Fixed include paths in documentation

I noticed that these are pointing to a perhaps older directory structure, as the include paths were incorrect in the documentation of Namespace Configuration in the README.md from how the document structure currently is attainable via Composer. I have a suspicion that the Yaml include path may be different, but I do not currently use this component.
Reverting change to create branch.
Fixed Include Paths in documentation and application.ini
Slight adjustment to ClassLoader include.
Updated resources.doctrine.orm.entityManagers.default.metadataDrivers.annotationRegistry.annotationFiles
This is correct for the ClassLoader
Merge pull request #55 from dustinmoorman/zf1-d2-include-path-fixes

Zf1 d2 include path fixes