Okay. I've added the change weapon SEXPs and I've updated the set-primary/secondary-ammo SEXPs to support a new feature. The rearm limit is now a specifiable option in all 4 SEXPs.
This means that you can have a mission where the player is given a brand new type of bomb and told that the 4 he is carrying are the only ones in existance. A support ship can still be present in the mission but will not rearm this weapon even though any other weapons would be rearmed. All you would have to do is make a SEXP like this.
When
-true
-Set-Secondary-Ammo
--Alpha 1
--2 <------------------------Name of the bank holding the weapon
--4 <------------------------Number of prototype weapons
--0 <------------------------Number of weapons a support ship should fill the player up to.
Previously your only option would have been to disallow support ships.
The Change-weapon SEXP will take arguments for the amount of ammo and rearm limit as optional extras too. It's worth noting that the names of the SEXPs only denote which banks are being changed NOT which weapons. It's perfectly possible to stick primary weapons in the secondary bank using the set-Secondary-weapon SEXP and visa versa. In fact you can stick capship weapons in either bank using these SEXP but I've got absolutely no idea what would happen if you tried.

Changes are in CVS.