Added setup script to project

The current setup script is incomplete but helps with a partial setup. There is
some generic error handling that checks for required programs.

Stages
 - Stage 1: Checks that required programs are installed.

 - Stage 2: Configures a local perl environment in the project directory and
   installs the required modules.

 - Stage 3: Generates a virtual host configuration file for apache2 and
   attempts to copy the file into the sites-available folder.

 - Stage 4: Builds the directory structure required by CoGe.

 - Stage 5: Generates the CoGe configuration file.

Limitations

 - Does not configure apache2 to use the virtual host file.

 - The script does not handle installing 3rd party tools required by coge.

 - Several of the options are not yet configurable.

 - The current script does not generate a usuable setup for CoGe.