When I change the filename to customBilayer.dll the function does not update it is still custom_bilayer

I think you'll need to recompile. I'll add the README.md from the matlab which contains the compilation instructions.

The compilation instructions are in the docs, no need to copy them over. What I am taking about is on the Matlab side if I do
problem.addCustomFile('DSPC Model','customBilayer.m','matlab',pwd);
The function is set to customBilayer but then if I do
problem.setCustomFile(1,'filename', 'custom_bilayer.py', 'path', path);
the function is set to 'custom_bilayer' unless I explicitly specified a function name

On the python side, the function stays the same after the filename is changed

Ok, I've set it up to have the function name mapped to the filename for matlab, and free otherwise. Let me know what you think of this behaviour.

Please add an __init__.py file to this folder also, otherwise it won't be copied when the user installs.

Does the "tests/test_data" directory need one as well then?

Not needed, at the moment, we don't copy tests for install