- Added lines from the zip of Codeigniter-3.1.2

Some files don't contain a line separator ('\n') at the end. Add the
missing eol.

In POSIX, all lines of text should end with a newline character by
definition. See
http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html
section 3.397 for more.

See https://gist.github.com/jacknagel/1020172 for a gist of the issue.

Environment support eliminates the need to ignore database.php.  Instead, ignore the entire development dir.
Logs and cache are now in application folder instead of system.

Improved CodeIgniter .gitignore to support an system directory in a different location to the default install. Fixed database.php ignore rule. The application directory can be moved to any location and the ignore will still operate