I create art in GIMP, test some animations in Aseprite, but the bulk of animating is done inside the game dev software itself (Construct 3).
I published the source files on my Patreon: https://www.patreon.com/collection/2053809?view=expanded
The basic gist is, each node except the first one has a parent node (right click -> Hierarchy -> add selection). When a parent node is clicked on, all its children nodes get unlocked and can now be interacted with.
Nodes have special parameters: Name + Description, Level, Upgrade Stat + Upgrade Number, Cost + Currency Type.