Adds the $DIR/Lib directory to the checked directories

In ref to this comment: https://github.com/loadsys/CakePHP-Shell-Scripts/pull/1/files#r9725295

Signed-off-by: Justin Yost <justin.yost@yostivanich.com>
Updated Coverage if/else statements

Updated comments with clarification of what happens with the reports

Signed-off-by: Justin Yost <justin.yost@yostivanich.com>