Fix cleanup

[yethee]

There were warnings at usage of an absolute path for a source.

For example:

root@ubuntu:/home/phpdox# ./phpdox.php -p /home/phpdox/src
phpdox %version% - Copyright (C) 2010 - 2011 by Arne Blankerts

.....................

PHP Warning:  rmdir(./xml/home/phpdox/src/backend/..): Directory not empty in /home/phpdox/src/application.php on line 192
PHP Warning:  rmdir(./xml/home/phpdox/src/docblock/element/..): Directory not empty in /home/phpdox/src/application.php on line 192
PHP Warning:  rmdir(./xml/home/phpdox/src/docblock/parser/.): Invalid argument in /home/phpdox/src/application.php on line 192
PHP Warning:  rmdir(./xml/home/phpdox/src/docblock/parser/..): Directory not empty in /home/phpdox/src/application.php on line 192
PHP Warning:  rmdir(./xml/home/phpdox/src/docblock/..): Directory not empty in /home/phpdox/src/application.php on line 192
   ...

[theseer]

Merged. Thank you.