It doesn't say who cloned Curly.
If we take Wind Fortress as canon and not a mini-game like Boss Rush...
Wind Fortress is located at the bottom of the island; it appears as though even the bottom of the island once had an lookout/palace or something (guarded by Gaudi no less?!)...
Above that, the actual Wind Fortress looks like something possibly newer, but still in ruins. That's the area you first see a Curly clone. Equipped with machineguns and some kind of projecticle weapon, they pack a punch!
And above that, in the heart of mod, there's some kind of weird lab. Full of pods of Curly clones. (btw all clones have red eyes, while Curly has blue)
They seem pretty helpless when they first awaken from the pod, crawling out towards you... Kinda makes you feel bad to shoot them ><
They all appear to be naked too lol, and they aren't cloned with guns. Only the clones in Wind Fortress had them.
Past the pods there is a strange machine..... with Curly inside. It's a machine with a giant display
with a big W and a circle on it!
From there a bunch of clones will attack you, and for each one that you kill; two will take its place! So, it's easy to become over-run....
Who made it? Hmmm.... Curly doesn't know when she wakes up, and Quote of course is as talkative as normal. I didn't see any insignia's on the machine...
Is it okay to post a picture of the machine?
If I were to speculate ... it doesn't look like technology from the island. Meaning it's probably a machine from the surface.
Is it from those who created Quote and Curly? Or perhaps more likely, some enemy of those who created Quote and Curly? ... Or is it a relic of the past? From the War for instance? A robot cloning machine running haywire? Or is there an intelligent force at work?
Did Curly just climb in, and take a nap? Was she lured in? Or was she kidnapped and put into the machine? Hmmm......
In the end, I imagine Wind Fortress isn't really canon, as it doesn't take itself very seriously. There's practically no plot, or text. It's just a fun teaser/mod made by Pixel.
However, it could be like a trailer/demo or an idea for an entirely new game. Even if he doesn't make it; you could take it as inspiration to craft a whole new game around some of those ideas. A Cave Story 2 beta?
Personally, I like to think the machine itself is pulling the strings. A giant intelligent computer (network?) AI is up to no good...
EDIT : Most importantly, what does G in G-CLONE stand for??
Thannnnnnnnk you 
