Improved and fixed command line help.

* Added calling main with '-jar' syntax to synopsis.
* Added placeholder for Java options to synopsis.
* Replaced '...Main' with 'java...' in examples to accommodate '-jar'
  invocation and Java options syntaxes.
* Clarified meaing of '-': that it represents input or output depending
  on context.
* Fixed documentation of '--scores-labels' default file which is
  actually standard input and not none.
* Improved and fixed example of processing standard input with default
  options.  Added example without options and statement of equivalence
  to example with options.  Removed non-existent option '--format'.
Switched command line help to stdout instead of stderr.