I always use YAML files for configuration files with MATLAB applications. I found them easy to read and editable, manageable versions and very easy to use.
They have an advantage (over the MATLAB script), also widely read by other languages (Perl, Python, Ruby, Java, etc.) if the configuration files should also be used by other parts of the wider application.
There is a YAML file reader for MATLAB (a wrapper around Apache's free Java SnakeYaml library), which is publicly available. I also wrote my own, with which I would be happy to share (it is based on the package I am associated with, with slightly less functionality, but a little easier to understand code and a bit more reliable).
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