I am still learning the game and I just got one of the upgrade kits for the clone phase one troopers. If I add the Commander trooper which counts as a personnel does that still increase the number of models in the unit to 5 (four normal clones and the commander as the leader) or is it still 4 models (three normal clones and the commander as the leader)?

you have 5 and the captain personnel as the leader of the unit as it states, "add one phase 1 clone captain mini"

Ok cool then what happens to the original leader model that came with the unit would I just treat that as a normal trooper for that unit?

42 minutes ago, Kayzen said:

Ok cool then what happens to the original leader model that came with the unit would I just treat that as a normal trooper for that unit?

Yes. Or you could use the extra trooper instead.

5 hours ago, SailorMeni said:

Yes. Or you could use the extra trooper instead.

Actually, it could happen that due to LoS rules, you get your captain killed. This means you lose the benefeits of the captain card and the new squad leader is the usual leader mini.

21 minutes ago, Qwar said:

Actually, it could happen that due to LoS rules, you get your captain killed. This means you lose the benefeits of the captain card and the new squad leader is the usual leader mini.

No it doesn't. Due to the captain being the Leader, you replace one of the standard minis with the Captain's mini. Same as what happens with the Heavy weapon in a strike team.
EDIT: Page 50 of the RRG:
"If a unit leader that was added by an upgrade card with the leader keyword is defeated, replace one of the remaining minis in the unit with the leader mini from that upgrade card."

My bad, I stand corrected.

2 hours ago, Qwar said:

My bad, I stand corrected.

I fully understand why you would think that after the other discussion about medics and such though.