This patch adds missing newlines, trims multiple redundant final
newlines into a single one, and trims redundant leading newlines.

According to POSIX, a line is a sequence of zero or more non-' <newline>'
characters plus a terminating '<newline>' character. [1] Files should
normally have at least one final newline character.

C89 [2] and later standards [3] mention a final newline:
"A source file that is not empty shall end in a new-line character,
which shall not be immediately preceded by a backslash character."

Although it is not mandatory for all files to have a final newline
fixed, a more consistent and homogeneous approach brings less of commit
differences issues and a better development experience in certain text
editors and IDEs.

[1] http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html#tag_03_206
[2] https://port70.net/~nsz/c/c89/c89-draft.html#2.1.1.2
[3] https://port70.net/~nsz/c/c99/n1256.html#5.1.1.2

This patch makes several scripts and PHP development tools files
executable and adds more proper shebangs to the PHP scripts.

The `#!/usr/bin/env php` shebang provides running the script via
`./script.php` and uses env to find PHP script location on the system.
At the same time it still provides running the script with a user
defined PHP location using `php script.php`.

Initial Pass, also fixing the extra space before the extract_tests function name to keep with standards.