Remove import redundancies and use full file paths in variable names.

A few import redundancies were moved into util.py, since routes.py
includes them anyway.
Several files need to be referenced by their file location, rather than
their name. For these files, I created variables that describes where
they are rather than what their name is.
Support stdin scripts. Remove dependency on output files.

You can now feed a program an input script rather than using
line-by-line feeding.
Dependency on the output directory was removed by using
subprocess.check_output rather than call. This feeds stdout and stderr
directly into the program, eliminating the need for a file buffer.