So got hosting controller installed and running.
 
Filled in the information for the server in the server panel and *boom* broke the PHP (and Perl) for apache.
 
Because it renamed the conf files with an hc extension. So instead of php.conf had php.conf.hc and of course apache is trying to load files with .conf ending and not finding them.
 
Why did this happen? Because that was not very good. 

If we don't rename conf file then its mean PHP/perl would be enabled by default with every website existed in the apache. And you wouldn't be able to enable/disable php/perl from HC control panel.
In order to manage these resource properties from HC panel we use our configuration and rename the file so then reseller would have choice to allow/disallow php and perl on specific domains.
 
In case you don't have any issue by enabling php/perl by default with every website then you can copy php.conf.hc and rename it with original name php.conf.