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fuzzylite does not deal with Files, and I think I will keep it that way for the foreseeable future. However, I will consider using custom vectors for the next version.

You need to investigate how to read and write files from your computer using C++. I have done reading files using std::ifstream and std::getline. For every line read, you can use std::istringstream as a tokenizer that reads the line and gets each of the values in the line and stores them in a matrix. Afterwards:
1) traverse the matrix using the values to prepare the input variables (using InputVariable::setInputValue)
2) call method Engine::process
3) defuzzify the values of each output variable and store them in the matrix
4) Write to file the matrix or part of the matrix

Also, I have changed the title of the post to reflect better its contents.