rough rough refactoring
added some important TODO comments

Also rewrote some of the function arguments a bit
return of determine_replacement()

see the comments in the code before and after this commit for
explanation why. Also did some other clean up stuff.
change null to NULL, rename C var to differentiate from C in main, and remove unused int
don't need errno.h include
Initialize FILE*s to NULL
label the columns of the logfile
added top-down.h and updated makefile
Merge branch 'dev' of github.com:johnmurrayvi/CS340-Spring-2013 into dev
altered top-down.c to reflect top-down.h
removed assignments inside conditional checks
merging back into dev
add initial specification doc. need to go through and trim unneeded stuff out
fix args_ok, update makefile, still need to make different builds though
initial stuff for make test. not fully functional yet
runs, now need to test replacements and logs?
fix missing $, clean up the tr-test.txt file
fix make clean, top-down needed to be a dependent of make test, and add top-down to gitignore
clean up comments a bit
Finish cleaning up comments