Worker: Improved flag handling, added error checks for config files,
minor fixes

Rewritten flag handling using GNUs getopt to prevent crashs in case the
arguments are shuffled or otherwise wrong.
Check first if files could be opened before working with them to prevent
crashs.
Removed misleading .rd0 comments and outputs since .rd0 files aren't
used by many people anymore. Replaced Rd0 variable names with Sim.