Our latest Maxfilter version is Maxfilter 2.2.14 (before that 2.2.12).
This command will apply Maxfilter including Signal Space Separation (SSS), its temporal extension (ST), and movement compensation.
maxfilter-2.2.14 -f input_file.fif -o output_file.fif -st -origin 0 0 45 -frame head -autobad on -movecomp -format short -force
For more information on these and other options, see the Maxfilter 2.2 manual..
You can get information about movement parameters using the command line script Fiff_HeadPositions (based on MNE-Python). There are also older Matlab scripts to analyse maxfilter output.
Standardising sensor arrays
If you want to interpolate your data to a common sensor array (e.g. across datasets), you may want to find the dataset with the most "average" sensor positions (to minimise interpolation errors). You can do this with the command line script AverageSensorArray, and an older Matlab script can be found here.