Regarding the space you should read the Disk Space policy
For unlimited features like emails, parked domain you should consider premium hosting
Check the comparison of free and premium hosting here --> http://x10hosting.com/free-hosting-comparison
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Re: Files are missing or it's the permissions on the server needs to be changed on VO
Just confirm that files are missing by looking into File Manager in Cpanel and then post a support ticket, The staff will restore your files. We have your backup.
If all files are there then regarding...