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/commands/git_commands/working_tree.go

@@ -49,8 +49,10 @@ func (self *WorkingTreeCommands) StageFiles(paths []string, extraArgs []string)
 }
 
 // StageAll stages all files
-func (self *WorkingTreeCommands) StageAll() error {
-	cmdArgs := NewGitCmd("add").Arg("-A").ToArgv()
+func (self *WorkingTreeCommands) StageAll(onlyTrackedFiles bool) error {
+	cmdArgs := NewGitCmd("add").
+		ArgIfElse(onlyTrackedFiles, "-u", "-A").
+		ToArgv()
 
 	return self.cmd.New(cmdArgs).Run()
 }