With the addition of new features, I find that the structure of the project is a mess and that it's hard to find your way around. It was already a bit of a mess and the structure wasn't very suitable, so it's not going to get any better. I think it would be a good idea to revise it a bit, and I don't think that would require too much effort.
Here's my proposal, it's just a start but I'd really like to have your thoughts on it.
/
globals/
id_gen.gd
path.gd
util.gd
[...]
ui/
assets/
fonts/
NotoSans-Bold.ttf
[...]
icons/
copy.svg
hand.svg
int_icon.svg
event.svg
[...]
theme_default/
main.tres
list_item.tres
[...]
scenes/
prefabs/
graph_nodes/
sentence/
icon.svg
sentence_node.tscn
sentence_node.gd
[...]
fields/
[...]
graph_edit/
monologue_graph_edit.tscn
monologue_graph_edit.gd
[...]
windows/
welcome_window/
welcome_window.tscn
welcome_window.gd
[...]
app/
app.tscn
[...]
run/ (old test)
menu/
menu.tscn
[...]
main/
main.tscn
[...]
examples/
[...]
docs/ (?)
[...]
With the addition of new features, I find that the structure of the project is a mess and that it's hard to find your way around. It was already a bit of a mess and the structure wasn't very suitable, so it's not going to get any better. I think it would be a good idea to revise it a bit, and I don't think that would require too much effort.
Here's my proposal, it's just a start but I'd really like to have your thoughts on it.