Cleaned directory, commented, added help

* Perl directory and program has been removed with this commit
* Moved all C files to the root directory
* Commented all previously undocumented code
* Updated makefile to use the C99 standard instead of GNU99
* input
** Fixed memory leak related to restructure of main in check_input
** Added code to print help in check_input
* parts_of_speech
** Added help and about strings