Close pairs files earlier than at_exit.

Closing the label and class pair files at program exit prevented the
ability to examine their contents during unit testing.  Part of the
work on NCBO-972.
Separate tests for label and class pairs.
Include manual annotations in known class pairs.
Check number of lines in class pairs file.
Clean up output directory in teardown.
Verify contents of class pairs file.
Merge branch 'ncbo-972'