remove defunct and broken functions
remove unused model evaluation functions
remove unused old skolemization functions
remove unused cnf, nnf functions
add Printing, Util, and Substitution sections
integrate term_to_str and args_to_str
integrate term_to_str and args_to_str
remove unused utility functions
remove unused utility functions
combine get_functions and skolemize_get_funcs to get_funcs
fix bug where get_funcs misses nested functions
change type of substitution to a map from variables to terms
combine skolemize replace and safe_replace
Combine substitution functions.

Combine skolemize_replace, parametrize, and safe_replace to use the
already-defined substitution fuctions for termlists.

Also fixed a bug where substitutions would apply to bound variables.
When the substitution enters the scope of a quantifier, it now
drops its references to bound variables.
fixed parse function