- 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.