Fix config_item() returning stale values

Use case fixed:

    config_item('foobar'); // returns "some value"
    $CI->config->set_item('foobar', 'new value');
    config_item('foobar'); // still returns "some value", expected "new value"
Remove documentation note obsoleted by previous commit
Merge pull request #2538 from vlakoff/develop-4

Fix config_item() returning stale values