Removed a lot of command-line flags.  The config file is sufficient.

  This is a temporary change until we've finished the neatening/tidying.
  perltidy.
  Major reorg. of code.

  We've moved away from having a list of single-use variables
 such as:

   $in   -> THe input directory.
   $out  -> The output directory (assuming in-place is not set).

  Now we use a global hash reference of all known options.  This
 allows is to move the generation code out of templer.in, and into
 Templer::Site where it belongs.