added a run file / included book in output

vhf wanted to see which book the broken urls came from so we have
to run the url testing inside the code where urls are regexped out
from each line. in the end this simplified the code by removing an
extra foreach loop to do the testing on all the collected @uris.

additionally, this had the unintended consequence of fixing a bug
where urls appearing more than once were only counted once. now,
they get printed for every instance they show up so that they may
be fixed in all instances.

./run file is to remind me how to run this program and save into
output.txt at the same time.