A Project class contains project-specific data like name, undo_redo, frames, layers, tags and brushes. These variables have been moved from Global. This is the first step towards multiple tab support, where each tab will be a different Project.
Instead of having 2 variables for left & right nodes, use an array instead. This will help with better looking code, automation and less repetitive code, as seen in ToolButtons.gd. Move related refactoring will follow.
Made a new "src" folder that will contain the source code files, like all the GDScript and scene files. Please read this for more details: https://www.gdquest.com/docs/guidelines/best-practices/godot-gdscript/
It made no sense to keep scenes separate from their scripts. More file organizing will follow soon.