[COOK-3990] Changed the conf.d files to end in .conf

The chef minitest fail. The apache2.conf file includes conf.d/*.conf but the minitests check the files created when installing the apache2 package on Ubuntu.  

For example the package creates the /etc/apache2/conf.d/security file, but the recipe creates the /etc/apache/conf.d/security.conf file.   The  /etc/apache2/conf.d/security wont be included since apache.conf only includes files ending in '.conf'

Therefore the test should be checking the conf.d/*.conf files, not the ones created by the apache2 package.