Fix for #3318

Fixes https://cakephp.lighthouseapp.com/projects/42648-cakephp/tickets/3318

It seems fixing this in the htaccess file(s) isn't going to work even though a url rewriting based solution was more clean. On the plus side this works for any web server.
If a url is called with "index.php" in it then the CakeRequest swallows this part and fixes the path. Any linked url from the requested page will have a clean url. Thus after following one of these urls this problem is gone anyway.

Some code docblock improvements to CakeRequestTest.php
Added test case for fix
Also now you can call just index.php even if you have url rewriting enabled
Merge pull request #1377 from ravage84/fix-for-3318

Trim off webroot/index.php when determining base and url.

Trimming off index.php from url and webroot/index.php from base url allows the correct values to be created when a path contains index.php in it.

Fixes #3318