Within each node of the Version Control tool window, you can display the modified files as a flat list, or as a directory tree.

To toggle grouping items by directories, do one of the following
  • Click the Folder icon.
  • Use ⌘P or ⌘P⌘P or ⌘P⌘P or ⌘P^ P, ⌃P or ⌃P^ P, ⌃P or ⌃P keyboard shortcut.