Marking notes are the data that will be applied to projects for marking. In the Gild Marker View, they are called line notes because, before they can affect the mark of a project, they must be applied to particular lines of text in files in that project.1
Though line notes are applied to particular projects and files, they are also contained within the sections of the scheme that the current session is using.
Below is an image for an example of how line notes are contained and applied within a session. It may help make these relationships a little more clear:
