I think it should be a good idea to use all space efficiently. On macOS the window topbar (grey bar) is a 20px high bar that only contains the close, maximise and minimise buttons (see screenshot, below). I think these buttons should be merged with the actual application, as shown in the screenshot below (Spark Mac Mail client).
To make this happen, ‘Project’ could go down on top of the file tree, so that the buttons could go left aligned on the spot of ‘project’. This would make the application window seem a bit more whole.
To visualise what I’m saying, see the quick mockup below.