Previously was called in TokamakEquilibrium.makeRegions() which had the
same effect as makeRegions is called from __init__, but it's clearer to
call directly from __init__.

Adds xpoint_offset option to control how far points that should be at
the X-point are shifted to avoid the null.

Some settings are needed in TokamakEquilibrium.__init(), so need to
create a new object if they are changed before run().

Allow settings to be adjusted to retry, instead of hypnotoad-gui
closing on any error.