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For every mod you make, any type, do you have to make a new side?

Nope. The game defaults to stock sides, and as long as you don't want to modify the units that came with the game, you can choose any premade unit you want through the .lua.

I want to give the Clone Commander a Rifle, will I need a custom side?

Well, does the Commander normally have a blaster rifle in the shipped sides?

That should answer your question, in fact Maveritchell already gave you the needed reply, this question was pointless.

Giving the Commander a Rifle= Custom unit= Custom Side, ergo, you need to make one.

However, you don't need to make an entire new side. Just a small one with the clone commander in it, the necessary files for him, and weapons.

in other words get its tgas msh's and odfs and weapon odfs and that should work.

Why do you have to make a new side?

How else do you think you make changes to units?

Just like you do in BF1... you edit the unit from his original side.

You can edit the original unit, but you still have to "make" a new side. The game just doesn't magically read what changes you make to something that's not even part of the game (i.e. whatever is in your modtools folders).

You can just edit the master side, and edit the odf. If you want a new unit that doesn't replace the master one, read the jedi creation doc to make a new side.

Of course sides don't magically munge themselces In BFII:
1. Units are stored under the assets/sides/ folder. (rep=republic etc.)
2. Copy any faction's folder (ex. REP, I'll just say FACID to be generic) AND THE COMMON FOLDER to any data_MODID/sides/ folder first.
3. Edit the content in the data_MODID/sides/FACID.
4. Go to data_MODID/_BUILD and run visual munge
5. Select the FACID from the sides dropdown.
6. Hit munge, then wait wait wait until it says it's done.
7. Go to C:\Program Files\LucasArts\Star Wars Battlefront II\GameData\Addon\MODID\SIDES\ and copy FACID.lvl and FACIDSHELL.lvl to \GameData\DATA\_LVL_PC\SIDE. BUT WAIT! DO NOT OVERWRITE THE EXISTING LVL'S!!! Cut them out and put them in My Document or something so you have them for backup.
8. Run Battlefront, and you should see your changes in the game

And this is what you do in BFI, so there is no confusion
Munging a side:
INFO: Everything pertaining to the Republic faction is stored in the sides folder REP. The REP folder should always be under the SIDES folder.

1. Open BFBuilder.hta
2. Create a new project, fill in the neccesary info. Let's just say you named your map test.
3. Copy the REP folder from assets/sides to Datatest/sides/
4. Edit the files in Datatest/sides/rep/, such as replacing a texture, or changing an ODF. Make sure the new files have the same name as the original.
5. Go to Datatest/_BUILD_PC/, and EDIT the munge.bat. You should get to a point where it says:

cd Sides
REM STARTSIDES
REM cd GAM
REM @call munge.bat
REM cd ..
REM ENDSIDES
cd ..

REM means to comment out. Lines with REM on it won't be ran. cd means to change directory, so cd sides means to change the directory to the sides folder. cd .. means to go up a folder. Notice how the side "GAM" (for gammorean) is already there (It was created by BFBuilder). All these lines do is run the munge.bat in _BUILD_PC/Sides/GAM. But we wan't to munge the REP side, so change GAM to REP, and remove the REM's so the lines are ran:

cd Sides
REM STARTSIDES
cd REP
@call munge.bat
cd ..
REM ENDSIDES
cd ..

6. Go to _BUILD_PC/Sides/REP. Well there isn't one, that's a problem. So create it! Ok copy the munge.bat and clean.bat from _BUILD_PC/Sides/GAM to _BUILD_PC/Sides/REP. \
7. EDIT the munge.bat that you just pasted. It should look like this.

@call ..\munge_side.bat Gam
@call ..\munge_fpm.bat Gam

Well that's bad, it should be Rep not Gam, so change it.

@call ..\munge_side.bat Rep
@call ..\munge_fpm.bat Rep

Phew, that's all the codework. Notice how there are more than one munge.bat's. One calls another, that calls another, and it gets confusing.
8. Open up BFBuilder, if it's not already open, and load your level, test, if it's not already loaded.
9. Hit the munge button, AND WAIT! NEVER INTERUPT A MUNGE! WAIT UNTILL NOTEPAD POPS UP WITH THE LOG. It may take a long time.
10. Go to BFBuilder/AddOn/Test/Data/_lvl_pc/Side/ . There should be a rep.lvl. If not, one of the munge.bat's is incorrect.
11. If you do indeed have a rep.lvl, congratulations! You're smart! Cut it out of there, and paste it in:
C:\Program Files\LucasArts\Star Wars Battlefront\GameData\Data\_LVL_PC\SIDE. BUT WAIT! DO NOT OVERWRITE THE ORIGINAL REP.LVL! Back up the original before you paste in yours.
12. Run the game. You should see your changes.

Get it?

Yes, thank you.