Moving output files to output subdirectory

# Please enter the commit message for your changes. Lines starting
# with '#' will be ignored, and an empty message aborts the commit.
# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#	modified:   Makefile
#	renamed:    output.cc -> output/output.cc
#	renamed:    output.h -> output/output.h
#
