' Linux '
hello Sir , There are Lot of possibilities why your Server is hacked , what im supposing is that You are on Dedicated ip , so if you are using dedicated ip i believe that The hacker have an exploit on your website or another website hosted on your server that way the hacker is able to control your server and all files under the linux username he is assigned to , second the hacker is able to exploit the local machine using vulnerability in the linux kernel ,it is 80% written in c , i will need to take look on your server to tell you what is there , message me so we can speak over chat for more details ,