The old way weren't causing any issues, but it would have caused with double-digit version numbers. Also fixed backwards compatibility issue with 0.6.2 and previous versions.
It used to save the linked cel array which contained the canvas nodes into the .pxo. This, however, does not make sense, because the canvas nodes are being recreated when a .pxo is loaded. Therefore, they are different nodes than they used to be.
Now, an array containing the frame numbers which have cels linked for each frame is being saved and loaded into the pxo.
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.