This is a big difference the two apps. PageFour’s structure was very simple — all notebooks existed inside a single parent folder, almost a ‘super notebook.’ Opening a different notebook was the same as opening a folder inside a notebook. PageFour folders and pages had corresponding folders and files with the same names in the Data folder.
One of the draw backs of this approach was that you could not create notebooks outside the PageFour Data folder, or easily copy them around and open them on different devices. A second drawback was the inability to create folders or pages with non-standard names, and to have pages within pages.
The Atomic Scribbler project structure is completely different. A project is stand-alone and can exist anywhere. The Project Manager is a loose way of opening recent projects, but it’s not a definitive list of projects — that doesn’t and can’t exist, as projects can be renamed, copied to external drives, not be accessible at a particular time, etc.
There is no direct link between a folder in a project to an actual folder on your PC. Atomic folders are virtual and don’t really exist as folders. A project’s meta data is stored in a single project database, completely separate to all other projects.
The core Atomic Scribbler window is directly linked to the open project. As such, you can’t open or access two projects at the same time in the same instance, not like you could with PageFour. Changing this would be a huge undertaking I’m afraid.