Using Relative Paths with Matlab Coder

I am trying to generate C code for a Matlab function. It uses mongoose web server for communication. If I place the .h/.c files in the same folder as the .m file I can compile everything fine using using matlab to an exe:
coder.cinclude('mongoose.h');
coder.updateBuildInfo('addSourceFiles','mongoose.c');
coder.cinclude('rest.h');
coder.updateBuildInfo('addSourceFiles','rest.c');
I would like to keep my .c files and .m files separate, so moving C files to a folder named native/ causes compilation to fail as expected. Thus, I tell Matlab where to find them using:
customDir = '/full/path/to/native';
coder.updateBuildInfo('addIncludePaths', customDir);
coder.updateBuildInfo('addSourcePaths', customDir);
Which works. However it works only with absolute paths and not with relative paths. This is a problem since each contributor to this projects keeps the source folder in a different location. What is the proper way to tell Matlab native file locations using relative paths to Matlab working directory?

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