How to upload file to the root of the site not via admin panel

So, yesterday I've got an e-mail from Google, which told me, that someone appears to registered as second owner of my website. How - I don't know. And in the list of owners there was only me! Strange.

When I've checked root folder of my website I've found, that there're 2 new files: google-site-verification.html file and instock.aspx, which presents an element of some T-shirts online-store.

Website, by the way, is on ASP.NET MVC 3 and works fine starting from 2012.

So, my question: how is it possible to upload a file to the root folder of the website? I know two ways:

1. Via FTP.
2. Via control panel.

So, is hacker just got access to my account (which is strange, why didn't he changed password and stole website at all?) or it's something else?

Any thoughts?

PS. I've managed to find that some turkish guy encountered the same problem with the same "new owner of the website". Here's branch of the forum with his complaints (google translator forever!):

https://www.r10.net/webmaster-genel-konular-sorunlar/2444605-web-sitem-hacklendi-bir-sorum-var-lutfen-yardim.html