Ashaekin: Yes, you can use a program to make weapons appear in your hand, just as you did in your profile. Weapons without specific commands attached to them usually appear with the armour, or can be chosen to appear through the user interface of the IMS.
Stohlen: Yes, you will be able to add programs throughout the campaign. You can also use the IMS' image interpretation capabilities to create effects without programs as mentioned in the opening post, but that is considered inferior to programs.
Also, as far as I understand, your Saber siege is a short-range siege weapon, and your Saber shot is a short-range rapid-fire weapon. Is that correct?