First you need to make sure that you have indeed created an enemy ship. Player ships won't do, Slipstream has a seperate setting for creating enemy ships. What ships can appear as enemies ingame is governed by bleuprint lists in
autoBlueprints.xml. Like this one for example:
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<blueprintList name="SHIPS_ZOLTAN">
<name>ZOLTAN_FIGHTER</name>
<name>ZOLTAN_BOMBER</name>
</blueprintList>
To mod in your ship first extract the game data with SMM. Now look at
autoBlueprints.xml and decide which ship lists you want the enemy to be part of. Create a
autoBlueprints.xml.append file containing those lists, with your ship added to them as a new entry. Like this;
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<blueprintList name="SHIPS_ZOLTAN">
<name>ZOLTAN_FIGHTER</name>
<name>ZOLTAN_BOMBER</name>
<name>MY_SHIP_ID_FOUND_IN_SHIP_BLUEPRINT</name>
</blueprintList>
(You can influence the likelihood of your ship appearing by adding it multiple times. Entries in lists are selected randomly with equal chance for each entry). Save your
.append file and place it in the data folder of your uncompressed ship mod. Re-compress your ship mod into an
.flt file and you are done.
If you want to ensure compatibility you can use SMMs advance tags to "inject" your ship into any existing lists. This ensure that your mod does not overwrite lists that have been changed by other mods. SMMs readme explains a little how to use the tags, but if you want details you'll have to ask someone else (I don't have much experience with that stuff).