moved application folder outside the systems folder.
moved systems/logs directory to the application directory.
adjusted git ignore list to accomodate for changed config file locations.
updated shibboleth configuration example due to changes in application directory layout.
updated filepaths/links from 'system/application/...' to application/...
synced autoload configuration with CI v2.0.0 distro.
updated paths from "system/application" to "application". adjusted relative include paths as well.