As of Martinize2 version 0.12.0, the defaults of the -scfix and -cys flags have been changed.
-scfix is now assumed by default, so it is no longer necessary to specify it. If you do, a warning will be raised. If you purposefully intend to generate protein models without side chain fixes, the -noscfix flag can be used.
Additionally, the default argument of -cys is changed to auto to search for disulfide bridges in your topology by default, so no longer needs to be explicitly specified unless you want to turn off the behaviour (-cys none) or specify the search distance for disulfide bridges manually (e.g. -cys 5 will enforce disulfide bridges between cysteines within 5 nm of each other).