Revert inputs and masterfiles changes.

It doesn't work in the test environment, and not on Windows either.

Due to Windows special casing, this needs to be fixed by having the default configure option be empty. Then, when calling these functions, it should only return the configured value if nonempty. If it is empty, it will return hard-coded values, which on Windows will resolve to ``C:\Program Files\Cfengine``, not ``/var/cfengine``.