Is github workable with stencyl?

Can you explain to me how to make it so every change is commitable to github if it is possible? right now, i can commit the original game folder but when i make changes to it, github does not recognize it as a different commit

I am also trying to work with a team using stencyl and the only way I can hook github up to stencyl was by copying and pasting the folder from stencyl in. Is there any way to link them using git or some other software or will we have to copy paste all summer.

Thanks in advance