I currently build two websites for two different companies. Each company runs PPC campaigns from these web sites.
If I use the same common files to build the two websites, would Google detect them as the same company? That's something I don't want. I want Google to see them as two separate companies.
Added to this, the two websites are hosted in the same server. And they share common files.
I have them share common files since they are similar in design and helps me have a cleaner code base.