Wolverine had the boneclaws but they were covered in adamantium right? So after his adamantium claws got chopped off he just grew new bone claws?

This plot is confusing. Why was there all the drama about Mariko being left everything in the will if Yashida knew he wasn't going to die? Where did his boneclaws come from? What were the ninjas trying to do and why was Viper even a character?