Various minor improvements to the run script in MC setup

1) Allows true 'silent' running by switching off tqdm and SFThist output
2) Generalise the check old run setup to take an arbitrary set of
parameters to check (provided) they are in the saved dict. Then adds
DeltaOmega and DeltaFs check
3) Pass through the log_table and gen_tex_tables options so that one can
switch off these outputs
4) Adds create_plots to FollowUp run
5) Simple reorder to Writer parameters to group amplitude parameters