Fix Bug in iterate_input Recursion

A parameter wasn't being passed in the recursive calls.
Add Populate Option

Add the --populate option which runs normally except it ignores the
rules file, thereby populating the output storage with all of the
existing possible targets.
Add Summary Output

Add a summary at the end that shows a list of processed (matched) and
unprocessed items.
Log Commands More Cleanly

The log statements muddied the output of the command (and the command
itself). This change groups them together so the output is easier to
read. They all come out in one log statement.