ -244,7 +244,7 @@ func (self *MergeAndRebaseHelper) PromptToContinueRebase() error {
 					Prompt: self.c.Tr.UnstagedFilesAfterConflictsResolved,
 					HandleConfirm: func() error {
 						self.c.LogAction(self.c.Tr.Actions.StageAllFiles)
-						if err := self.c.Git().WorkingTree.StageAll(); err != nil {
+						if err := self.c.Git().WorkingTree.StageAll(true); err != nil {
 							return err
 						}