I made a extra side for the fighter, but just copying over the whole vehicle side from the convo pack assets is the safer (and easier) way.
The procedure you did should be like following:
1. Copy over the vehicle side assets into your sides folder (???\BF2_ModTools\data_***\Sides). Make sure that when you open it you get right to the odf, msh etc. folders, not another folder called vehicles (double foldering can happen with extracted files).
2. Go to ???\BF2_ModTools\assets\sides and copy the Common folder into your sides folder. It contains most of the base classes, most custom sides need them. Now you should have a Common folder and a vehicles folder in your sides folder (and propably one called tur, but that one is irrelevant. It contains the turrets that are placed around stock maps).
3. Go to ???\BF2_ModTools\data_***\_BUILD\Sides (never mistake that for your sides folder). Make a copy of a folder that has is no munged files in it (not called Common and contains nothing more than a clean.bat and a munge.bat), GAR for example. Now rename the copy to VEHICLES.
4. Now go to ???\BF2_ModTools\data_***\Common\scripts\*** and open the LUA that belongs to your gamemode/era. Add
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ReadDataFile("dc:SIDE\\vehicles.lvl",
"cis_fly_geofighter")
to the other side-loading ReadDataFile stuff, like so:
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ReadDataFile("sound\\yav.lvl;yav1cw")
ReadDataFile("SIDE\\rep.lvl",
"rep_inf_ep3_rifleman",
"rep_inf_ep3_rocketeer",
"rep_inf_ep3_engineer",
"rep_inf_ep3_sniper",
"rep_inf_ep3_officer",
"rep_inf_ep3_jettrooper",
"rep_hover_fightertank",
"rep_hero_anakin",
"rep_hover_barcspeeder")
ReadDataFile("dc:SIDE\\vehicles.lvl",
"cis_fly_geofighter")
ReadDataFile("SIDE\\cis.lvl",
"cis_inf_rifleman",
"cis_inf_rocketeer",
"cis_inf_engineer",
"cis_inf_sniper",
"cis_inf_officer",
"cis_inf_droideka",
"cis_hero_darthmaul",
"cis_hover_aat")
If you scroll a bit down you'll see lots of SetMemoryPoolSize lines.
Add
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SetMemoryPoolSize("EntityFlyer", 36)
to the list. The number defines how much flyers can spawn at maximum on the map.
(5. While you are at it, scroll a few lines higher to
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SetMaxFlyHeight(30)
SetMaxPlayerFlyHeight (30)
And set the numbers from 30 to something like 500. The value defines how high you can get with flyers and jetpacks. 30 isn't enough if flyers are involved.)
The LUA can be saved and closed now.
6. Open your map in ZE. Go into the conquest layer, go into object mode, select the CommandPost you want your vehicle to be assosiated with and type into the property tab (to the right) cp1_control (or cp2_control, cp3_control or whatever, depends on wich CommandPost you edit, I'll take cp1 for this tut) into the space below ControlRegion. This tells the CommandPost that it has a control region and that it is called cp1_control.
7. Switch into region mode click on New Group and place the box close to your CommandPost. Select it, keep the letter C on your keyboard pressed and move the box to where you like it and pull it a bit into the ground using the 3 mouse buttons (#3 is the wheel). THere are two Edits called Region ID and Class Properties. Type cp1_control into both. Now it's the region your CommandPost is looking for.
8. Now place a vehicle spawner into your Region, select it, put cp1 (varies if you decided to take another Post) into the ControlZone, type cis_fly_geofighter into the ClassCISATK Edit, Click on the Page Dn button and do the same with the ClassCISDEF Edit (I assumed you want the vehicle for the CIS).
Save the map, close ZE, run Modtools VisualMunge.exe (???\BF2_ModTools\data_***\_BUILD), keep checkbox called common checked, open the Sides list and select vehicle, then munge.