Fix the handling of options nopreprocessoroutput, onlyjson and onlymacro when...

Fix the handling of options nopreprocessoroutput, onlyjson and onlymacro when they appear at the top of the .mod file

The nopathchange is still not supported in this context, so document it.

Also recommend the whitespace-separated syntax instead of the comma-separated
syntax, since the latter is inconsistent with the way options are passed on the
command-line.

Closes: #1667
(cherry picked from commit d3e90a8d)