Wanted to make a sily side mod where you're clones fighting clones and i was wondering if such a thing is even possible since i have never seen anything like that being made in any mod. I assume it's more difficult than just dropping the rep files in the cis side folder and replacing everything, right?

you can try copying the rep folder and rename everything to cis

You would have to put the Rep files in the CIS side, but you would have to change all of them so they start with "CIS" instead of "REP". You would also have to go into all of the CIS Clone trooper files and change instances of "REP" to "CIS". Considering the number of files, this is likely to be a time consuming task. JediMoose32 has YouTube Videos on editing a stock side that should provide more details on what you would need to do to achieve this.

It also might not be a practical idea unless you make significant changes to one side's color scheme or armor so players know who to shoot at.

Answering this as a technical question: It doesn't matter what side folder a unit is from. You can stay in the REP folder, make a new side or move everything to the CIS if you want; it won't change anything. The only problem I can see with this, is if you try assigning the same unit to 2 different teams. I think that might crash the game. But all you need to do to work around that is make 2 copies of the unit odf files. Then you can load one unit odf and put it on team 1, load the other unit odf to put the same unit on team 2. ie make rep_inf_ep3_rifleman_1 and rep_inf_ep3_rifleman_2 exactly the same. Then put rep_inf_ep3_rifleman_1 on team 1 and rep_inf_ep3_rifleman_2 on team 2. Changing the team names to Republic, Republic would need some changes in the mission lua and I think uses the editlocalize tool.

Creatively though, I agree with INMR that you should probably make the sides more distinguished. Even in the context that the same group is fighting amongst themselves, actually name the teams and have lots of visual cues like different coloured laser bolts, armour markings, etc. to make the game less confusing. (If you're ambitious you can have subtle sound cues too).