Including custom config files in builds

Several of my classes save and load their own configuration files. Some are saved in a sub folder of Assets, some are saved in the top level folder of the project. The files in the Assets folder appear in the project window, but the ones in the top level do not.
However none of these files get included when I make a build, and I have to manually copy them into the build folder. How do I tell Unity they are required so it will include them? Some of them have hardcoded filenames, but others do not, with the file name set as a public variable on the script.

komatii

I need this answered as well. I have the exact same needs however, I am also doing an Android version of my game and since it builds to a single *.apk file, I have no way of including my custom files at all…

Have you guys considered using Resources?

Runtime Classes - Resources