D'oh! Haven't seen this.
Anyway, you shouldn't change the original gameplay or missions and just enhance the game and fix some bugs. So player like me can enjoy playing the game like back in the 90s.

(I still now and then play through the campaign

)
So please don't change the original missions (except bug fixing).
But what you could do is renaming all the covert ops missions in sc-001.mix so they start with scg20ea.ini/scb20ea.ini and are then consecutively numbered. This makes them appear always on top of the new missions menu. Then self-made maps aren't listed between them and you can simply say that new maps should get numbers starting with scg27ea / scb28ea and higher.
This post has been edited by Lin Kuei Ominae: Aug 26 2009, 03:26 PM