The MonoDevelop Solution Pad shows projects and folders that correspond to real folders on disk, but by default it only shows files and folders within them that have been included in the project. This behaviour can be changed using the Display Options->Show All Files toggle option in the Solution Pad context menu. The option is contextual — it applies only to the item on which it is toggled, and recursively applies to all its children. To have it apply to the whole Solution Pad, toggle it on the root solution or workspace.
When Show All Files is enabled, files that are not included in the project will be shown in the folder hierarchy, but with semi-transparent icons to indicate their status. They can be edited and moved and so on, though they will not be included in the code completion system. Perhaps the most useful thing that this option enables is the Include in project context menu command on non-included files, which can be used to include them in the project quickly and easily.