I should have been more clear, but I was really only replying to the last part of the original post:

...
&NET::SSH::sshopen2()

And I could grep the expanded output to find the packages that ARE used and do my own bookeeping, but Deparse does not fully-qualify function calls.

The problem here was that you can easily grep your own code for Foo::x() to find uses of Foo's x method, but if your code just calls x(), you need to know that x is a method of Foo. If you can find out what all the methods of Foo are, then you can grep for non-fully-qualified calls to those methods in your code and flag those parts of your code for review.

-Joe

Update: I just read some more of the replies, and of course I agree that there's no way to automate this task and get it 100% right. But I think that a simple solution like this could save some effort by categorizing each script/module as "definitely used" or "probably not used". Then you'd want to manually review the "probably not used" cases.