Zf1 d2 include path fixes

Hello Guilherme! I noticed that these include paths in the documentation and application.ini are not the same per the directory structure we receive from installing this project via Composer using the composer.json file in the README.md. It looks like they are using a new structure, and I have adjusted the include paths in both files to follow suit.

I have adjusted all but the Yaml component, as I didn't receive that due to my project's configuration.