Add error checking for missing arguments

[rjyounes]

All arguments may be specified on the commandline. Some options may be specified in the config file as well; these values are overridden by commandline arguments. Some but not all options have a programmatic default. Need to implement error-checking for arguments with no default value that remain unspecified either in the config file or on the commandline.

[rjyounes]

Write error messages to logfile as well as to stderr