Perhaps one of the most prominent examples of a combined GUI + CLI is AutoCAD. AutoCAD has reached the point where (almost?) everything that can be done with the CLI can now be done with the GUI too, but it was not always this way.
The CLI still remains as a super important tool for those proficient with AutoCAD, since it allows them ready access to many "GUI shortcuts" (even if these commands existed well before the GUI functionality they now act as a shortcut for).
Another interesting fact is that in AutoCAD, the CLI is also designed for use with one hand (say the left hand), while the other hand remains free to use the mouse.
The CLI interface for text editors for Emacs and Vim might also be interesting examples, although I know far less about them.
In general, I am interested in CLIs that aren't meant to be UNIX/DOS-like, but are meant to augment the user's productivity while using a particular tool (be it CAD software, text editing, or other). If looking at UNIX/DOS-like CLIs, I am interested in knowing what research-based/non-ideological ideas people have for improving such CLI.
Are there any established pattern libraries or style guides (similar to the iOS Human Interface Guidelines or the Windows User Experience Interaction Guidelines) for combined graphical and command line interfaces?