Now on V2, theres a "update library" button that would simple update your music list when you add new music, v3 does not have this.

I uploaded files using Filezilla (uploaded in .rar, and then unrared them using SSH)

So the files "Are" showing under "Files", but when I click on "Media" Its not showing any of the music, it shows 1 song that I uploaded using the internal file uploader.

Is there a way to update the files manually so it knows they are there?

I did upload the rar file and unrared using "root" And I tried running this:
/usr/local/centovacast/sbin/fixperms

But that didnt help much.   Any Suggestions to get the Media to update?

(EDIT)
I also wanted to add that on Firefox and Internet Explorer, the Flash player at the top in the right hand corner there, the "play" button doesnt work...( I thought maybe it was my version of flash so I updated, but it still doesnt work) But the "Music note" works just fine.

Am I the only one having this issue?   

ssh
/usr/local/centovacast/bin/ccmanage reindex <username> --updateall

I hope it helps

Now on V2, theres a "update library" button that would simple update your music list when you add new music, v3 does not have this.

By design.

I uploaded files using Filezilla (uploaded in .rar, and then unrared them using SSH)

So the files "Are" showing under "Files", but when I click on "Media" Its not showing any of the music, it shows 1 song that I uploaded using the internal file uploader.

That means either you are not using Centova Cast v3's built-in FTP server (eg: you have an FTP server of your own running on the machine), OR Centova Cast's cron jobs are not running.

When set up correctly using CCv3's built-in FTP server, FTP-based uploads will be pulled into the media library within a minute or so of uploading them.

Is there a way to update the files manually so it knows they are there?

Yes, per LifeFM's reply.