Handle file path arguments in the natural way

The diff looks big, but that's mostly from reindentation; the changes
are actually pretty simple:

* In gather_dups(), move the file-handling core of the first loop
  ("for root in roots:") into a new inner function, gather_file().
  Invoke gather_file() on file roots directly, and walk directory
  roots as before.

* Add the --ignore-missing flag.

* Add conditionals to handle the case of symbolic links that may be
  broken, in the interaction between the new file-target code and
  the new --ignore-missing flag.

* Document all the above.