New behat feature for `wp cli` tasks

features/cli.feature:
 - wp cli check-updates should return at least one update after version 0.0.0
 - wp cli update should perform a successful update of version 0.0.0
Add a version param to "Given a new Phar"
Move version changes to make-phar.php

- make-phar.php gains a new optional flag --store-version which defaults to false.
  The script will change the contents of VERSION only if this is true.
  This is false when building temporary Phars with custom versions for tests.

- Because of that there is a new function set_file_contents() in make-phar.php
  This is similar to add_file(), but the contents of the new file are passed
  as an argument, instead of reading them via file_get_contents()

- Behat test for building a temporary Phar with a fake version
  Also ensure that VERSION is not modified