Can you make that items automatically stacks when updated?

Example:
I made Potion stackable so filling a Glass Bottle with water create one stack of one option and if I fill one more Glass Bottle it create one other stack of one option. I have to sort manually my items.

That is the goal of the plugin, but as you've found, there are some cases that are not covered yet. I'll certainly look into glass bottle filling and see what I can do.

I think that will be the same issue with bucket, water bucket and lava bucket :)

Those are already supported

Water bottle filling has been fixed in v1.0.8