MDL-43266 Testing sites are cleaning all test dataroot contents
MDL-43266 testing: Removing duplicated keys
Merge branch 'MDL-43266_25-last-fixes' of git://github.com/dmonllao/moodle into MOODLE_25_STABLE
MDL-43266 testing: avoid assoc arrays for json

Last commit switched from raw arrays to associative
arrays. That leads to json_encode() to generate an
object instead of an array, ultimately leading to
problems with the rest of code expecting an array.

By using array_values() we are moving back to the
non-associative array.

Also, fix some file permissions.
weekly release 2.5.5+
MDL-44148 Portfolios: set_user_config usage fix

Amended user/portfolio.php's use of portfolio_plugin_base::set_user_config to be consistent with the API.