From looking at Cooldown.lua, Cooldown:SetCooldown now has charges and maxCharges as additional arguments.

function CooldownFrame_SetTimer(self, start, duration, enable, charges, maxCharges)
    self:SetCooldown(start, duration, charges, maxCharges)
end

Side note:
Your branch of OmniCC appears to be out of date vs the latest release on Curse. Otherwise, I'd have created a pull request myself :)

Oh crap, sorry about that.

I will update the branch soon as I get home (on work now).

Ok, master updated.