Upgraded to PHPMyAdmin 4.1.7.
Added file to ignore .git directory and manifest.yml, no need to push them.
Moved extra folder to proper location.  Updated php.ini.
Removed unnecessary configuration option.
Revert "Removed unnecessary configuration option."

This reverts commit 4ab0c01087518b5de84055276c2be5e5033acd50.
Fixed URL to respect http or https.